From 17d6c7ab12abe7c5e1647ee6d3d5c8a7eef17b8c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 09:08:22 -0500 Subject: [PATCH 0001/1813] Update bowtie2 to 2.5.3 (#45261) --- recipes/bowtie2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bowtie2/meta.yaml b/recipes/bowtie2/meta.yaml index 0d332684fac38..ece3f06a3d3f0 100644 --- a/recipes/bowtie2/meta.yaml +++ b/recipes/bowtie2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.2" %} +{% set version = "2.5.3" %} package: name: bowtie2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/BenLangmead/bowtie2/archive/v{{ version }}.tar.gz - sha256: 2f86dbfbf3dcb8521d559f830594fe28ac6e4c40d81313a8c2bfb17c82a501e0 + sha256: 4ac3ece3db011322caab14678b9d80cfc7f75208cdaf0c58b24a6ea0f1a0a60e build: number: 0 From 3df2df5f03b92fb0e3d109391354fb60c92c4640 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Wed, 17 Jan 2024 17:16:32 +0100 Subject: [PATCH 0002/1813] Update raptor (#45270) --- recipes/raptor/meta.yaml | 2 +- recipes/raptor/raptor | 11 ++++++----- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/raptor/meta.yaml b/recipes/raptor/meta.yaml index 0b38ef4ed151c..cf815b6a65db9 100644 --- a/recipes/raptor/meta.yaml +++ b/recipes/raptor/meta.yaml @@ -10,7 +10,7 @@ source: sha256: be44e7b2635e110c940cf40ff132956200551a2e25765d9f057e844f7a3ccebb build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/raptor/raptor b/recipes/raptor/raptor index 180b5b084c99f..107b82cc749f2 100644 --- a/recipes/raptor/raptor +++ b/recipes/raptor/raptor @@ -6,11 +6,12 @@ set -eu # -m 1 : stop after first match, i.e. count is either 0 or 1 # -E : use extended regular expressions # \b : matches any non alphanumeric character, i.e. space, tab, newline, etc. -HAS_SSE2=$(grep -c -m 1 -E '\bsse2\b' /proc/cpuinfo) -HAS_SSE4_2=$(grep -c -m 1 -E '\bsse4_2\b' /proc/cpuinfo) -HAS_AVX2=$(grep -c -m 1 -E '\bavx2\b' /proc/cpuinfo) -HAS_AVX512F=$(grep -c -m 1 -E '\bavx512f\b' /proc/cpuinfo) -HAS_AVX512BW=$(grep -c -m 1 -E '\bavx512bw\b' /proc/cpuinfo) +# || true: ignore `grep -c` returning a non-zero exit code (behavior depends on OS) +HAS_SSE2=$(grep -c -m 1 -E '\bsse2\b' /proc/cpuinfo || true) +HAS_SSE4_2=$(grep -c -m 1 -E '\bsse4_2\b' /proc/cpuinfo || true) +HAS_AVX2=$(grep -c -m 1 -E '\bavx2\b' /proc/cpuinfo || true) +HAS_AVX512F=$(grep -c -m 1 -E '\bavx512f\b' /proc/cpuinfo || true) +HAS_AVX512BW=$(grep -c -m 1 -E '\bavx512bw\b' /proc/cpuinfo || true) if [ ${HAS_AVX512F} -eq 1 ] && [ ${HAS_AVX512BW} -eq 1 ]; then HAS_AVX512=1 else From 0892d7949226b76d97e57bfcfbae758276a9fa1c Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 17 Jan 2024 10:31:28 -0600 Subject: [PATCH 0003/1813] Add recipe for MAEGATK v0.2.0 (#45272) * Add recipe for MAEGATK v0.2.0 * edit entry_points and tests --- recipes/maegatk/meta.yaml | 63 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 recipes/maegatk/meta.yaml diff --git a/recipes/maegatk/meta.yaml b/recipes/maegatk/meta.yaml new file mode 100644 index 0000000000000..6e622c1497f78 --- /dev/null +++ b/recipes/maegatk/meta.yaml @@ -0,0 +1,63 @@ +{% set name = "maegatk" %} +{% set version = "0.2.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/maegatk-{{ version }}.tar.gz + sha256: fce1ec287914e03ce2b317a4f6a338f1806cd82e5c77f4e4cb1efbd48c87bdda + +build: + number: 0 + noarch: python + entry_points: + - maegatk = maegatk.cli:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('maegatk', max_pin="x.x") }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - click + - pysam + - pytest + - snakemake-minimal + - biopython + - optparse-pretty + - regex + - ruamel.yaml + - openjdk + - fgbio + - bwa + - samtools + - freebayes + - r-base + - r-dplyr + - r-data.table + - r-matrix + - bioconductor-genomicranges + - bioconductor-summarizedexperiment + +test: + imports: + - maegatk + commands: + - maegatk --help + +about: + home: https://github.com/caleblareau/maegatk + summary: Mitochondrial Alteration Enrichment and Genome Analysis Toolkit + license: MIT + license_family: MIT + license_file: LICENSE.txt + description: Processing and quality control of mitochondrial genome variants from MAESTER data. + +extra: + recipe-maintainers: + - mencian From 7fd5966de6e43848d563e23af8af3115f97c4990 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 11:31:40 -0500 Subject: [PATCH 0004/1813] Update matchms to 0.24.1 (#45267) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/matchms/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 20b110efe079c..9cb15af6297b8 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.24.0" %} +{% set version = "0.24.1" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e62b1591782b01c3ef83850245609d85e3d612a7f7c350b4fc2ad067d8bc9d15 + sha256: 8cb7098f0e5149c3ab5ad7b39789472b35e12f7668a79c12a3c58e51b50c255c build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps -vvv" noarch: python run_exports: From 434fe6b42d3df4223b639be3343afb6411f627d4 Mon Sep 17 00:00:00 2001 From: Jacob Morrison Date: Wed, 17 Jan 2024 12:44:22 -0500 Subject: [PATCH 0005/1813] Update to biscuit version 1.4.0 (#45118) * remove unused file * patch file no longer needed * update to biscuit v1.4.0 * correct pthread requirement name * modify sgsl and utils Makefiles in build * add CC to make call * try finding zlib * try C_INCLUDE_PATH * edit build.sh * revert to CPATH * try make * edit tests * try adding perl to host for testing * add shebang via sed for asset builder --------- Co-authored-by: mencian --- recipes/biscuit/build.sh | 21 ++++++++----- recipes/biscuit/meta.yaml | 24 +++++++-------- recipes/biscuit/patch | 64 --------------------------------------- recipes/biscuit/script.sh | 1 - 4 files changed, 26 insertions(+), 84 deletions(-) delete mode 100644 recipes/biscuit/patch delete mode 100644 recipes/biscuit/script.sh diff --git a/recipes/biscuit/build.sh b/recipes/biscuit/build.sh index b69c7a1e293f1..f19d32dd1e12f 100644 --- a/recipes/biscuit/build.sh +++ b/recipes/biscuit/build.sh @@ -1,9 +1,16 @@ #!/bin/bash -BIN=$PREFIX/bin -mkdir -p $BIN -make CC="$CC $LDFLAGS" CFLAGS="$CFLAGS" -cp biscuit $BIN -cp QC.sh $BIN -cp build_biscuit_QC_assets.pl $BIN -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $BIN/build_biscuit_QC_assets.pl +# Needed for building utils dependency +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -pthread -L${PREFIX}/lib" + +mkdir -p "${PREFIX}/bin" +mkdir -p build +cd build || exit 1 +cmake -DCMAKE_INSTALL_PREFIX:PATH="${PREFIX}" .. +make CC="${CC} ${LDFLAGS}" CFLAGS="${CFLAGS} -O3" +make install + +# Needed to run asset builder +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/build_biscuit_QC_assets.pl diff --git a/recipes/biscuit/meta.yaml b/recipes/biscuit/meta.yaml index 380b874c46af9..39e7a090e8671 100644 --- a/recipes/biscuit/meta.yaml +++ b/recipes/biscuit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.0.20231027" %} +{% set version = "1.4.0.20240108" %} package: name: biscuit @@ -11,36 +11,36 @@ build: source: - url: https://github.com/huishenlab/biscuit/releases/download/v{{ version }}/release-source.zip - sha256: 027d4343a49fde7c497f4a0292a2cb5bb475b4bcacedb17f251680dbf4f56995 - patches: - - patch - - url: https://github.com/huishenlab/biscuit/releases/download/v{{ version }}/QC.sh - sha256: f2b9237f1166681a5f4e2cb0b297b2c2a086ea4975948a292b4871e391244b13 - - url: https://github.com/huishenlab/biscuit/releases/download/v{{ version }}/build_biscuit_QC_assets.pl - sha256: 7967240b63c8f816e7da79c3c0eb890933ec47df1114f6893b9e9736c8e564a8 + sha256: 58625f286a4bda4a3884feb10be575e4cb205f09b9ddb1075d099ca2259c1c17 requirements: build: - make + - cmake - {{ compiler('c') }} host: - zlib - ncurses + - pthread-stubs - libcurl run: - zlib - ncurses + - pthread-stubs - libcurl - perl test: commands: - - biscuit 2>&1 || true - - QC.sh -h 2>&1 | grep Usage - - build_biscuit_QC_assets.pl -h 2>&1 | grep Usage + - biscuit 2>&1 | grep "Usage" + - QC.sh -h 2>&1 | grep "Usage" + - build_biscuit_QC_assets.pl -h 2>&1 | grep "Usage" about: home: https://github.com/huishenlab/biscuit license: MIT + license_family: MIT + license_file: LICENSE summary: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data - + dev_url: https://github.com/huishenlab/biscuit + doc_url: https://huishenlab.github.io/biscuit/ diff --git a/recipes/biscuit/patch b/recipes/biscuit/patch deleted file mode 100644 index 2ef00a4400ab0..0000000000000 --- a/recipes/biscuit/patch +++ /dev/null @@ -1,64 +0,0 @@ -diff --git a/Makefile b/Makefile -index d54b6c2..8ee48a2 100644 ---- a/Makefile -+++ b/Makefile -@@ -1,5 +1,5 @@ --CC = gcc --CFLAGS = -W -Wall -finline-functions -fPIC -std=gnu99 -Wno-unused-result -O3 -+CC ?= gcc -+CFLAGS ?= -W -Wall -finline-functions -fPIC -std=gnu99 -Wno-unused-result -O3 - CLIB = -lncurses -lpthread -lz -lm - CF_OPTIMIZE = 1 - -diff --git a/lib/htslib/Makefile b/lib/htslib/Makefile -index 9c4ce60..c6722fd 100644 ---- a/lib/htslib/Makefile -+++ b/lib/htslib/Makefile -@@ -22,7 +22,7 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc -+CC ?= gcc - AR = ar - RANLIB = ranlib - -diff --git a/lib/klib/Makefile b/lib/klib/Makefile -index 15ad2fc..aebbf64 100644 ---- a/lib/klib/Makefile -+++ b/lib/klib/Makefile -@@ -1,4 +1,4 @@ --CC = gcc -+CC ?= gcc - AR = ar - CFLAGS = -g -Wall - -diff --git a/lib/sgsl/Makefile b/lib/sgsl/Makefile -index c939453..bc5fd6e 100644 ---- a/lib/sgsl/Makefile -+++ b/lib/sgsl/Makefile -@@ -1,4 +1,4 @@ --CC = gcc -+CC ?= gcc - AR = ar - CFLAGS = -g -Wall - # -std=gnu11 travis complains about this -@@ -25,7 +25,7 @@ libgsl.a: $(OBJECTS) - $(AR) -csr $@ $^ - - test: libgsl.a -- gcc -I. test/test.c libgsl.a -std=c99 -lm -o test-main -+ $(CC) -I. test/test.c libgsl.a -std=c99 -lm -o test-main - - clean: - rm -f $(OBJECTS) -diff --git a/lib/utils/Makefile b/lib/utils/Makefile -index 9c7f457..3b0cfef 100644 ---- a/lib/utils/Makefile -+++ b/lib/utils/Makefile -@@ -1,4 +1,4 @@ --CC = gcc -+CC ?= gcc - AR = ar - CFLAGS = -g -Wall - diff --git a/recipes/biscuit/script.sh b/recipes/biscuit/script.sh deleted file mode 100644 index 80e0ff397a83b..0000000000000 --- a/recipes/biscuit/script.sh +++ /dev/null @@ -1 +0,0 @@ -echo efrat From bc519e338182d580828de28e281ea1a882dcc24b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:44:54 -0500 Subject: [PATCH 0006/1813] Update gtfparse to 2.5.0 (#45262) --- recipes/gtfparse/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gtfparse/meta.yaml b/recipes/gtfparse/meta.yaml index e67367f8fe766..41e4bd86031e9 100644 --- a/recipes/gtfparse/meta.yaml +++ b/recipes/gtfparse/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gtfparse" %} -{% set version = "2.4.1" %} -{% set sha256 = "dbb6dd88bc5535b1d6ca8fab3154f3408c9b67d7215bbc1762d8f855919cc8a5" %} +{% set version = "2.5.0" %} +{% set sha256 = "9fea54811cd87f597a110a49dc1b1b6a3325ffb7d1f36ecc62c32d14d3eb9493" %} package: name: {{ name|lower }} From ef065033fdd7bd389480d756374699ac6ab0da8b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:45:03 -0500 Subject: [PATCH 0007/1813] Update pyensembl to 2.3.9 (#45263) * Update pyensembl to 2.3.7 * Update pyensembl to 2.3.9 --- recipes/pyensembl/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index 9693ad2d94240..cb30778055db9 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PyEnsembl" %} -{% set version = "2.3.6" %} -{% set sha256 = "206981651d926d455ee85fa813fefb0d6e8bd29983821aef1136df28337b8597" %} +{% set version = "2.3.9" %} +{% set sha256 = "444c4f489818fd639c34a631a9527cd6bb6586bf20b58daffe1b79d1d1ef86f4" %} package: name: {{ name|lower }} From 089b51a1277de64289369f0313d897c8272e6397 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:45:34 -0500 Subject: [PATCH 0008/1813] Update peaks2utr to 1.2.5 (#45271) --- recipes/peaks2utr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/peaks2utr/meta.yaml b/recipes/peaks2utr/meta.yaml index b0f5d08d094ca..03cb588cdd03b 100644 --- a/recipes/peaks2utr/meta.yaml +++ b/recipes/peaks2utr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "peaks2utr" %} -{% set version = "1.2.4" %} +{% set version = "1.2.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/peaks2utr-{{ version }}.tar.gz - sha256: 9fb91c2361e8de95994f1de7bf8414710777ecd52b23d35628270f0bb2e2412e + sha256: d24ed841692059e237800cceca00adb4f17638c6751b214d4146ca0fe26cf97e build: number: 0 From 7547a6dbfa4e6b93b863890eba16b31e1eb10a62 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 15:51:41 -0500 Subject: [PATCH 0009/1813] Update pbstarphase to 0.8.1 (#45278) --- recipes/pbstarphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml index 9b43d0bc72b8f..1416f4902aaa7 100644 --- a/recipes/pbstarphase/meta.yaml +++ b/recipes/pbstarphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbstarphase" %} -{% set version = "0.8.0" %} -{% set sha256 = "df207d5aa29f0e0088dff838403664ca624f71d1f6c176374f2354234b74850e" %} +{% set version = "0.8.1" %} +{% set sha256 = "cea59d70ebefe3660e90b566944e5c2928ce5a1107916199f5700b1117cc85ee" %} package: name: {{ name }} From 9e6c9c92b204445fe18137cf57bc78ae0f292e20 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 15:52:14 -0500 Subject: [PATCH 0010/1813] Update snakemake to 8.2.1 (#45279) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index cedec7fc176f7..1904589e0671a 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.2.0" %} +{% set version = "8.2.1" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 4226179d344152e046d5ceaa589f4a77c2b19af99976322ca2ede58a57942a63 + sha256: f177ada98188a10602aa2ed758fc9b7ff13e7107c5e582463ae681c525c28f0c build: number: 0 From 04022c7af3eea41b565af98f08198d37e9c12386 Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Wed, 17 Jan 2024 16:18:09 -0600 Subject: [PATCH 0011/1813] Update HTSeq version (#45273) * Update HTSeq version * Change url for osx build * Remove extra url line * Add wheel * Try pypi link for osx * Update url --------- Co-authored-by: Natasha Pavlovikj --- recipes/htseq/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/htseq/meta.yaml b/recipes/htseq/meta.yaml index a68cff9aff26b..2d524cc2a529a 100644 --- a/recipes/htseq/meta.yaml +++ b/recipes/htseq/meta.yaml @@ -1,17 +1,18 @@ -{% set version = '2.0.4' %} +{% set name = "HTSeq" %} +{% set version = "2.0.5" %} +{% set sha256 = "2519675246dd1639115a76c9aacf19ab5bc5bed2f3598bf89cd97be5c0d066b3" %} package: - name: htseq + name: {{ name|lower }} version: {{ version }} source: - url: https://files.pythonhosted.org/packages/ed/ca/6f1e2f556cb2aad34ea8481f41a5a16dc52bef2e4fa55e7107b0b8e6bfe5/HTSeq-{{ version }}.tar.gz - sha256: 5510d855617d61efff2287af4cdc60a73e94bd735e44c15b57f189ea0634e6e0 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: {{ sha256 }} build: number: 0 - skip: True # [py2k or py == 36] - script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation run_exports: - {{ pin_subpackage('htseq', max_pin="x") }} @@ -25,6 +26,7 @@ requirements: - pip - cython - numpy + - wheel - pysam >=0.15.1 - swig >=3.0.8 run: @@ -32,6 +34,8 @@ requirements: - {{ pin_compatible('numpy') }} - matplotlib-base >=1.4 - pysam >=0.15.1 + - scipy >=1.5.0 + - pandas >=1.1.0 test: # Python imports From f76d69172066dbf8ae1dc060fae4082f95e05b6f Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Wed, 17 Jan 2024 14:32:52 -0800 Subject: [PATCH 0012/1813] Add tntblast (thermonucleotideBLAST) (#45186) * Add tntblast * Add run_exports * move run_exports to correct location * Remove extra url * Add openmp, use g++ * use CXX_FOR_BUILD * Filter out USE_MPI flag * Add zlib * unsed BLAST_DIR * Add LIBS when compiling cpp files * Revert adding LIBS * zlib check * adjust variables * Try CXX instead of CC * Add true to test, to force exit code 0 * Add quotes to test definition * Try removing quotes from grep cmd in test * Add dummy test * Create bin dir before copying * Remove dummy test * Limit openmp to linux --------- Co-authored-by: Thanh Lee Co-authored-by: Robert A. Petit III --- recipes/tntblast/build.sh | 16 +++++++++++++ recipes/tntblast/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 recipes/tntblast/build.sh create mode 100644 recipes/tntblast/meta.yaml diff --git a/recipes/tntblast/build.sh b/recipes/tntblast/build.sh new file mode 100644 index 0000000000000..9faf1b0cc953d --- /dev/null +++ b/recipes/tntblast/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash + +sed -i.bak 's/-DUSE_MPI//g' Makefile +sed -i.bak '/BLAST_DIR =/d' Makefile + +export INCLUDE_PATH="${BUILD_PREFIX}/include" +export LIBRARY_PATH="${BUILD_PREFIX}/lib" +export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BUILD_PREFIX}/lib" + +export LDFLAGS="-lm -lz -L${BUILD_PREFIX}/lib" +export CPPFLAGS="-I${BUILD_PREFIX}/include" + +make CC="${CXX}" INC="${CPPFLAGS}" LIBS="${LDFLAGS}" all + +mkdir -p $PREFIX/bin +cp tntblast $PREFIX/bin diff --git a/recipes/tntblast/meta.yaml b/recipes/tntblast/meta.yaml new file mode 100644 index 0000000000000..1879071879028 --- /dev/null +++ b/recipes/tntblast/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "tntblast" %} +{% set version = "2.61" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage( name|lower, max_pin="x") }} + +source: + url: https://github.com/jgans/thermonucleotideBLAST/archive/refs/tags/v{{ version }}.tar.gz + sha256: c2c8862ea772e7a655183b037995d02f319a04e3b359b447069b5f8fc0d11ec4 + +requirements: + build: + - make + - {{ compiler('cxx') }} + - openmp #[linux] + - llvm-openmp #[osx] + - zlib + host: + - openmp #[linux] + - llvm-openmp #[osx] + - zlib + run: + - openmp #[linux] + - llvm-openmp #[osx] + - zlib + +test: + commands: + - '{ tntblast 2>&1 || true; } | grep v.{{ version }}' + +about: + home: https://github.com/jgans/thermonucleotideBLAST + license: BSD License + license_file: LICENSE + license_family: BSD + summary: Searching DNA/RNA sequence databases with PCR and/or probe queries + dev_url: https://github.com/jgans/thermonucleotideBLAST + doc_url: https://github.com/jgans/thermonucleotideBLAST#readme + +extra: + identifiers: + - doi:10.1093/nar/gkn301 From 09f152fa6e3a4bb5ced537579a24fde21f71fdc6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 18:53:17 -0500 Subject: [PATCH 0013/1813] Update pypolca to 0.3.0 (#45268) --- recipes/pypolca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pypolca/meta.yaml b/recipes/pypolca/meta.yaml index 6981ef124abde..84b6e54e58dca 100644 --- a/recipes/pypolca/meta.yaml +++ b/recipes/pypolca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypolca" %} -{% set version = "0.2.1" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 104f9a794d21f36454eb8e89ef317bd086d452a7fc1d4e2433b1afaa8d649c5c + sha256: 8f65a6f010a65ced2f0e470d6f1ae9703236fece666674afe76cfb4475bfa440 build: number: 0 From f78e23eefc8b4c87c0a1d444bc6afe8fea9fe960 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 18:53:40 -0500 Subject: [PATCH 0014/1813] Update pharokka to 1.6.1 (#45264) --- recipes/pharokka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pharokka/meta.yaml b/recipes/pharokka/meta.yaml index f4cc32edee438..fad8abba9cbc1 100644 --- a/recipes/pharokka/meta.yaml +++ b/recipes/pharokka/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.6.1" %} {% set name = "pharokka" %} -{% set sha256 = "67a6459e1d7a3e22801a3eba0149056fcf9b3e61ea614d55893fdaa0cca7f5be" %} +{% set sha256 = "b172d91d182bc0d25610bd6241c489e3efd947c2f4bdc4204cc5bf2b07a55afd" %} {% set user = "gbouras13" %} package: From b1a2d9a12bfa65e8685f526d9ae0329ffd109c5e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:14:39 -0500 Subject: [PATCH 0015/1813] Update itolapi to 4.1.3 (#45265) --- recipes/itolapi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/itolapi/meta.yaml b/recipes/itolapi/meta.yaml index 89d85e715441f..14938580238b2 100644 --- a/recipes/itolapi/meta.yaml +++ b/recipes/itolapi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "itolapi" %} -{% set version = "4.1.2" %} +{% set version = "4.1.3" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 37a866a117a80d3d72a6eb6b2cba30444751c644cc6bc4242f050750375a8397 + sha256: b4f683630e4c816529b79a326de515809ad6174e473b6a25bc3954aaadd16778 build: noarch: python From b617d82d4252dab4c8cf13e3794aa83984b2cdc9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:15:24 -0500 Subject: [PATCH 0016/1813] Update recentrifuge to 1.13.2 (#45269) --- recipes/recentrifuge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/recentrifuge/meta.yaml b/recipes/recentrifuge/meta.yaml index 2490ce7708084..8f89c36bb4498 100644 --- a/recipes/recentrifuge/meta.yaml +++ b/recipes/recentrifuge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recentrifuge" %} -{% set version = "1.13.1" %} +{% set version = "1.13.2" %} package: name: {{ name }} @@ -14,7 +14,7 @@ build: source: url: https://github.com/khyox/{{ name }}/archive/v{{ version }}.tar.gz - sha256: a8c3826302c7a39fe0735176b49fc635964b83d5cc110fc3139c83783c27984d + sha256: 548cfe12d075e3d9e9c01e380891acc5278eae20e075818d7863136e7cf20b81 requirements: host: From ae089eb5324afcb7c48d16c5020ad57bdc7a0fbe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:16:15 -0500 Subject: [PATCH 0017/1813] Update synapseclient to 4.0.0 (#45275) --- recipes/synapseclient/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/synapseclient/meta.yaml b/recipes/synapseclient/meta.yaml index 3b475ae73277e..58be08dcd1ec8 100644 --- a/recipes/synapseclient/meta.yaml +++ b/recipes/synapseclient/meta.yaml @@ -1,5 +1,5 @@ {% set name = "synapseclient" %} -{% set version = "3.2.0" %} +{% set version = "4.0.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/synapseclient-{{ version }}.tar.gz - sha256: 87c91f03dbca7074efd18144325df07db24e07ea92e0b7c8691aaec46c28329a + sha256: 9b1acfa4fc9d76c3d69fab3a362e80a4f3cb8dbd60cea0dd6ab34fbb120a9b34 build: noarch: python From 3070dd823a2800f825ab33ebffead993ff69f863 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:20:31 -0500 Subject: [PATCH 0018/1813] Update hybracter to 0.6.0 (#45286) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index 8e85a27f1af6e..aca31cdfc5401 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.5.0" %} +{% set version = "0.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 6bdc2376e0000556622b957e765f27014972784700f306943b345956739d4592 + sha256: 2d7d79818f6b896e47c0ad4c4e4583d2028019a2d43c5aa502762c4a22cbacd1 build: number: 0 From 830891e5b4aecf9179d70bf13b19588fed2178e4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:29:58 -0500 Subject: [PATCH 0019/1813] Update abromics_galaxy_json_extractor to 0.8.3.4 (#45288) --- recipes/abromics_galaxy_json_extractor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abromics_galaxy_json_extractor/meta.yaml b/recipes/abromics_galaxy_json_extractor/meta.yaml index 9b20f38f812b2..ab4d067298934 100644 --- a/recipes/abromics_galaxy_json_extractor/meta.yaml +++ b/recipes/abromics_galaxy_json_extractor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.3" %} +{% set version = "0.8.3.4" %} context: {} @@ -8,7 +8,7 @@ package: source: url: https://gitlab.com/ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/archive/{{ version }}/abromics-galaxy-json-extractor-{{ version }}.tar.gz - sha256: '81fc614902567dfe83d57fc978bf98cc22e26a58f0e25e359c9d647df6f05bb9' + sha256: '4106ed76eb759f3bd3fcb866d18fdafce64f4ef6d364967f7ccee29b6af06d19' build: noarch: python From c4ac2a8a7535c67da720647ef6b80dd5b28de8df Mon Sep 17 00:00:00 2001 From: "Le (Lena) Huang" Date: Thu, 18 Jan 2024 10:31:36 -0500 Subject: [PATCH 0020/1813] update (#45283) --- recipes/dbcan/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/dbcan/meta.yaml b/recipes/dbcan/meta.yaml index 7be1bbfbd0487..34d2f399cac8b 100644 --- a/recipes/dbcan/meta.yaml +++ b/recipes/dbcan/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dbcan" %} -{% set version = "4.1.2" %} +{% set version = "4.1.3" %} package: name: "{{ name|lower }}" @@ -9,7 +9,7 @@ source: # the sha256 sum is generated by doing # wget -0- [URL] | shasum -a 256 url: https://github.com/linnabrown/run_dbcan/releases/download/{{ version }}/dbcan-{{ version }}.tar.gz - sha256: 3a675683379d1afc9f3444fc9894272f1485956df266a6ee4fc11a8f628e6d51 + sha256: 6346e0b6b2c810e2f808bc0bc901643c16f3eda2652d50b8f8470eb722fb419b build: number: 0 @@ -46,6 +46,7 @@ requirements: - openpyxl - matplotlib-base - session-info + - blast test: imports: From b0f7eb23b7952ec2ea96a8af5ea116e4abafa8e0 Mon Sep 17 00:00:00 2001 From: hjulienne Date: Thu, 18 Jan 2024 16:38:08 +0100 Subject: [PATCH 0021/1813] Raiss 4.0 (#45162) * added new tag for RAISS * corrected raiss recipe * formatted version constraints * added run export * updated dependancies * corrected sha sum * fixed version issue with scipy * update version number --------- Co-authored-by: hjulienn --- recipes/raiss/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/raiss/meta.yaml b/recipes/raiss/meta.yaml index 07f2b3b1215de..6ba190e766b4d 100644 --- a/recipes/raiss/meta.yaml +++ b/recipes/raiss/meta.yaml @@ -1,5 +1,6 @@ {% set name = "raiss" %} -{% set version = "4.0" %} + +{% set version = "4.0.1" %} package: name: {{ name }} @@ -7,7 +8,8 @@ package: source: url: https://gitlab.pasteur.fr/statistical-genetics/{{ name }}/-/archive/{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: 771a4ec126967daa367daa599178909cd182ed5d564c169b64e0491f1bb19714 + sha256: eb5cc6b67b395fbf5c2678a253dd7fd2c30c5f62a7358253778b1c6c1161a89f + build: noarch: python @@ -29,7 +31,7 @@ requirements: - pandas - python-dateutil - pytz - - scipy + - scipy >=1.7.0 - six - tzdata From 3b70fadff6e3a2b61b17490516ced91816f5d228 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 11:00:27 -0500 Subject: [PATCH 0022/1813] Update wgd to 2.0.25 (#45282) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index c67fb54a19082..aabbc58070e0f 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.24" %} +{% set version = "2.0.25" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: 60c986d848cacff15037567e02931c908d7644306e201ba48952810c1ff0545a + sha256: d43295772471abbade56b343f8e2152682594ed16fc8ca779a2a0ec642a784f5 build: number: 0 From 2800ff208b2cbad2cb35751e1bc1e2d1b895f178 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 13:00:39 -0500 Subject: [PATCH 0023/1813] Update nanometa-live to 0.4.2 (#45293) --- recipes/nanometa-live/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanometa-live/meta.yaml b/recipes/nanometa-live/meta.yaml index ab801d6964c57..8c98e0ee36a38 100644 --- a/recipes/nanometa-live/meta.yaml +++ b/recipes/nanometa-live/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanometa-live" %} -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/FOI-Bioinformatics/nanometa_live/archive/{{ version }}.tar.gz - sha256: bc241b82277b641df9d419cb014a80a223a5f2db47a596925663589d8dbda5c2 + sha256: 82bbb858a17468c481837bd17a32ec7b9e09789ce32a0dd9ec01dcc4e7dbdbe5 build: number: 0 From 28831fbe790028870c3ce309f03214084f94987c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 16:09:34 -0500 Subject: [PATCH 0024/1813] Update annonars to 0.34.0 (#45290) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index d7d44551f9f50..61ae02aad9578 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.33.0" %} +{% set version = "0.34.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 258cfc2aee680718fc1acc8bccddb571416e425198ca258ee295cdc42cc19f71 + sha256: 8b0725fc8d7e861bc08c96882f6e9e489b5079c10eb723295b26d2100e6e86f9 requirements: build: From 4be472d605a562570c4e9688cbe7008df335246a Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 18 Jan 2024 16:31:11 -0600 Subject: [PATCH 0025/1813] Add recipe for MGATK v0.7.0 (#45297) * Add recipe for MGATK v0.7.0 * add additional dependencies --- recipes/mgatk/meta.yaml | 66 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 recipes/mgatk/meta.yaml diff --git a/recipes/mgatk/meta.yaml b/recipes/mgatk/meta.yaml new file mode 100644 index 0000000000000..dcc431be31cd5 --- /dev/null +++ b/recipes/mgatk/meta.yaml @@ -0,0 +1,66 @@ +{% set name = "mgatk" %} +{% set version = "0.7.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgatk-{{ version }}.tar.gz + sha256: f42f5eb8fcfd38dd6ef3db853764071311cb70d841a73ff2f40f0a0c9e9d7de9 + +build: + number: 0 + noarch: python + entry_points: + - mgatk = mgatk.cli:main + - mgatk-del-find = mgatk.deletioncalling.clifind:main + - mgatk-del = mgatk.deletioncalling.clidel:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('mgatk', max_pin="x.x") }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - click + - pysam + - pytest + - snakemake-minimal + - biopython + - numpy + - pandas + - optparse-pretty + - regex + - ruamel.yaml + - openjdk + - picard-slim + - r-base + - r-dplyr + - r-data.table + - r-matrix + - bioconductor-genomicranges + - bioconductor-summarizedexperiment + +test: + imports: + - mgatk + commands: + - mgatk --help + - mgatk-del-find --help + - mgatk-del --help + +about: + home: https://github.com/caleblareau/mgatk + summary: Mitochondrial genome analysis toolkit. + license: MIT + license_family: MIT + license_file: LICENSE.txt + doc_url: https://github.com/caleblareau/mgatk/wiki + +extra: + recipe-maintainers: + - mencian From 9e5b2289a69862c3b9e1bfd77306b60eb41f1f28 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 18:04:20 -0500 Subject: [PATCH 0026/1813] Update nextstrain-cli to 8.0.0 (#45298) --- recipes/nextstrain-cli/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml index cdd7f714d9895..ea7189f07bb13 100644 --- a/recipes/nextstrain-cli/meta.yaml +++ b/recipes/nextstrain-cli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "7.4.0" %} +{% set version = "8.0.0" %} package: name: nextstrain-cli @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain-cli-{{ version }}.tar.gz - sha256: bc678d817dac6351466728122dff1ce37d7e8f3f8b8402fd2cef5822287b7de4 + sha256: 515fb4be3c013a9a30ef8cc28d8e7430d20e2edd840a9a3aa3419764b57e8268 build: - number: 1 + number: 0 noarch: python entry_points: - nextstrain = nextstrain.cli.__main__:main From 6f3f76d5ac2a87e58cd55ca7036ffff867c09632 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 19 Jan 2024 20:41:47 +1300 Subject: [PATCH 0027/1813] LTR_FINDER_parallel is now also exposed to /usr/local/bin (#45280) --- recipes/edta/build.sh | 9 +++++++++ recipes/edta/meta.yaml | 3 ++- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/recipes/edta/build.sh b/recipes/edta/build.sh index 729d94a5a9379..e47cfd13c7302 100644 --- a/recipes/edta/build.sh +++ b/recipes/edta/build.sh @@ -20,3 +20,12 @@ for name in ${EDTA_OTHER_PROGRAMS} ; do done ln -sf ${EDTA_DIR}/development/EDTA_processI.pl ${PREFIX}/bin/ + +LTR_FINDER_PARALLEL_DIR=${EDTA_DIR}/bin/LTR_FINDER_parallel + +cat <>${PREFIX}/bin/LTR_FINDER_parallel +#!/bin/bash +perl ${LTR_FINDER_PARALLEL_DIR}/LTR_FINDER_parallel \$@ +END + +chmod a+x ${PREFIX}/bin/LTR_FINDER_parallel \ No newline at end of file diff --git a/recipes/edta/meta.yaml b/recipes/edta/meta.yaml index 3e5f7651efd27..eb2e7f1763bc2 100644 --- a/recipes/edta/meta.yaml +++ b/recipes/edta/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('edta', max_pin='x') }} @@ -59,6 +59,7 @@ test: - EDTA_processI.pl -h 2>&1 | grep -i "Perform EDTA" - EDTA_raw.pl -h 2>&1 | grep -i "Obtain raw" - lib-test.pl -h 2>&1 | grep -i "To test" + - LTR_FINDER_parallel -check_dependencies > /dev/null about: home: https://github.com/oushujun/EDTA From 05df3a8ae4bf93e45fb8dd2167e8126dee8565e1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:43:19 -0500 Subject: [PATCH 0028/1813] Update ppanggolin to 2.0.1 (#45245) * Update ppanggolin to 2.0.0 * update with new requirements of 2.0.0 * add run_exports and relax version of mafft and mmseq2 * fix run_exports location * Fix name variable * test with cython <3 to solve os fail * move to v2.0.1 with patches to let the recipe compile on macOS --------- Co-authored-by: JeanMainguy --- recipes/ppanggolin/meta.yaml | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/recipes/ppanggolin/meta.yaml b/recipes/ppanggolin/meta.yaml index 4e0712795ef53..fe77191e7d636 100644 --- a/recipes/ppanggolin/meta.yaml +++ b/recipes/ppanggolin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.105" %} +{% set version = "2.0.1" %} package: name: ppanggolin @@ -6,36 +6,39 @@ package: source: url: https://github.com/labgem/PPanGGOLiN/archive/{{ version }}.tar.gz - sha256: 410a51029302d9aae534846fc5dde9c01c17aa63ae91c9d48db47e399d2d2a47 + sha256: 0e13410a03f825894ceccb7c7a85f8acee060cd98c720486fbb90df71cbd5275 build: - number: 1 + number: 0 skip: True # [py<37] + run_exports: + - {{ pin_subpackage("ppanggolin", max_pin="x") }} requirements: build: - {{ compiler('c') }} + host: - python - pip - - cython + - cython <3 run: - python - tqdm =4 - pytables =3 - - prodigal =2.6 + - pyrodigal =3 - aragorn =1.2 - infernal =1.1 - mmseqs2 - - networkx =2 + - networkx =3 - scipy =1 - - plotly =4 + - plotly =5 - gmpy2 =2 - numpy =1 - - pandas =1 + - pandas =2 - colorlover =0.3 - mafft - - bokeh =2 + - bokeh =3 test: commands: @@ -48,6 +51,7 @@ test: about: license: CeCiLL 2.1 home: https://github.com/labgem/PPanGGOLiN + doc_url: https://ppanggolin.readthedocs.io summary: "PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph" extra: From fd4d62f9eb7bfd41e258356f38938a2e838dde0c Mon Sep 17 00:00:00 2001 From: Justin Sing <32938975+singjc@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:48:07 -0500 Subject: [PATCH 0029/1813] Add recipe for massdash (#45189) * [ADD] recipe for massdash * [FIX] description * [FIX] run_exports, dependency version spacing and matplotlib-base * [FIX] dependency version spacing * [ADD] dev requirements * [ADD] dev requirements * [MOVE] dev requirements to host * [FIX] license --- recipes/massdash/meta.yaml | 56 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 recipes/massdash/meta.yaml diff --git a/recipes/massdash/meta.yaml b/recipes/massdash/meta.yaml new file mode 100644 index 0000000000000..ea81e6b4d1607 --- /dev/null +++ b/recipes/massdash/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "massdash" %} +{% set version = "0.0.5" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: f5258b934d09df5e6d9f22e3dc82bb806aeb28a987b6d90bba49fd7b6fe9f8be + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('massdash', max_pin='x.x') }} + +requirements: + host: + - pip + - python + - flake8 + - flit + - flit-core + - pylint + - snapshottest + run: + - bokeh ==2.4.3 + - click + - joblib + - matplotlib-base + - matplotlib-venn + - upsetplot + - numpy >=1.9.0 + - pandas >=0.17 + - plotly + - psutil + - pyopenms + - scipy + - streamlit + - tqdm + +test: + imports: + - massdash + +about: + home: https://github.com/Roestlab/massdash + license: BSD + license_family: BSD + summary: MassDash is a streamlined DIA mass spec visualization, analysis, optimization, and rapid prototyping. + +extra: + recipe-maintainers: + - singjc From 5f1c15147ba175b447ea7d0ddb6037f7fab7ab7b Mon Sep 17 00:00:00 2001 From: BenoitMorel Date: Fri, 19 Jan 2024 08:49:13 +0100 Subject: [PATCH 0030/1813] update generax (#45153) * update generax * update generax build number * add run exports * Remove patch * Remove patch * recompile * rerun checks * rerun checks --------- Co-authored-by: BenoitMorel --- recipes/generax/meta.yaml | 12 ++++++------ recipes/generax/patch | 12 ------------ 2 files changed, 6 insertions(+), 18 deletions(-) delete mode 100644 recipes/generax/patch diff --git a/recipes/generax/meta.yaml b/recipes/generax/meta.yaml index 6463eb3db5c99..0c662c20d3c3d 100644 --- a/recipes/generax/meta.yaml +++ b/recipes/generax/meta.yaml @@ -1,6 +1,7 @@ {% set name = "generax" %} -{% set version = "2.0.4" %} - +{% set version = "2.1.3" %} + + package: name: {{ name|lower }} version: {{ version }} @@ -9,12 +10,11 @@ source: git_url: https://github.com/benoitmorel/{{ name|lower }}.git git_rev: {{ version }} sha256: unused - patches: - - patch build: - number: 3 - + number: 0 + run_exports: + - {{ pin_subpackage('generax', max_pin="x") }} requirements: build: - make diff --git a/recipes/generax/patch b/recipes/generax/patch deleted file mode 100644 index 20728f85402ef..0000000000000 --- a/recipes/generax/patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/src/core/IO/Model.hpp b/src/core/IO/Model.hpp -index 0eb6ce1..3a16942 100644 ---- a/src/core/IO/Model.hpp -+++ b/src/core/IO/Model.hpp -@@ -6,6 +6,7 @@ - - #include - #include -+#include - extern "C" { - #include - #include From 2fbf82fb9672764f191f69c2450048232caa4cf0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:50:12 -0500 Subject: [PATCH 0031/1813] Update pyfaidx to 0.8.1.1 (#45294) * Update pyfaidx to 0.8.1 * Update pyfaidx to 0.8.1.1 --- recipes/pyfaidx/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyfaidx/meta.yaml b/recipes/pyfaidx/meta.yaml index 9209e777f8e00..eb721ce14f0d7 100644 --- a/recipes/pyfaidx/meta.yaml +++ b/recipes/pyfaidx/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.8.0" %} +{% set version = "0.8.1.1" %} package: name: pyfaidx version: {{ version }} source: - url: https://files.pythonhosted.org/packages/ef/95/aa7e6d1c1b68e64234d5ed985a761edbbce124baea17c2056935626958d2/pyfaidx-0.8.0.tar.gz - sha256: 1eed70f4eafb4ba9c4cf7022cd748947b8ebe0f4c86cb56f42f587ab7f2da027 + url: https://files.pythonhosted.org/packages/0e/32/a89e956d4f27bd8ab4d92f6b27e46386975add4ad13e54504012afa3d025/pyfaidx-0.8.1.1.tar.gz + sha256: 6f0482352619f2cc56003ca22321bdb0d0764b656795bc1e4062b1fa9b08686b build: number: 0 From 3f9448ed474f12985d9c455805ace9e65ca33fb1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:50:42 -0500 Subject: [PATCH 0032/1813] Update protmapper to 0.0.29 (#45301) --- recipes/protmapper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/protmapper/meta.yaml b/recipes/protmapper/meta.yaml index a7fa1af749531..fe4ac6f625278 100644 --- a/recipes/protmapper/meta.yaml +++ b/recipes/protmapper/meta.yaml @@ -1,6 +1,6 @@ {% set name = "protmapper" %} -{% set version = "0.0.28" %} -{% set sha256 = "0cd18592dc6ae67e2ec723395c6adfe5221f8ce73e7185c3ac85348639c29a1e" %} +{% set version = "0.0.29" %} +{% set sha256 = "d0d10198fb000401d03ba6c271869970caf8e1c8b46db686d2eed153fa8c2257" %} package: name: {{ name|lower }} From ddb238c975b11f820dcfdd3d3b5f166686c7fa50 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:51:08 -0500 Subject: [PATCH 0033/1813] Update pango-designation to 1.24 (#45300) --- recipes/pango-designation/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pango-designation/meta.yaml b/recipes/pango-designation/meta.yaml index 869455a8746fb..3c559b4e5981f 100644 --- a/recipes/pango-designation/meta.yaml +++ b/recipes/pango-designation/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.23" %} +{% set version = "1.24" %} package: name: pango-designation @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pango-designation/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5692d92d4b7ff902464552e81d71fc25dcafd0ada175af3b143246c14fc6d9c1 + sha256: 9b84365c503a71ac5aadf47b977aa022450457492b24955149f26469f733f898 build: number: 0 From f6bc7c6c69f4ef78e4829d5f39e96bd4c383f430 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:51:35 -0500 Subject: [PATCH 0034/1813] Update vg to 1.54.0 (#45289) --- recipes/vg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml index 8549c995de117..c67d295ba6970 100644 --- a/recipes/vg/meta.yaml +++ b/recipes/vg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vg" %} -{% set version = "1.53.0" %} +{% set version = "1.54.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg - sha256: a86dfc47c143af9f9a89c5e4595ed32b493384aac2b067f97d0684ec2d9a413b + sha256: 84bee2444b3714b5b8672ea4a4e28063c0eb41a22b8b7359641c10467fe8b247 build: number: 0 From 4a90b4a7dedfdaeb04f967573fc676fdf53caee7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:52:07 -0500 Subject: [PATCH 0035/1813] Update metdatamodel to 0.6.0 (#45276) Co-authored-by: Helge Hecht --- recipes/metdatamodel/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metdatamodel/meta.yaml b/recipes/metdatamodel/meta.yaml index e83742363e601..a36b4b670c13c 100644 --- a/recipes/metdatamodel/meta.yaml +++ b/recipes/metdatamodel/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metdatamodel" %} -{% set version = "0.5.5" %} +{% set version = "0.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metDataModel-{{ version }}.tar.gz - sha256: 8ed0c978ffe4e1a75d169ae58687cb86f15c991d05529748791c554c9f1103a9 + sha256: 58bdbf5099c059d6e481921b017bc667e73623c1a1ba840d8b3f42d79e15b2cc build: noarch: python From 1141839f5c65ac656949a481d2ec628e015f4ebc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 10:38:35 -0500 Subject: [PATCH 0036/1813] Update vsearch to 2.27.0 (#45305) --- recipes/vsearch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index fdfb483ba13ff..d453c4b0d1b98 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.26.1" %} -{% set sha256 = "dc8513376405fc01ca3742624177113752870b05bb682fe1bf62d190d0a696bd" %} +{% set version = "2.27.0" %} +{% set sha256 = "18d6fc919adce684c01fe57797e2adbf5b4d4f6cf5ef169378ad473797be38ae" %} package: name: vsearch From 869b1ba4d53494b5295d68c2182678687aa4c295 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:38:02 -0500 Subject: [PATCH 0037/1813] Update pyrodigal to 3.2.2 (#45327) --- recipes/pyrodigal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml index 79aae4b1a1021..94764527e29ad 100644 --- a/recipes/pyrodigal/meta.yaml +++ b/recipes/pyrodigal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal" %} -{% set version = "3.2.1" %} +{% set version = "3.2.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7c0bb83eafa888bdc5d931fb3a1f6abc35247f96abc3f9e557a0109e85cbdd35 + sha256: 0e02b2089df29c3c0f1379364664f4a83da12373233bb74d7a95d24a346b02ec build: number: 0 From 89c8ce1fa0872483742412d80a6f3b8ca473f02c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:38:36 -0500 Subject: [PATCH 0038/1813] Update pyopal to 0.5.1 (#45324) * Update pyopal to 0.5.0 * Update pyopal to 0.5.1 --- recipes/pyopal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyopal/meta.yaml b/recipes/pyopal/meta.yaml index 300e327a6f612..fe7ef5a8f3e0e 100644 --- a/recipes/pyopal/meta.yaml +++ b/recipes/pyopal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyopal" %} -{% set version = "0.4.1" %} +{% set version = "0.5.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: abfc3cb741eaaaf0185af6efb44b56f458f54fe7b1d4d5b9c54bf60da73e245a + sha256: debc526d00f605f1a9f75ece2bb124b6b370f8649857bc33ec7bdc264e8cc6cb build: number: 0 From e0f5986c1994307ae37266d439ee85d6ee114436 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:38:48 -0500 Subject: [PATCH 0039/1813] Update pymochi to 1.0 (#45323) --- recipes/pymochi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pymochi/meta.yaml b/recipes/pymochi/meta.yaml index 6d20abd0c7781..7ce09a732e24f 100644 --- a/recipes/pymochi/meta.yaml +++ b/recipes/pymochi/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9" %} +{% set version = "1.0" %} {% set github = "https://github.com/lehner-lab/MoCHI" %} package: @@ -7,7 +7,7 @@ package: source: url: {{ github }}/archive/v{{ version }}.tar.gz - sha256: cec741cc8cda6affc9f4c2fd470afd28ee7c5ec9282bd59a4d4102a6e3afe005 + sha256: 93bd3c32b5a686d5bacecf3d48678497eeed3bf799198ab453e21accefecbae7 build: noarch: python From 7d8e8183b097bb1615e4e9ed7af052a706403a03 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:39:24 -0500 Subject: [PATCH 0040/1813] Update itolapi to 4.1.4 (#45322) --- recipes/itolapi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/itolapi/meta.yaml b/recipes/itolapi/meta.yaml index 14938580238b2..0e664d28481a5 100644 --- a/recipes/itolapi/meta.yaml +++ b/recipes/itolapi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "itolapi" %} -{% set version = "4.1.3" %} +{% set version = "4.1.4" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b4f683630e4c816529b79a326de515809ad6174e473b6a25bc3954aaadd16778 + sha256: 68e87ba51d209da556b0e373b3b0456b644a1a732c193fedbd7785ff37b6a2cb build: noarch: python From b026ec2d1773da68fdcf81a38ed7424c5dfb2e98 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:39:54 -0500 Subject: [PATCH 0041/1813] Update assemblycomparator2 to 2.5.16 (#45310) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index f0d50c8973c9b..b5640b7519dd6 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.15" %} +{% set version = "2.5.16" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9605f4021710e975365090fba1c13c2005c46978cec48c6cabe678167c86d33e + sha256: 197d157e67a04df4f63b88191106dce7219eab8ee4aa146b74d4fb796a505e93 build: From 8529035b2aef6fffbbe53df4df6dd1ef393d341f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:40:53 -0500 Subject: [PATCH 0042/1813] Update dajin2 to 0.4.0 (#45319) --- recipes/dajin2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index eca8b4b9afad9..9c3310af914d4 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.3.6" %} +{% set version = "0.4.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: cf9e686f78041682589c8e90bcac8eb2ad6473987c96bd574faf36e0b461613c + sha256: 0b0abcc8f40679bec605c85643b069b55914ac1ac9031f6ad73c319899abd002 build: entry_points: From d77f275f964c2a242787d6c4ab5327d2fa5e41cb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:41:01 -0500 Subject: [PATCH 0043/1813] Update orthoflow to 0.3.1 (#45317) --- recipes/orthoflow/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/orthoflow/meta.yaml b/recipes/orthoflow/meta.yaml index ca8111d636967..e693187f59ef0 100644 --- a/recipes/orthoflow/meta.yaml +++ b/recipes/orthoflow/meta.yaml @@ -1,5 +1,5 @@ {% set name = "orthoflow" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/orthoflow-{{ version }}.tar.gz - sha256: bdfb03dbdccec636adee9be5c8a5a8eec682c82f3435da90ae7c504a2899f9e6 + sha256: fb7b14dcc52d3d4ce3ef39cf50a2bf68a43f5cd2b46898b3b50a054b78fc91c8 build: entry_points: From 4a1471aedb23d7292bc674ab049086527078411c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:41:13 -0500 Subject: [PATCH 0044/1813] Update dupsifter to 1.2.1.20240119 (#45315) --- recipes/dupsifter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dupsifter/meta.yaml b/recipes/dupsifter/meta.yaml index 7a256ef424987..2d91cf55de8e3 100644 --- a/recipes/dupsifter/meta.yaml +++ b/recipes/dupsifter/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.2.0.20230926' %} +{% set version = '1.2.1.20240119' %} package: name: dupsifter @@ -11,7 +11,7 @@ build: source: url: https://github.com/huishenlab/dupsifter/releases/download/v{{ version }}/release-source.zip - sha256: 7a4dfe194d51ac09b30f85f6c77f9e8c31c62e636f56c09748688b32755d9521 + sha256: ca3db67e36f9a3d054acf9fbaf0dee1037781d468d7f094ea5d3852610448e7a patches: - patch From 5dc9dcaef1ee50ba9ab8f6f60a9fc63fdcf3a9ae Mon Sep 17 00:00:00 2001 From: Joerg Fallmann Date: Sun, 21 Jan 2024 20:47:01 +0100 Subject: [PATCH 0045/1813] snakemake pinning, version 8 major changes that break everything (#45302) --- recipes/monsda/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/monsda/meta.yaml b/recipes/monsda/meta.yaml index d923fef7e8211..68ab0c3b3a547 100644 --- a/recipes/monsda/meta.yaml +++ b/recipes/monsda/meta.yaml @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --use-pep517 --no-deps --ignore-installed -vvv" entry_points: - monsda = MONSDA.RunMONSDA:main @@ -35,7 +35,7 @@ requirements: - pandas >=1.4.1 - perl >=5.32.1 - scipy >=1.7.0 - - snakemake >=7.32.3 + - snakemake >=7.32.3,<8.0.0 - versioneer >=0.20 - yaml >=0.2.5 - black >=21.5b2 From 2020eee1405a4cee8f9cbc62f34bfd0574c5b33b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 15:28:44 -0500 Subject: [PATCH 0046/1813] Update massdash to 0.0.6 (#45303) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/massdash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/massdash/meta.yaml b/recipes/massdash/meta.yaml index ea81e6b4d1607..b3ae8c95452b5 100644 --- a/recipes/massdash/meta.yaml +++ b/recipes/massdash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "massdash" %} -{% set version = "0.0.5" %} +{% set version = "0.0.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f5258b934d09df5e6d9f22e3dc82bb806aeb28a987b6d90bba49fd7b6fe9f8be + sha256: f2b4160745ddcd96698f92c7d9c86b5a354970ace233924a0e26cba88421a761 build: number: 0 From a6d43de65f9c235d118503f82068198f9184625c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 15:44:41 -0500 Subject: [PATCH 0047/1813] Update cyvcf2 to 0.30.27 (#45308) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cyvcf2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cyvcf2/meta.yaml b/recipes/cyvcf2/meta.yaml index b959105c2467d..26df81e5b90b8 100644 --- a/recipes/cyvcf2/meta.yaml +++ b/recipes/cyvcf2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cyvcf2" %} -{% set version = "0.30.26" %} -{% set sha256 = "e8473957181ef7b037213d110217046d107cd6a0eb4671f13c47a7a24412db05" %} +{% set version = "0.30.27" %} +{% set sha256 = "f1b12c1fb78bd039c5d94b0ff2d838edfa0716c0e4902ad3ecec3d48da3d4ff9" %} package: name: {{ name }} From 1ca04427dd322d5cc86e9385f5328218f703253e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 15:51:18 -0500 Subject: [PATCH 0048/1813] Update galah to 0.4.0 (#45285) * Update galah to 0.4.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/galah/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/galah/meta.yaml b/recipes/galah/meta.yaml index 362a196815042..3259624da0826 100644 --- a/recipes/galah/meta.yaml +++ b/recipes/galah/meta.yaml @@ -1,14 +1,16 @@ -{% set version = "0.3.1" %} +{% set version = "0.4.0" %} {% set name = "galah" %} -{% set sha256 = "78a278a2a4d2e5f074115e41a38c426fab328d3deaac84cb55cded77e9c97428" %} +{% set sha256 = "9b40cc805df15461e5b07fd3108663cc92d286030c17fefe5a33716b5b8fa10a" %} package: name: {{ name }} version: {{ version }} build: - number: 3 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('galah', max_pin="x.x") }} source: url: https://github.com/wwood/{{ name }}/archive/v{{version}}.tar.gz @@ -29,5 +31,6 @@ test: about: home: https://github.com/wwood/galah license: GPL-3.0-only + license_family: GPL3 license_file: LICENCE.txt summary: Galah aims to be a more scalable metagenome assembled genome (MAG) dereplication method. From 72a0061ff5a9ae87d5a9728017bcecf07d2b035c Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sun, 21 Jan 2024 21:53:31 +0100 Subject: [PATCH 0049/1813] bump ampvis2 and update URL (#45313) * bump ampvis2 and update URL * add run_exports * reset build * fix run_exports copy paste error --- recipes/r-ampvis2/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/r-ampvis2/meta.yaml b/recipes/r-ampvis2/meta.yaml index fc5c07195db77..57c01fefc9001 100644 --- a/recipes/r-ampvis2/meta.yaml +++ b/recipes/r-ampvis2/meta.yaml @@ -1,20 +1,22 @@ {% set name = "r-ampvis2" %} -{% set version = "2.7.32" %} +{% set version = "2.8.6" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/MadsAlbertsen/ampvis2/archive/refs/tags/v{{ version }}.tar.gz - sha256: b75f2e92e3d8999e47b8004824b7d1e0a9bb7b0c5fb116296e11a0d87ec0ac4a + url: https://github.com/KasperSkytte/ampvis2/archive/refs/tags/v{{ version }}.tar.gz + sha256: 98ef7a7f899b5d866552f10ae9a005c1c4bd41667e88cb771006811f8d6f50d7 build: - number: 2 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-ampvis2', max_pin="x.x") }} requirements: host: From 3f6faa391a04f806d9c3490896cc7f7d2eb193c7 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sun, 21 Jan 2024 21:55:06 +0100 Subject: [PATCH 0050/1813] add revoluzer (#45296) * add revoluzer * add reun_exports * try 0.1.1 * fix link and sha * add glpk requirement * cmake trace * fix debug and add CMAKE_INCLUDE_PATH * debug * BUILD_PREFIX? * BUILD_PREFIX?? * CXXFLAGS * add boost * bump and test * cleanup * skip osx for now --- recipes/revoluzer/build.sh | 9 ++++++++ recipes/revoluzer/meta.yaml | 44 +++++++++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 recipes/revoluzer/build.sh create mode 100644 recipes/revoluzer/meta.yaml diff --git a/recipes/revoluzer/build.sh b/recipes/revoluzer/build.sh new file mode 100644 index 0000000000000..175ed562969c8 --- /dev/null +++ b/recipes/revoluzer/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash +CXXFLAGS="-I${BUILD_PREFIX}/include $CXXFLAGS" + + +cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' +cmake --build build +mkdir -p $PREFIX/bin +echo "installing: $(find build/src -type f -executable)" +mv $(find build/src -type f -executable) $PREFIX/bin diff --git a/recipes/revoluzer/meta.yaml b/recipes/revoluzer/meta.yaml new file mode 100644 index 0000000000000..1bb05b1981a8b --- /dev/null +++ b/recipes/revoluzer/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "revoluzer" %} +{% set version = "0.1.2" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: https://gitlab.com/Bernt/{{ name }}/-/archive/{{ version }}/{{ name }}-{{ version }}.tar.gz + sha256: f2957266157797c4fe2338e07ea756ad8fc688efe90b6b48a83744a0b82c986a + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('revoluzer', max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - cmake + - make + - boost-cpp + - glpk + host: + run: + - boost-cpp + - glpk + +test: + commands: + - crex --help + - trex -h + +about: + home: https://gitlab.com/Bernt/revoluzer/ + license: GPL-3.0-or-later + license_file: LICENSE + summary: Genome rearrangement analysis tools + +extra: + recipe-maintainers: + - bernt-matthias From c0d60345c5c7835b419237c59e7488af673ff878 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 15:58:11 -0500 Subject: [PATCH 0051/1813] Update snakemake to 8.2.3 (#45311) * Update snakemake to 8.2.2 * Update snakemake to 8.2.3 --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 1904589e0671a..e40d63fbdb441 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.2.1" %} +{% set version = "8.2.3" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: f177ada98188a10602aa2ed758fc9b7ff13e7107c5e582463ae681c525c28f0c + sha256: d31b7e5ceaa255038475287154b641a973cba9ff7cca6880f109f18ab703351a build: number: 0 From db343dee025d05f380b1fb06a2b24aa7c78a57bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 16:04:48 -0500 Subject: [PATCH 0052/1813] Update pegasusio to 0.9.0 (#45093) * Update pegasusio to 0.8.2 * add pegasusio * Update pegasusio to 0.9.0 --------- Co-authored-by: joshuazhuang7 --- recipes/pegasusio/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/pegasusio/meta.yaml b/recipes/pegasusio/meta.yaml index 046eedbbb6559..c217cf33b836f 100644 --- a/recipes/pegasusio/meta.yaml +++ b/recipes/pegasusio/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pegasusio" %} -{% set version = "0.8.1" %} +{% set version = "0.9.0" %} package: name: {{ name|lower }} @@ -7,14 +7,16 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "ea18b963315726a18819740b91df316f43c50b87f248092be601756b30f49d44" + sha256: "fc7d1b33d46418a216de50426e29af101268e510ea171b36458498293b5dfdcc" build: number: 0 - skip: True # [py<37] + skip: True # [py < 37] entry_points: - pegasusio = pegasusio.__main__:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('pegasusio', max_pin="x.x") }} requirements: build: @@ -56,6 +58,7 @@ about: home: https://github.com/lilab-bcb/pegasusio doc_url: https://pegasusio.readthedocs.io license: BSD-3-Clause + license_family: BSD license_file: LICENSE summary: "PegasusIO is the IO package for Pegasus." From e243eb5343a3bc8fae259f283624c87dbf8a913a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 16:06:37 -0500 Subject: [PATCH 0053/1813] Update parsnp to 2.0.2 (#45085) * Update parsnp to 2.0.0 * Update meta.yaml * add tqdm * Update parsnp to 2.0.1 * Update parsnp to 2.0.2 * Update meta.yaml * Update meta.yaml * hack partition into directory (need to change to proper python build) * Update run_test.sh --------- Co-authored-by: Bryce Kille Co-authored-by: joshuazhuang7 --- recipes/parsnp/build.sh | 1 + recipes/parsnp/meta.yaml | 30 +++++++++++++++--------------- recipes/parsnp/run_test.sh | 1 + 3 files changed, 17 insertions(+), 15 deletions(-) diff --git a/recipes/parsnp/build.sh b/recipes/parsnp/build.sh index f8fa0b7b71356..8c6ca7f6a253e 100644 --- a/recipes/parsnp/build.sh +++ b/recipes/parsnp/build.sh @@ -34,6 +34,7 @@ rm -R muscle/m4 cp parsnp $PREFIX/bin cp extend.py $PREFIX/bin cp logger.py $PREFIX/bin +cp partition.py $PREFIX/bin cp src/parsnp_core $PREFIX/bin/bin cp template.ini $PREFIX/bin cp -R bin $PREFIX/bin diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index acc3bfddfea80..5591dab327142 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -1,16 +1,18 @@ -{% set version = "1.7.4" %} +{% set version = "2.0.2" %} package: name: parsnp version: '{{version}}' source: - url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" - sha256: c24a1b395b1ddb6ab2a1f1c41e7e575b45da2ffed99581225be05fdad761684f + url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" + sha256: 1d9a4c6e5b414511ebc0052e3c9e6e32984b545ef8816086ed1d74af69c27c8f build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('parsnp', max_pin="x") }} requirements: build: @@ -19,31 +21,29 @@ requirements: - autoconf - libtool - make - - llvm-openmp # [osx] - - openmp # [linux] host: - zlib - llvm-openmp # [osx] - - openmp # [linux] + - openmp # [linux] run: - python >=3.7 - llvm-openmp # [osx] - - openmp # [linux] - - harvesttools - - fasttree - - phipack + - openmp # [linux] - biopython - - numpy + - numpy - zlib - phipack - raxml - fasttree - - fastani # [linux] - - mash + - fastani # [linux] + - mash - harvesttools - - mafft + - pyspoa + - tqdm about: home: https://github.com/marbl/parsnp license: "custom; see https://raw.githubusercontent.com/marbl/parsnp/master/LICENSE" summary: Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. + doc_url: "https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html" + dev_url: https://github.com/marbl/parsnp diff --git a/recipes/parsnp/run_test.sh b/recipes/parsnp/run_test.sh index d8e2ab432847e..73e2775eda56a 100644 --- a/recipes/parsnp/run_test.sh +++ b/recipes/parsnp/run_test.sh @@ -9,3 +9,4 @@ parsnp -r ! -d mers_virus/genomes/*.fna -o test2 --verbose parsnp -g mers_virus/ref/England1.gbk -d mers_virus/genomes/*.fna -p 2 -C 1000 -c -o test --verbose --use-fasttree parsnp -r ! -d mers_virus/genomes/*.fna -o test2 --verbose -p 2 parsnp -r ! -d mers_virus/genomes/*.fna -o test3 --verbose -p 2 --extend-lcbs +parsnp -r ! -d mers_virus/genomes/*.fna -o test4 --verbose -p 2 --partition --partition-size 10 From 8a2ab394779cc9ee57d1290adef89ddf31ec5afc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 16:33:12 -0500 Subject: [PATCH 0054/1813] Update r-pathfindr to 2.3.1 (#45316) --- recipes/r-pathfindr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-pathfindr/meta.yaml b/recipes/r-pathfindr/meta.yaml index 7b75c815daaee..4a76e0d8a98db 100644 --- a/recipes/r-pathfindr/meta.yaml +++ b/recipes/r-pathfindr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.3.0' %} +{% set version = '2.3.1' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -11,7 +11,7 @@ source: url: - {{ cran_mirror }}/src/contrib/pathfindR_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/pathfindR/pathfindR_{{ version }}.tar.gz - sha256: e7fc4f10859890af5ab17cc7870efac64614f234059f5734ddd7af705f67281b + sha256: 03b766e4799dbf2083717cd9a8a302beaaa58eaec9499b3b9b9e5e55e50c5694 build: merge_build_host: True # [win] From 3b1e17b03c7ddfda73351da7cc2b6228bbaef5bf Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sun, 21 Jan 2024 16:50:32 -0600 Subject: [PATCH 0055/1813] Update MOODS to 1.9.4.2 (#45330) --- recipes/moods/build.sh | 24 ++++++++++++------------ recipes/moods/meta.yaml | 28 +++++++++++++++------------- 2 files changed, 27 insertions(+), 25 deletions(-) diff --git a/recipes/moods/build.sh b/recipes/moods/build.sh index 9fd7ba71a6699..689926c02722e 100644 --- a/recipes/moods/build.sh +++ b/recipes/moods/build.sh @@ -1,17 +1,17 @@ #!/bin/bash -cat >setup_compile.patch << EOF ---- setup.py 2018-07-18 09:44:45.000000000 -0700 -+++ new_setup.py 2018-07-18 09:46:32.000000000 -0700 -@@ -7,7 +7,7 @@ - from distutils.core import setup, Extension - +cat > setup.py.patch << EOF +--- a/setup.py ++++ b/setup.py +@@ -4,7 +4,7 @@ from setuptools import setup, Extension + from os import path + common_includes = ["core/"] --common_compile_args = ['-march=native', '-O3', '-fPIC', '--std=c++11'] +-common_compile_args = ['-O3', '-fPIC', '--std=c++11'] +common_compile_args = ['-mtune=generic', '-O3', '-fPIC', '--std=c++11'] - - + tools_mod = Extension('MOODS._tools', + sources=['core/tools_wrap.cxx', EOF -patch setup.py setup_compile.patch -rm setup_compile.patch -$PYTHON setup.py install --record=record.txt +patch setup.py setup.py.patch +rm setup.py.patch +${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation diff --git a/recipes/moods/meta.yaml b/recipes/moods/meta.yaml index d516f94e805d6..01727f6f25eda 100644 --- a/recipes/moods/meta.yaml +++ b/recipes/moods/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "1.9.4.1" %} +{% set name = "moods" %} +{% set version = "1.9.4.2" %} package: - name: moods + name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/jhkorhonen/MOODS/releases/download/v{{ version }}/MOODS-python-{{ version }}.tar.gz - sha256: 7fd4d634bc2258421859d720afb9e38b4015b92d1ffc7aaeeb5422ce8b26d65e + url: https://pypi.io/packages/source/{{ name[0] }}/mira-moods/mira-moods-{{ version }}.tar.gz + sha256: e694e37c7487286801bffcda3e0576157960007919dd5ceb8b5a1626dc2968e1 build: - number: 4 + number: 0 + skip: True # [py < 36] + run_exports: + - {{ pin_subpackage('moods', max_pin="x") }} requirements: build: - - {{ compiler('c') }} - {{ compiler('cxx') }} host: - python - - swig # [py3k] - + - pip run: - python - - swig # [py3k] test: imports: - MOODS.scan about: - home: https://github.com/jhkorhonen/MOODS - license: GPLv3 - license_family: GPL + home: https://www.cs.helsinki.fi/group/pssmfind/ + summary: 'MOODS: Motif Occurrence Detection Suite' + license: GPL-3.0-or-later + license_family: GPL3 license_file: COPYING.GPLv3 - summary: MOODS, Motif Occurrence Detection Suite + dev_url: https://github.com/jhkorhonen/MOODS extra: identifiers: From a3e81745a4901de00c6e5f0af56b3b2f5e2882c3 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino <62253982+AndreaGuarracino@users.noreply.github.com> Date: Sun, 21 Jan 2024 18:42:16 -0600 Subject: [PATCH 0056/1813] Update irissv to 1.0.5 (#45329) * update version, sha256 and build number * add `run_exports` * update url --- recipes/irissv/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/irissv/meta.yaml b/recipes/irissv/meta.yaml index 88b85d9548522..842485ab0d1d9 100644 --- a/recipes/irissv/meta.yaml +++ b/recipes/irissv/meta.yaml @@ -1,16 +1,19 @@ -{% set version = "1.0.4" %} +{% set name = "irissv" %} +{% set version = "1.0.5" %} package: - name: irissv + name: "{{ name }}" version: {{ version }} source: - url: https://github.com/mkirsche/Iris/archive/{{ version }}.tar.gz - sha256: 1a7b609fa582abf901ef7392dd84fbcdabdca930be28cb0decb9fd7389aff6a2 + url: https://github.com/mkirsche/Iris/archive/refs/tags/v{{ version }}.tar.gz + sha256: a71718d418fb8b1afacbe2b3a6b91fd50cadc9e12c0b532739b955e455913b0b build: noarch: generic - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: run: From b100b748dfd500ab3fc8aed49174d7008b58007a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 19:58:42 -0500 Subject: [PATCH 0057/1813] Update kingfisher to 0.4.1 (#45281) --- recipes/kingfisher/meta.yaml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/recipes/kingfisher/meta.yaml b/recipes/kingfisher/meta.yaml index 855fa0bd6e4fb..82a4ed31a27c7 100644 --- a/recipes/kingfisher/meta.yaml +++ b/recipes/kingfisher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kingfisher" %} -{% set version = "0.3.1" %} +{% set version = "0.4.1" %} package: name: {{ name }} @@ -7,12 +7,12 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/kingfisher-{{ version }}.tar.gz - sha256: 2d2dae22f7345a5ad7ba8d64e310a9033667ca09aabdf3bea4ace05a629c388f + sha256: b74510c997db71432b4feb03398b8432b883d873d0d05eb2f0e5a1dafbce42f6 build: noarch: python number: 0 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps -vvv run_exports: - {{ pin_subpackage('kingfisher', max_pin="x") }} @@ -39,15 +39,13 @@ test: imports: - kingfisher commands: - - pip check - kingfisher --version | grep {{ version }} - requires: - - pip about: home: https://github.com/wwood/kingfisher-download summary: Download/extract biological FASTA/Q read data and metadata license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENCE.txt extra: From a6fb9ddea53979436535adca225ce559e01ef0d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 00:07:07 -0500 Subject: [PATCH 0058/1813] Update phables to 1.3.0 (#45333) --- recipes/phables/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phables/meta.yaml b/recipes/phables/meta.yaml index a021fa80dec1f..c2f2754b2359c 100644 --- a/recipes/phables/meta.yaml +++ b/recipes/phables/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phables" %} -{% set version = "1.2.2" %} +{% set version = "1.3.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/Vini2/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 316b6f3c9c2a0267745b0ebbaf2f8e82084f3863695274a4c0c6c58d248b4842 + sha256: bded81ddbfdce0b5143da3ebf51e56b1fe61f3b23c282433940c0e357014e642 build: number: 0 From c3ba9525199eceb0033d2a9a6acff9b25677730c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Mon, 22 Jan 2024 13:15:04 +0100 Subject: [PATCH 0059/1813] new recipe svync (#45338) --- recipes/svync/build.sh | 4 ++++ recipes/svync/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 recipes/svync/build.sh create mode 100644 recipes/svync/meta.yaml diff --git a/recipes/svync/build.sh b/recipes/svync/build.sh new file mode 100644 index 0000000000000..888542f1bb2ed --- /dev/null +++ b/recipes/svync/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +chmod a+x svync* +mkdir -p $PREFIX/bin +cp svync* $PREFIX/bin/svync \ No newline at end of file diff --git a/recipes/svync/meta.yaml b/recipes/svync/meta.yaml new file mode 100644 index 0000000000000..a19463ec08781 --- /dev/null +++ b/recipes/svync/meta.yaml @@ -0,0 +1,36 @@ +{% set version = '0.1.0' %} +{% set name = 'svync' %} + +package: + name: {{ name }} + version: {{ version }} + +source: + - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-darwin-amd64.tar.gz # [osx-amd64] + md5: 62bc02c3f3dc52fd02b998f6f0223216 # [osx] + - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-linux-amd64.tar.gz # [linux] + md5: dbc6b403d5ce1bcef9ba07ad7e1a5dc9 # [linux] + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + run: + - tabix + +test: + commands: + - "{{ name }} --help" + - bgzip -h + +extra: + skip-lints: + - should_be_noarch_generic # uses per platform binaries + - should_not_be_noarch_source # uses binaries + +about: + home: https://github.com/nvnieuwk/svync + license: MIT + summary: A tool to standardize VCF files from structural variant callers From 7f79bd0cbfdba03d8cb632de375df4e12456a79f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 07:16:18 -0500 Subject: [PATCH 0060/1813] Update varlociraptor to 8.4.3 (#45337) --- recipes/varlociraptor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index 8fb5cf321e92c..a499dd821034d 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.2" %} +{% set version = "8.4.3" %} package: name: varlociraptor @@ -11,7 +11,7 @@ build: source: url: https://github.com/varlociraptor/varlociraptor/archive/v{{ version }}.tar.gz - sha256: 41dd246d34e0e0d277681e9114bbc5bdfa95d0ef01b884be975a8f00bc3b492a + sha256: bbb192ea88f22a85a95273ef425425f2d60686d58ae104c2d182effbd3d61ae9 requirements: build: From 11517b31f0117c9dd4a81635ec5594029947e0ed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 07:27:58 -0500 Subject: [PATCH 0061/1813] Update treetime to 0.11.2 (#45335) --- recipes/treetime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/treetime/meta.yaml b/recipes/treetime/meta.yaml index 804bad35fbd08..06d0ced896a94 100644 --- a/recipes/treetime/meta.yaml +++ b/recipes/treetime/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.11.1" %} -{% set sha256 = "294cf2f72e145f0642784befa8f31766469d20aeb4b798b78fed211a586577a1" %} +{% set version = "0.11.2" %} +{% set sha256 = "c6fe577580a1ed83dcfc7530f85b678bd9d890366ba83d50444cd8e7371a71af" %} package: name: treetime From 9653071348559befe4a37e09461166560e24d8cd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 09:07:30 -0500 Subject: [PATCH 0062/1813] Update nanometa-live to 0.4.3 (#45342) --- recipes/nanometa-live/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanometa-live/meta.yaml b/recipes/nanometa-live/meta.yaml index 8c98e0ee36a38..4ccbcf3cfba8b 100644 --- a/recipes/nanometa-live/meta.yaml +++ b/recipes/nanometa-live/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanometa-live" %} -{% set version = "0.4.2" %} +{% set version = "0.4.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/FOI-Bioinformatics/nanometa_live/archive/{{ version }}.tar.gz - sha256: 82bbb858a17468c481837bd17a32ec7b9e09789ce32a0dd9ec01dcc4e7dbdbe5 + sha256: 9c8e0cb9eddaf8cfde3a752424717447319afd2af357a815e0ba4d4112e58e5c build: number: 0 From 3af81d41e301dd40365566fe77ba906faeb2e273 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Mon, 22 Jan 2024 16:11:29 +0100 Subject: [PATCH 0063/1813] toil update for 6.0.0 (#45343) - add semantic version run exports - and patch to remove need for ruamel.yaml.string dependency (which is not yet packaged for conda) --- .../drop_ruamel_yaml_string_dependency.patch | 52 +++++++++++++++++++ recipes/toil/meta.yaml | 49 +++++++++-------- 2 files changed, 78 insertions(+), 23 deletions(-) create mode 100644 recipes/toil/drop_ruamel_yaml_string_dependency.patch diff --git a/recipes/toil/drop_ruamel_yaml_string_dependency.patch b/recipes/toil/drop_ruamel_yaml_string_dependency.patch new file mode 100644 index 0000000000000..e2121b54bca4b --- /dev/null +++ b/recipes/toil/drop_ruamel_yaml_string_dependency.patch @@ -0,0 +1,52 @@ +commit 893aa9b3295400829a86054cab028635e9bd2dd2 +Author: Michael R. Crusoe +Date: Mon Jan 22 14:58:45 2024 +0100 + + remove ruamel.yaml.string dependency for a simpler solution + +diff --git a/requirements.txt b/requirements.txt +index c34aceb56..b0e85191d 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -11,6 +11,5 @@ pytz>=2012 + enlighten>=1.5.2, <2 + configargparse>=1.7,<2 + ruamel.yaml>=0.15 +-ruamel.yaml.string>=0.1.1 + pyyaml>=6,<7 + typing-extensions>=4.6.2, <5 +diff --git a/src/toil/common.py b/src/toil/common.py +index d2531d3aa..c8852c8ce 100644 +--- a/src/toil/common.py ++++ b/src/toil/common.py +@@ -23,6 +23,7 @@ import tempfile + import time + import uuid + import warnings ++from io import StringIO + + from ruamel.yaml import YAML + from ruamel.yaml.comments import CommentedMap +@@ -580,15 +581,16 @@ def generate_config(filepath: str) -> None: + with AtomicFileCreate(filepath) as temp_path: + with open(temp_path, "w") as f: + f.write("config_version: 1.0\n") +- yaml = YAML(typ=['rt', 'string']) ++ yaml = YAML(typ='rt') + for data in all_data: + if "config_version" in data: + del data["config_version"] +- for line in yaml.dump_to_string(data).split("\n"): # type: ignore[attr-defined] +- if line: +- f.write("#") +- f.write(line) +- f.write("\n") ++ with StringIO() as data_string: ++ yaml.dump(data, data_string) ++ for line in data_string.readline(): ++ if line: ++ f.write("#") ++ f.write(f"{line}\n") + + + def parser_with_common_options( diff --git a/recipes/toil/meta.yaml b/recipes/toil/meta.yaml index 6baaf6c98595c..0f3965135414e 100644 --- a/recipes/toil/meta.yaml +++ b/recipes/toil/meta.yaml @@ -1,6 +1,6 @@ {% set name = "toil" %} -{% set version = "5.12.0" %} -{% set sha256 = "fb21c85b8654b0e628087ebd403fa5f53644d86a33a4c1e039ba5769dcaf6654" %} +{% set version = "6.0.0" %} +{% set sha256 = "6cf772b744b886a53eaaf700e51ea2fd03bac15d384c34ee9e53455cbe00b33b" %} package: name: {{ name|lower }} @@ -9,39 +9,43 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz sha256: {{ sha256 }} + patches: + - drop_ruamel_yaml_string_dependency.patch # https://github.com/DataBiosphere/toil/pull/4760 build: number: 0 noarch: python script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} entry_points: - toil = toil.utils.toilMain:main - _toil_worker = toil.worker:main - toil-cwl-runner = toil.cwl.cwltoil:main [cwl] - toil-wdl-runner = toil.wdl.wdltoil:main [wdl] - - toil-wdl-runner-old = toil.wdl.toilwdl:main [wdl] - toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main [server] - _toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos] - _toil_contained_executor = toil.batchSystems.contained_executor:executor requirements: host: - - python >=3.7 + - python >=3.8 - pip run: - - python >=3.7 - - dill >=0.3.2 - - requests >=2 - - docker-py >=3.7.2,<6 - - urllib3 >=1.26.0 + - python >=3.8 + - dill >=0.3.2,<0.4 + - requests >=2,<3 + - docker-py >=3.7.2,<8 + - urllib3 >=1.26.0,<3 - python-dateutil - - psutil >=3.0.1 - # - py-tes >=0.4.2,<1 - - pypubsub >=4.0.3 - - addict >=2.2.1 + - psutil >=3.0.1,<6 + - pypubsub >=4.0.3,<5 + - addict >=2.2.1,<2.5 - pytz >=2012 - - enlighten >=1.5.2 - - typing-extensions + - enlighten >=1.5.2,<2 + - configargparse >=1.7,<2 + - typing-extensions >=4.6.2,<5 + - pyyaml >=6,<7 #mesos pymesos isn't available #server reqs # - wes-service is missing @@ -49,8 +53,8 @@ requirements: # - connexion >=2.10.0, <3 # - flask >=2.0,<3 # - werkzeug >=2.0,<3 - # - flask-cors ==3.0.10 - # - gunicorn ==20.1.0 + # - flask-cors ==4.0.0 + # - gunicorn ==21.2.0 # - celery >=5.1.0, <6 #aws reqs # mypy-boto3-{iam,sdb} are not yet in Conda @@ -66,20 +70,19 @@ requirements: - apache-libcloud >=2.2.1 - google-cloud-storage >=2,<=2.8.0 #cwl reqs - - cwltool ==3.1.20230601100705 + - cwltool ==3.1.20240112164112 - schema-salad >=8.4.20230128170514 - - galaxy-tool-util - - ruamel.yaml >=0.15,<=0.17.21 + - galaxy-tool-util <23 + - ruamel.yaml >=0.15,<=0.18.3 - ruamel.yaml.clib >=0.2.6 - - networkx >=2,<2.8.9 + - networkx <4 #htcondor reqs - python-htcondor >=10.2.0.post1 #kubernetes reqs - python-kubernetes >=12.0.1,<22 - idna >=2 #wdl reqs - # - wdlparse ==0.1.0 # not yet packaged for Conda - - mock >=4.0.3 + - miniwdl ==1.11.1 test: imports: From 6d1aefbd3487f3677c74e262f4a35443b6c93cfd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 10:12:06 -0500 Subject: [PATCH 0064/1813] Update dimet to 0.2.0 (#45344) --- recipes/dimet/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dimet/meta.yaml b/recipes/dimet/meta.yaml index fcc2e26a6ff37..fd7147d1ce9d8 100644 --- a/recipes/dimet/meta.yaml +++ b/recipes/dimet/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dimet" %} -{% set version = "0.1.4" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dimet-{{ version }}.tar.gz - sha256: 372537f9c9aef2035868357df2c04e5f94bf3f6bef39f69988e25d114a8009ab + sha256: 40d5dee29232deb5722392c745a70f757c78128829b372ce0093fe2fbaf9411e build: noarch: python From 8c89d23e4111af930211ce4452c1ea9095e376d8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:40:33 -0500 Subject: [PATCH 0065/1813] Update htslib to 1.19.1 (#45340) --- recipes/htslib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml index de1440505082b..de0c0dc0023c1 100644 --- a/recipes/htslib/meta.yaml +++ b/recipes/htslib/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.19" %} +{% set version = "1.19.1" %} package: name: htslib @@ -11,7 +11,7 @@ build: source: url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 - sha256: 8751c40c4fa7d1f23a6864c5b20a73744f8be68239535ae7729c5f7d394d0736 + sha256: 222d74d3574fb67b158c6988c980eeaaba8a0656f5e4ffb76b5fa57f035933ec requirements: build: From 09f68e5f1df75b623b4028e38c2e8722e0798c17 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 15:47:57 -0500 Subject: [PATCH 0066/1813] Update samtools to 1.19.1 (#45353) --- recipes/samtools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index b17cf299e837e..3d45b94379193 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.19" %} +{% set version = "1.19.1" %} package: name: samtools @@ -11,7 +11,7 @@ build: source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - sha256: fa6b3b18e20851b6f3cb55afaf3205d02fcb79dae3b849fcf52e8fc10ff08b83 + sha256: 1f94915cc32dcb6095049ed57560d99b409ba9297f4316bab551d05bb57ff355 requirements: build: From fda2a046eed6669a40f973f51e20ede45bba52a7 Mon Sep 17 00:00:00 2001 From: Bede Constantinides Date: Mon, 22 Jan 2024 22:10:01 +0000 Subject: [PATCH 0067/1813] Update hostile to 1.0.0, add new dep, update DOI (#45352) --- recipes/hostile/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/hostile/meta.yaml b/recipes/hostile/meta.yaml index 4f8c76370bf62..88d7df7ebd535 100644 --- a/recipes/hostile/meta.yaml +++ b/recipes/hostile/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.0" %} +{% set version = "1.0.0" %} package: name: hostile @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/h/hostile/hostile-{{ version }}.tar.gz - sha256: dd003b09a7f17a8fc126bc81c2b402d1ab5946916f1f55dbcffa4c9c3014a56a + sha256: abe985acf384703ff482d5712cc4b3367e7f777818a66cbd389e7bfc6c6ac76a build: noarch: python @@ -25,6 +25,7 @@ requirements: run: - bowtie2 ==2.4.5 - defopt >=6.4.0 + - dnaio >=1.2.0 - gawk >=5.1.0 - httpx >=0.24.1 - minimap2 >=2.26 @@ -50,4 +51,4 @@ about: extra: identifiers: - - doi:10.1101/2023.07.04.547735 + - doi:10.1093/bioinformatics/btad728 From 8a6416cdc3be64e9e5b4f6c53073d5ff0ff60176 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 20:52:07 -0500 Subject: [PATCH 0068/1813] Update deeplc to 2.2.27 (#45346) --- recipes/deeplc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/deeplc/meta.yaml b/recipes/deeplc/meta.yaml index 51849c0d6507f..053b4fee421bc 100644 --- a/recipes/deeplc/meta.yaml +++ b/recipes/deeplc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLC" %} -{% set version = "2.2.26" %} -{% set sha256 = "b4cbb3612a89fe82ddac6149a261f7440c721f4b87235ce534c4cbd95d424e1b" %} +{% set version = "2.2.27" %} +{% set sha256 = "611cd06f1a12a543289c4fa0bbb5364bc3dbeeca905464c7c2668f45fa2fa781" %} package: name: {{ name|lower }} From 4e5525a959401a4ee67132bdefe6668b285fb89f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 20:52:24 -0500 Subject: [PATCH 0069/1813] Update pangolin-data to 1.24 (#45347) --- recipes/pangolin-data/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangolin-data/meta.yaml b/recipes/pangolin-data/meta.yaml index 99468f431af4a..d8b1f3721fb4d 100644 --- a/recipes/pangolin-data/meta.yaml +++ b/recipes/pangolin-data/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.23.1" %} +{% set version = "1.24" %} package: name: pangolin-data @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pangolin-data/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3a845838cf31131d8bc7e0c19cb3e78e2c99a5894ac44452bfa5f86a91dca056 + sha256: 63e3eb2598b90d0b0c3ab6b9be34cd520c7b060751f5511e653616146407f839 build: number: 0 From 80e61ad1a6627e0b488378acf9776c7c16e04f1d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 20:53:22 -0500 Subject: [PATCH 0070/1813] Update tides-ml to 1.1.3 (#45354) --- recipes/tides-ml/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tides-ml/meta.yaml b/recipes/tides-ml/meta.yaml index c3a3d4bc436e8..8700a6649354a 100644 --- a/recipes/tides-ml/meta.yaml +++ b/recipes/tides-ml/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tides-ml" %} -{% set version = "1.1.2" %} +{% set version = "1.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/TIdeS-ML-{{ version }}.tar.gz - sha256: 17ad86b841d5e8fca4dbad58d114aa919d332a22190c7d002472ec6c1541609a + sha256: a2a872ac26c24705a6f538823b53081ae456a313fa587520997418fbda8e612e build: entry_points: From 454ad5e153125e87a69b7a0ed23ca3e668aac07e Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Mon, 22 Jan 2024 17:56:06 -0800 Subject: [PATCH 0071/1813] Update augur to 24.0.0 (#45357) Includes dependency changes. --- recipes/augur/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index 21d5c1cf2ebbe..c890f6e104b18 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "23.1.1" %} +{% set version = "24.0.0" %} package: name: augur @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: 1b6f8fb1f20c147d24806764761f8e977c8e100a58e04e06d3110bb72268518f + sha256: 6766330e7db7d6ceab8256b1f815882fdf3a9dccdeb224f316266d7983f2a407 build: - number: 1 + number: 0 noarch: python entry_points: - augur = augur.__main__:main @@ -24,7 +24,7 @@ requirements: run: - python >=3.8 - bcbio-gff >=0.7.0,<0.8 - - biopython >=1.73,!=1.77,!=1.78 + - biopython >=1.73,!=1.77,!=1.78,<1.82 - cvxopt >=1.1.9,<2 - importlib_resources >=5.3.0 # [py<311] - isodate >=0.6.0,<0.7 @@ -35,7 +35,7 @@ requirements: - pandas >=1.0.0,<2 - pyfastx >=1.0.0,<3 - scipy >=1.0.0,<2 - - treetime >=0.10.0,<0.12 + - treetime >=0.11.2,<0.12 - xopen[zstd] >=1.7.0,<2 - fasttree From 33aceb21ef8aedd53c9f1c42853fca95f6d8d02e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 03:12:00 -0500 Subject: [PATCH 0072/1813] Update koverage to 0.1.8 (#45360) --- recipes/koverage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/koverage/meta.yaml b/recipes/koverage/meta.yaml index 385acafa06329..e9a66d5265d47 100644 --- a/recipes/koverage/meta.yaml +++ b/recipes/koverage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "koverage" %} -{% set version = "0.1.7" %} +{% set version = "0.1.8" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 75561037d21f1577200b659d097ef72ccb305f2cf5323eabda5d86cee15916ff + sha256: 0680e72916022fbedbf14c9dc5daa0e159e41196f81da15b5e9367d93af0832a build: noarch: python From 2dd3d83f170c6bc1e059a788517689a959a53011 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 23 Jan 2024 11:15:33 +0100 Subject: [PATCH 0073/1813] Bump svync to v0.1.1 (#45365) --- recipes/svync/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/svync/meta.yaml b/recipes/svync/meta.yaml index a19463ec08781..57d179ecbcf9d 100644 --- a/recipes/svync/meta.yaml +++ b/recipes/svync/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.0' %} +{% set version = '0.1.1' %} {% set name = 'svync' %} package: @@ -7,9 +7,9 @@ package: source: - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-darwin-amd64.tar.gz # [osx-amd64] - md5: 62bc02c3f3dc52fd02b998f6f0223216 # [osx] + md5: 2fb00fc49591526cc61e445cc75526d5 # [osx] - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-linux-amd64.tar.gz # [linux] - md5: dbc6b403d5ce1bcef9ba07ad7e1a5dc9 # [linux] + md5: c119b00f23e0e4310e7971fbb6aef9a9 # [linux] build: number: 0 From 563c94422524b7ef8849d021885d8485b9916a3d Mon Sep 17 00:00:00 2001 From: aguus8 <139561482+aguus8@users.noreply.github.com> Date: Tue, 23 Jan 2024 14:20:31 +0100 Subject: [PATCH 0074/1813] [biobb_pdb_tools] update 4.1.1 (#45348) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [v4.1.0] update 2023.4 * [v4.1.0] update 2023.4 * [biobb_pdb_tools] update 4.1.1 * [biobb_pdb_tools] update 4.1.1 --------- Co-authored-by: Agustín García Doñate Co-authored-by: Agustin Garcia Doñate Co-authored-by: Genís Bayarri --- recipes/biobb_pdb_tools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biobb_pdb_tools/meta.yaml b/recipes/biobb_pdb_tools/meta.yaml index 2de77d46048e3..44c5d7c9dec38 100644 --- a/recipes/biobb_pdb_tools/meta.yaml +++ b/recipes/biobb_pdb_tools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_pdb_tools" %} -{% set version = "4.1.0" %} +{% set version = "4.1.1" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: a956ceb461219df25154a59c8b319c79802f0f7975095837aef40d6b057c0744 + sha256: 7510052e89c534f935f1b70b575943fe391dc0bc837c4c0982c7cb3d944adb29 build: number: 0 From a41f3d72ddfa757ecd500d4a8c783447c309e88f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 08:22:06 -0500 Subject: [PATCH 0075/1813] Update gget to 0.28.3 (#45355) --- recipes/gget/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gget/meta.yaml b/recipes/gget/meta.yaml index 0c155d5a9aec3..fa18fdcf7a298 100644 --- a/recipes/gget/meta.yaml +++ b/recipes/gget/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gget" %} -{% set version = "0.28.2" %} -{% set sha256 = "2bc24c484e26fdd25646f66089e08edf101c344e9ddb9aaeb1484fac3e1d2a99" %} +{% set version = "0.28.3" %} +{% set sha256 = "4f9e2f3e445b7e898e1a12fa7460604330e73d917c8e357a91a09c0c005b64b9" %} package: name: "{{ name|lower }}" From 0cc31d78b9e1fda396fefe7018bc6115375f3bd1 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 23 Jan 2024 16:17:02 +0100 Subject: [PATCH 0076/1813] Bump svync to v0.1.2 (#45371) --- recipes/svync/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/svync/meta.yaml b/recipes/svync/meta.yaml index 57d179ecbcf9d..9430c018d9b6c 100644 --- a/recipes/svync/meta.yaml +++ b/recipes/svync/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.1' %} +{% set version = '0.1.2' %} {% set name = 'svync' %} package: @@ -7,9 +7,9 @@ package: source: - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-darwin-amd64.tar.gz # [osx-amd64] - md5: 2fb00fc49591526cc61e445cc75526d5 # [osx] + md5: 2f64a4d9b81124917766bd8a754ea470 # [osx] - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-linux-amd64.tar.gz # [linux] - md5: c119b00f23e0e4310e7971fbb6aef9a9 # [linux] + md5: 298f930c1f30918bd41d07db5bbfd348 # [linux] build: number: 0 From 32d57a440c157481dc1cb700f053b641a627763d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 11:11:53 -0500 Subject: [PATCH 0077/1813] Update sevenbridges-python to 2.10.1 (#45369) --- recipes/sevenbridges-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index 7c534eeee72b4..7bdcd4c93f64a 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.10.0" %} -{% set sha256 = "6e370de45b5af6574a2937e8a8aba76108f779f55982b360eb796a113e9399e6" %} +{% set version = "2.10.1" %} +{% set sha256 = "5db46a3fce7b0235be9273ec070092775be43e4bb1b2787c349f3598eaa3fd07" %} package: name: sevenbridges-python From d8ec881b580be85e9242a48874e8b0020b0071ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 11:13:31 -0500 Subject: [PATCH 0078/1813] Update assemblycomparator2 to 2.5.17 (#45368) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index b5640b7519dd6..6c929a7075290 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.16" %} +{% set version = "2.5.17" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 197d157e67a04df4f63b88191106dce7219eab8ee4aa146b74d4fb796a505e93 + sha256: 5c15c4882529d33d56678eb3b710e243e3f5adc49b7d0ad1871f26ecab69d97e build: From 6c6580ac39f66032ecf8d4ba3d82cb39b13cdd3c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 11:13:55 -0500 Subject: [PATCH 0079/1813] Update snakemake-interface-common to 1.15.2 (#45367) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index c5e119044e696..4cfc57b3f3c14 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.15.1" %} +{% set version = "1.15.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 5a779c7a0f27412bce26e1dfe4ccc712d04e0c0b9ceaa1640335a35d02509732 + sha256: f2a4908a5ec5d6e657723f90221da3c136e70a1c5897b4e1d65a703bc08e8d7a build: noarch: python From 4d4e022327218d499431ccdf9c7e0b01747fee18 Mon Sep 17 00:00:00 2001 From: Samuel Aroney <41124903+AroneyS@users.noreply.github.com> Date: Wed, 24 Jan 2024 06:31:23 +1000 Subject: [PATCH 0080/1813] Update CoverM to v0.7.0 (#45332) * bump CoverM to v0.7.0 * fix name * update sha256 * add cmake to build * add make to build --- recipes/coverm/meta.yaml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/recipes/coverm/meta.yaml b/recipes/coverm/meta.yaml index 7e12b62eb8ef2..90634a04ae368 100644 --- a/recipes/coverm/meta.yaml +++ b/recipes/coverm/meta.yaml @@ -1,14 +1,16 @@ -{% set version = "0.6.1" %} +{% set version = "0.7.0" %} {% set name = "coverm" %} -{% set sha256 = "b6211e6f89ef986691b910d7d7b4c6d1e9eb9beb64e4f71902178ed60d27f4e6" %} +{% set sha256 = "539142529d2590166e98ed399db36913fbf8b256d8c74a1966acae849c18a828" %} package: name: {{ name }} version: {{ version }} build: - number: 6 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('coverm', max_pin="x.x") }} source: url: https://github.com/wwood/{{ name }}/archive/v{{ version }}.tar.gz @@ -21,6 +23,8 @@ requirements: - {{ compiler('cxx') }} - clangdev # one of the rust submodules explicitly requires clang. As it's statically compiled that will hopefully work - pkg-config + - make + - cmake host: - zlib - gsl @@ -43,4 +47,5 @@ test: about: home: https://github.com/wwood/CoverM license: GPL3 + license_family: GPL3 summary: CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications From 8ae689e106a22dc6c425ceef7aafa8b66b9b89ae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 19:47:49 -0500 Subject: [PATCH 0081/1813] Update pybiolib to 1.1.1691 (#45383) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index b4b1f16fe1b7d..bbcec685a8ceb 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1689" %} +{% set version = "1.1.1691" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: f33b444bdbde72a8b93f236777544de8d2a5fc0633f7cdb4c1e73f392eae0040 + sha256: 5f25f9028e05b606a32a452fb065288915d94a010481db935ddc2379812abec6 build: noarch: python From 2502722966ac2b0f1abd9a8b8d0eea5ab710fdea Mon Sep 17 00:00:00 2001 From: "Le (Lena) Huang" Date: Tue, 23 Jan 2024 20:38:36 -0500 Subject: [PATCH 0082/1813] update dbcan to 4.1.4 (#45374) --- recipes/dbcan/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/dbcan/meta.yaml b/recipes/dbcan/meta.yaml index 34d2f399cac8b..4c247128ceb5f 100644 --- a/recipes/dbcan/meta.yaml +++ b/recipes/dbcan/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dbcan" %} -{% set version = "4.1.3" %} +{% set version = "4.1.4" %} package: name: "{{ name|lower }}" @@ -9,7 +9,8 @@ source: # the sha256 sum is generated by doing # wget -0- [URL] | shasum -a 256 url: https://github.com/linnabrown/run_dbcan/releases/download/{{ version }}/dbcan-{{ version }}.tar.gz - sha256: 6346e0b6b2c810e2f808bc0bc901643c16f3eda2652d50b8f8470eb722fb419b + sha256: 12dc906b56c3b1bfea667aa617d46d3f292857fc360730e4fe1d35f5b5557215 + build: number: 0 From 2dab87ef8028f1026ff81023537e63deca7cca7a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 20:40:42 -0500 Subject: [PATCH 0083/1813] Update earlgrey to 4.0.5 (#45361) * Update earlgrey to 4.0.4 * Update earlgrey to 4.0.5 --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index caa4eddb4e6a7..268616558bed9 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.3" %} -{% set sha256 = "5715301151d7d6609aa703c9c174f00e1bde61c6d2f0493f5c01831d95152fb0" %} +{% set version = "4.0.5" %} +{% set sha256 = "5fe1341dad3da2bf322415cb048a846173e386b1998be188828f3c905349daa8" %} package: name: {{ name|lower }} From 1b5f25d1d6b0170ba55d5c4deb4cf2e1bf520762 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 20:41:35 -0500 Subject: [PATCH 0084/1813] Update bakta to 1.9.2 (#45373) Co-authored-by: Oliver Schwengers --- recipes/bakta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml index 98a9068bd9875..f33a11054a52e 100644 --- a/recipes/bakta/meta.yaml +++ b/recipes/bakta/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.9.1" %} +{% set version = "1.9.2" %} package: name: bakta @@ -6,7 +6,7 @@ package: source: url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz - sha256: 'd8eb7ea1321ad6884002cfac670c33031b8dfa219a62b90c556f7cf402a64fe4' + sha256: '145b0209fe6a0c67a1a1a6e5c108e99bad0a86e3b1db0a9d24261744725fe257' build: noarch: python From 045837857ebada429fcc95877b2793a439463046 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 20:43:49 -0500 Subject: [PATCH 0085/1813] Update igv-reports to 1.11.0 (#45378) --- recipes/igv-reports/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/igv-reports/meta.yaml b/recipes/igv-reports/meta.yaml index 6335f9d235f6d..8b464c54de237 100644 --- a/recipes/igv-reports/meta.yaml +++ b/recipes/igv-reports/meta.yaml @@ -1,5 +1,5 @@ {% set name = "igv-reports" %} -{% set version = "1.10.0" %} +{% set version = "1.11.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8cbe26d120ca4d599c7ffb8077dc4501a5ef29cf76a69f187ce1cd948ef0f451 + sha256: 8a524c53f4bbcf93d58a2b2246d8473b22bea1955a492f81365c4c27164efe86 build: noarch: python From 679b0a1a2ce6e4003618f6bb721b073e28b0a237 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 20:44:04 -0500 Subject: [PATCH 0086/1813] Update taxmyphage to 0.2.7 (#45379) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index 0d0b81c087803..379c12a36a2bd 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.2.6" %} +{% set version = "0.2.7" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: 1058adb02296ec0493b21dedd899447a144804230a4e13f4c98f94dcc0548076 + sha256: 8208758ca9814435a72ffd11ba76538a829c355c73b276f567962c2334b149ec build: entry_points: From 865ac419441208c10b6ab85831cf3ce05a968821 Mon Sep 17 00:00:00 2001 From: Arafat Rahman Date: Tue, 23 Jan 2024 17:47:06 -0800 Subject: [PATCH 0087/1813] 1.1.0 release update (#45385) --- recipes/beav/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/beav/meta.yaml b/recipes/beav/meta.yaml index 51c26396cf4a7..61b78a68727b4 100644 --- a/recipes/beav/meta.yaml +++ b/recipes/beav/meta.yaml @@ -1,6 +1,6 @@ {% set name = "beav" %} -{% set version = "1.0.0" %} -{% set sha256 = "b0e65b26c2e5760bfa31587d153d3df902ee34606bc0f4059622dbcb8269ffc4" %} +{% set version = "1.1.0" %} +{% set sha256 = "f9a65ac152b33c8649b51e152cc7137036140f5e2d7460f162ebd180aac3f868" %} {% set dbscan_git = "condabeav0.5" %} {% set dbscan_sha256 = "2fe08873026fe63a9992bfb997e59fecce7facb903778983dc6917c962573463" %} {% set gapmind_git = "Beav0.5.1conda" %} From 5b298cdae5ebf6bd6ea92bd4752abb3fe4a1ba0e Mon Sep 17 00:00:00 2001 From: Kristy Horan Date: Wed, 24 Jan 2024 13:01:07 +1100 Subject: [PATCH 0088/1813] Add missing deps tbtamr (#45359) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * added in tbtamr * added in tbtamr * added in tbtamr * added in tbtamr * added in tbtamr * added in tbtamr * Update recipes/tbtamr/meta.yaml Co-authored-by: Björn Grüning * addressed issues with licence * adding licence file * added max_pin x.x * adding in missing dependencies tqdm, xlsxwriter, requests * bump build --------- Co-authored-by: Björn Grüning --- recipes/tbtamr/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/tbtamr/meta.yaml b/recipes/tbtamr/meta.yaml index 435271ec684fd..459fa16a643f1 100644 --- a/recipes/tbtamr/meta.yaml +++ b/recipes/tbtamr/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - tbtamr=tbtamr.tbtamr:main run_exports: @@ -36,6 +36,10 @@ requirements: - bcftools - bedtools - delly + - xlsxwriter + - requests + - tqdm + test: imports: From 60ee1021c3e984b3584dd456258ed6f2eabe9316 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 21:25:01 -0500 Subject: [PATCH 0089/1813] Update trackplot to 0.3.7 (#45362) * Update trackplot to 0.3.7 * pin python to <3.12 --------- Co-authored-by: mencian --- recipes/trackplot/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/trackplot/meta.yaml b/recipes/trackplot/meta.yaml index 0c723aed874f0..f0d3984428fb9 100644 --- a/recipes/trackplot/meta.yaml +++ b/recipes/trackplot/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trackplot" %} -{% set version = "0.3.6" %} +{% set version = "0.3.7" %} package: name: trackplot @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f1f8706c954abd0f8c426f1c3ed51b458d69940c8a275aa61544864788a93956 + sha256: 5e650448e71d81eaae61fbbdcf88e8130b79f008278128ee1311c2b16a24b803 build: noarch: python @@ -20,11 +20,11 @@ build: requirements: host: - - python >=3.8 + - python >=3.8,<3.12 - pip - poetry-core run: - - python >=3.8 + - python >=3.8,<3.12 - adjusttext >=0.7.3 - cairocffi >=1.4.0 - click From 6285313032a680dcb71dbf52e7b441c660674c48 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 21:49:19 -0500 Subject: [PATCH 0090/1813] Update varfish-cli to 0.6.2 (#45363) --- recipes/varfish-cli/meta.yaml | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml index cc5fa0f456492..30c63c249cf4e 100644 --- a/recipes/varfish-cli/meta.yaml +++ b/recipes/varfish-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.5.3" %} -{% set sha256 = "ae8ee0314f0ebcfacf44518d7dcca4d9aba74d3fa50159fd0adbc04017671677" %} +{% set version = "0.6.2" %} +{% set sha256 = "62633a89b55e8fa0d93acd91deb5d231ac567ecdc76b530ae0e4b000a7c5dea7" %} package: name: varfish-cli @@ -10,9 +10,13 @@ source: sha256: '{{sha256}}' build: - script: python -m pip install --no-deps --ignore-installed . - noarch: python + noarch: python number: 0 + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + entry_points: + - varfish-cli = varfish_cli.__main__:main + run_exports: + - {{ pin_subpackage('varfish-cli', max_pin="x.x") }} requirements: host: @@ -29,9 +33,11 @@ requirements: - tqdm - tabulate - polyleven + - pydantic - python-dateutil - simplejson - typeguard + - typer test: imports: From 3e0cbca3284c346c6cef25cbb45bdf6f9169c4ca Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 21:50:29 -0500 Subject: [PATCH 0091/1813] Update r-conos to 1.5.1 (#45364) * Update r-conos to 1.5.1 * add run_exports --------- Co-authored-by: mencian --- recipes/r-conos/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/r-conos/meta.yaml b/recipes/r-conos/meta.yaml index 78c4f6043b388..d7c122620cdaf 100644 --- a/recipes/r-conos/meta.yaml +++ b/recipes/r-conos/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.5.0' %} +{% set version = '1.5.1' %} package: name: r-conos @@ -8,13 +8,15 @@ source: url: - {{ cran_mirror }}/src/contrib/conos_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/conos/conos_{{ version }}.tar.gz - sha256: dcf4afbbf3c744e8e4f1bd4472bb4c8f18a1d18d9f2bf854372d12d8e558b0f1 + sha256: bb479d63a2836bfa163b6abc9f8f2bac9e081cdcc5b781f1bee201e7b99da205 build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-conos', max_pin="x") }} requirements: build: From e173f20a15d225bf7defeada47fb414f368db445 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 21:50:45 -0500 Subject: [PATCH 0092/1813] Update r-tinyarray to 2.3.2 (#45336) * Update r-tinyarray to 2.3.2 * add run_exports --------- Co-authored-by: mencian --- recipes/r-tinyarray/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/r-tinyarray/meta.yaml b/recipes/r-tinyarray/meta.yaml index 1a61d8ba0282c..2284c61513a42 100644 --- a/recipes/r-tinyarray/meta.yaml +++ b/recipes/r-tinyarray/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.3.1' %} +{% set version = '2.3.2' %} package: name: r-tinyarray @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/tinyarray_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/tinyarray/tinyarray_{{ version }}.tar.gz - sha256: 68ea15eb8d726368919faa54c89e2d18806b94e73e21fdee365c350b7ee79eb3 + sha256: 32d74c2e64b88fb973a2ade4162f4a2c3ec9127d41966768301b518cdcac5654 build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-tinyarray', max_pin="x") }} requirements: host: From faf579b10faff5195c3485c5ddf320e3161a7955 Mon Sep 17 00:00:00 2001 From: Guy Assa <78320514+theAguy@users.noreply.github.com> Date: Wed, 24 Jan 2024 04:56:34 +0200 Subject: [PATCH 0093/1813] better translocation detection (#45345) * better translocation detection * better translocation detection take 2 * better translocation detection take 3 * better translocation detection take 4 --- recipes/crispector/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/crispector/meta.yaml b/recipes/crispector/meta.yaml index eead4a143981d..0032615c4b7e3 100644 --- a/recipes/crispector/meta.yaml +++ b/recipes/crispector/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.4" %} +{% set version = "1.0.7" %} package: name: crispector @@ -10,10 +10,12 @@ build: - crispector = crispector.cli:main noarch: python script: python -m pip install . --no-deps -vv + run_exports: + - {{ pin_subpackage('crispector', max_pin="x") }} source: - url: https://github.com/YakhiniGroup/crispector/archive/v{{ version }}.tar.gz - sha256: 66b4ecc6f73958221eed868200c00d3c39718e9a146c389da9fcbd16440f6f1f + url: https://github.com/YakhiniGroup/crispector/archive/refs/tags/V{{ version }}.tar.gz + sha256: f88a8807e9793c7fb9db341f5ba9f130e59f557ecac55b625eb0dcd61ad38b9c requirements: host: @@ -35,6 +37,7 @@ requirements: - pandas >=0.24.2 - statsmodels - jinja2 + - mpmath >=1.3.0 test: commands: From 820dc543676bd7ab402bb55c14a3fbb75f1dd46a Mon Sep 17 00:00:00 2001 From: Travis Wrightsman Date: Tue, 23 Jan 2024 21:59:20 -0500 Subject: [PATCH 0094/1813] Build shared library for quicktree (#45326) * Build shared library for quicktree * Make BSD mkdir happy --- recipes/quicktree/build.sh | 9 +++- recipes/quicktree/meta.yaml | 11 +++-- ...001-Add-rule-to-build-shared-library.patch | 43 +++++++++++++++++++ 3 files changed, 59 insertions(+), 4 deletions(-) create mode 100644 recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch diff --git a/recipes/quicktree/build.sh b/recipes/quicktree/build.sh index 6796b7efd05b6..7d776e66d9e68 100644 --- a/recipes/quicktree/build.sh +++ b/recipes/quicktree/build.sh @@ -1,5 +1,12 @@ #!/bin/bash -mkdir -p $PREFIX/bin +set -eux + +mkdir -p "$PREFIX"/{bin,lib,include/quicktree} + make CC=$CC + cp quicktree $PREFIX/bin +cp libquicktree.so "${PREFIX}/lib/" +# some header files are named generic enough to warrant namespacing +cp include/*.h "${PREFIX}/include/quicktree/" diff --git a/recipes/quicktree/meta.yaml b/recipes/quicktree/meta.yaml index b663ce6822c58..5c6cb7814f9f8 100644 --- a/recipes/quicktree/meta.yaml +++ b/recipes/quicktree/meta.yaml @@ -1,21 +1,26 @@ +{% set name = "quicktree" %} {% set version = "2.5" %} package: - name: quicktree + name: {{ name }} version: {{ version }} source: url: https://github.com/khowe/quicktree/archive/v{{ version }}.tar.gz sha256: 731aa845ce3f1f0645bd0df2b54df75f78fce065d6a3ddc47fedf4bdcb11c248 + patches: + - patches/0001-Add-rule-to-build-shared-library.patch build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + requirements: build: - make - {{ compiler('c') }} - run: test: commands: diff --git a/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch b/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch new file mode 100644 index 0000000000000..509748c0811eb --- /dev/null +++ b/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch @@ -0,0 +1,43 @@ +From 390c2db84a0fd0ff3a05d77407d18da3b9c26d63 Mon Sep 17 00:00:00 2001 +From: Travis Wrightsman +Date: Sat, 20 Jan 2024 17:46:20 -0500 +Subject: [PATCH] Add rule to build shared library + +--- + Makefile | 9 ++++++--- + 1 file changed, 6 insertions(+), 3 deletions(-) + +diff --git a/Makefile b/Makefile +index 14e42a4..7fe8385 100644 +--- a/Makefile ++++ b/Makefile +@@ -15,15 +15,18 @@ QUICKTREEOBJ = $(COMMON) $(OBJ)/quicktree.o $(OBJ)/buildtree.o $(OBJ)/tree.o + + + CC = gcc +-CFLAGS = -c -I$(INC) -O2 -Wunused-result ++CFLAGS = -c -I$(INC) -O2 -Wunused-result -fPIC + + LFLAGS = -g + +-all: quicktree ++all: quicktree libquicktree.so + + quicktree : $(QUICKTREEOBJ) + $(CC) $(LFLAGS) -o $@ $(QUICKTREEOBJ) -lm + ++libquicktree.so: $(QUICKTREEOBJ) ++ $(CC) -shared $(LFLAGS) -o $@ $(QUICKTREEOBJ) -lm ++ + $(OBJ)/quicktree.o : $(SRC)/quicktree.c $(INC)/version.h + $(CC) $(CFLAGS) -o $(OBJ)/quicktree.o $(SRC)/quicktree.c + +@@ -52,4 +55,4 @@ $(OBJ)/options.o : $(SRC)/options.c $(INC)/options.h + $(CC) $(CFLAGS) -o $(OBJ)/options.o $(SRC)/options.c + + clean: +- rm $(OBJ)/*.o quicktree ++ rm $(OBJ)/*.o quicktree libquicktree.so +-- +2.39.2 + From 35084337b0e967e524e2efc871dd153863f4a451 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 23:29:07 -0500 Subject: [PATCH 0095/1813] Update presto to 0.7.2 (#45381) * Update presto to 0.7.2 * add run_exports * add name variable * add packaging --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/presto/build.sh | 9 --------- recipes/presto/meta.yaml | 27 ++++++++++++++++++++------- 2 files changed, 20 insertions(+), 16 deletions(-) delete mode 100755 recipes/presto/build.sh diff --git a/recipes/presto/build.sh b/recipes/presto/build.sh deleted file mode 100755 index 4899c226c8dd0..0000000000000 --- a/recipes/presto/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/presto/meta.yaml b/recipes/presto/meta.yaml index 8db5c41676eea..e3fdd0365f366 100644 --- a/recipes/presto/meta.yaml +++ b/recipes/presto/meta.yaml @@ -1,19 +1,26 @@ +{% set name = "presto" %} +{% set version = "0.7.2" %} +{% set sha256 = "b4f4b34413af4207eb2052316d31d7bc2067b864286498476d89013ad5423dd9" %} + package: - name: presto - version: "0.7.1" + name: {{ name }} + version: {{ version }} source: - url: https://files.pythonhosted.org/packages/ca/12/09123b431758827082924054e03277207067853c6af19803f67d1ad1dea9/presto-0.7.1.tar.gz - sha256: 8b5787b3a3206fda5e5cd0fd1804a6c0ecb8821f9de2b78d9a5e5a5a31ba43e9 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/presto-{{ version }}.tar.gz + sha256: {{ sha256 }} build: number: 0 noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('presto', max_pin="x.x") }} requirements: host: - python >=3 - - setuptools + - pip run: - python >=3 - numpy >=1.8 @@ -23,6 +30,7 @@ requirements: - blast >=2.5 - muscle >=3.8 - vsearch >=2.3.2 + - packaging test: commands: @@ -41,7 +49,12 @@ test: - SplitSeq.py --version about: - home: https://presto.readthedocs.io - license: AGPL-3.0 + home: https://bitbucket.org/kleinstein/presto + license: AGPL-3.0-or-later summary: 'A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.' license_family: AGPL + doc_url: https://presto.readthedocs.io + +extra: + identifier: + - doi:10.1093/bioinformatics/btu138 From f116a1f00de46f99ea0680a87f3e94912a470bef Mon Sep 17 00:00:00 2001 From: Jim Shaw Date: Tue, 23 Jan 2024 23:30:05 -0500 Subject: [PATCH 0096/1813] Add floria recipe. (#45334) * add floria * removed extra file --- recipes/floria/build.sh | 8 ++++++++ recipes/floria/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 recipes/floria/build.sh create mode 100644 recipes/floria/meta.yaml diff --git a/recipes/floria/build.sh b/recipes/floria/build.sh new file mode 100644 index 0000000000000..3662f6efb60db --- /dev/null +++ b/recipes/floria/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX diff --git a/recipes/floria/meta.yaml b/recipes/floria/meta.yaml new file mode 100644 index 0000000000000..ff7c268607c96 --- /dev/null +++ b/recipes/floria/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "0.0.1" %} + +package: + name: floria + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('floria', max_pin="x") }} + +source: + url: https://github.com/bluenote-1577/floria/archive/v{{ version }}.tar.gz + sha256: 48430783e411225a90282f65afb05a1e7e3d1d2bfb78fa838e359802530f4be1 + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.62 + - make + - cmake >=3.12 + +test: + commands: + - floria --help + +about: + home: https://github.com/bluenote-1577/floria + license: MIT + summary: Floria is method for recovering strain-level haplotypes and clusters of reads from metagenomic short or long read sequencing data by haplotype phasing. + + +extra: + recipe-maintainers: + - bluenote-1577 + From f8199d1bcad0d5d61a33c517a4ecdf845b03a348 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 00:54:05 -0500 Subject: [PATCH 0097/1813] Update dnaapler to 0.5.2 (#45386) --- recipes/dnaapler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index 5737d45fcec6a..699f0fa47dae3 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.5.1" %} +{% set version = "0.5.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 9bc6289ebefaa2e9725709cae2dbfa2723ad0d4e7f073f781a23e9b799bac8a8 + sha256: 3e0a03afdf00c20943892184062d9b778d3d8b2b549605a69c883a8f5e68e946 build: number: 0 From 67608bab9863aed87e4feefe819a9612ab1a9dac Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 08:36:13 -0500 Subject: [PATCH 0098/1813] Update varfish-cli to 0.6.3 (#45391) --- recipes/varfish-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml index 30c63c249cf4e..f65d88b9dd723 100644 --- a/recipes/varfish-cli/meta.yaml +++ b/recipes/varfish-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.2" %} -{% set sha256 = "62633a89b55e8fa0d93acd91deb5d231ac567ecdc76b530ae0e4b000a7c5dea7" %} +{% set version = "0.6.3" %} +{% set sha256 = "7a7344b3d88b8ac303f0a54f7709fa528fe1555dd6e935c45e6ec452d955871d" %} package: name: varfish-cli From 05e30d19fb906992fb0605bed65cd35f93253a08 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 10:51:30 -0500 Subject: [PATCH 0099/1813] Update vcf2variants to 1.3 (#45402) --- recipes/vcf2variants/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vcf2variants/meta.yaml b/recipes/vcf2variants/meta.yaml index ce21048d701da..1e86cba1234ab 100644 --- a/recipes/vcf2variants/meta.yaml +++ b/recipes/vcf2variants/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcf2variants" %} -{% set version = "1.2" %} +{% set version = "1.3" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 7830202ec67de08e7b223649365eed4a4a66d1339c985123d21c65cca7283728 + sha256: 152f8e97ae8d23613672e93b33713e4fb620a92bbae72bd052e75e2fc409db12 build: number: 0 From 5986b8bdeec8bc6b98582ce94103cc5b9ceb4bf0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 10:52:40 -0500 Subject: [PATCH 0100/1813] Update scirpy to 0.15.0 (#45395) * Update scirpy to 0.15.0 * Update meta.yaml --------- Co-authored-by: Gregor Sturm --- recipes/scirpy/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml index 1d42f7a62616a..91d97a5982193 100644 --- a/recipes/scirpy/meta.yaml +++ b/recipes/scirpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scirpy" %} -{% set version = "0.14.0" %} +{% set version = "0.15.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 26a5a5374503925c1db16595ef67b1814a6389a4932edc2aa48607a47a00bf43 + sha256: 4b0e5ce9fa8a874f0dd502a9493d9201dd6afc673512ab0287644a98c77b3744 folder: "{{ name }}-{{ version }}" build: @@ -45,6 +45,7 @@ requirements: - numba >=0.41.0 - pooch >=1.7.0 - pycairo >=1.20 # [win] + - joblib >=1.3.1 test: imports: From aa2441d96db4d1d8fa6ba92b3a88ef85e7c33681 Mon Sep 17 00:00:00 2001 From: tlacroix Date: Wed, 24 Jan 2024 16:55:07 +0100 Subject: [PATCH 0101/1813] Update icescreen v1.3.1 (#45377) * Update icescreen v1.3.1 * added run_exports section * try rerun tests because of weird CircleCI Pipeline No configuration error --- recipes/icescreen/meta.yaml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/recipes/icescreen/meta.yaml b/recipes/icescreen/meta.yaml index aac6a83ed3f11..a1d4fdde1d551 100644 --- a/recipes/icescreen/meta.yaml +++ b/recipes/icescreen/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ICEscreen" %} -{% set version = "1.2.0" %} +{% set version = "1.3.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,13 @@ package: source: url: https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/archive/v{{ version }}/icescreen-v{{ version }}.tar.gz - sha256: 21b163a5dc0f6a745d97aa6185aa94ccc4ecfe14553cc75ed71429ee1da9c122 + sha256: 283fb2bf95eb9066a535a25f7df94f6ec9d4b78083d62bd5237f801e94ac02d5 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('icescreen', max_pin="x") }} requirements: host: @@ -20,10 +22,10 @@ requirements: - hmmer =3.3.2 run: - python - - pandas >=2.0.0 - - snakemake-minimal >=7.25.0 - - biopython >=1.81 - - bcbio-gff >=0.7.0 + - pandas >=2.1.0 + - snakemake-minimal >=7.32 + - biopython =1.81 + - bcbio-gff =0.7.0 - blast =2.12 - hmmer =3.3.2 @@ -35,9 +37,10 @@ about: home: https://forgemia.inra.fr/ices_imes_analysis/icescreen license: AGPL-3.0-or-later license_family: AGPL - summary: "ICEscreen detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes." + summary: "ICEscreen detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes." doc_url: icescreen.migale.inrae.fr extra: recipe-maintainers: - thomas-lacroix + From 51bcb008de89c5bae858c82f899e5cdee4a23b4b Mon Sep 17 00:00:00 2001 From: "Moritz E. Beber" Date: Wed, 24 Jan 2024 16:56:27 +0100 Subject: [PATCH 0102/1813] Add memote (#43071) * feat: add first version of memote recipe * fix: pip install click-configfile * chore: ignore dependencies * fix: add run_exports section * fix: use name directly * fix: pin depinfo * fix: add missing dependencies * fix: use updated version with new dependencies * fix: change how the Python version is pinned * Apparently, <3.11 is not honored. * Statistics is only available for Python <3. This makes use of goodtables impossible for which we currently don't have a replacement. * fix: update dependencies --- recipes/memote/meta.yaml | 77 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 recipes/memote/meta.yaml diff --git a/recipes/memote/meta.yaml b/recipes/memote/meta.yaml new file mode 100644 index 0000000000000..ee4d6467bc3cd --- /dev/null +++ b/recipes/memote/meta.yaml @@ -0,0 +1,77 @@ +{% set name = "memote" %} +{% set version = "0.17.0" %} +{% set sha256 = "b61b222c6fe7719f0f916f01a5c68679567bad8884ed36eb634311ddbc565f19" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + entry_points: + - memote = memote.suite.cli.runner:cli + script: + - {{ PYTHON }} -m pip install --no-deps -vv . + noarch: python + number: 0 + run_exports: + - {{ pin_subpackage("memote", max_pin="x") }} + +requirements: + host: + - python >=3.9,<=3.11 + - setuptools >=40.6.0 + - versioneer-518 + - wheel + - versioneer + - pip + run: + - click + - click-configfile + - click-log + - cobra >=0.28 + - cookiecutter + - depinfo >=2.2 + - future + - git + - gitpython + - importlib_resources + - jinja2 + - jsonschema + - numpy + - numpydoc + - optlang >=1.8 + - pandas + - pandera + - pygithub <2 + - pylru + - pytest + - python >=3.9,<=3.11 + - requests + - ruamel.yaml + - six + - sqlalchemy + - sympy + +test: + imports: + - memote + commands: + - memote --help + - pip check + requires: + - pip + +about: + home: https://memote.readthedocs.io/ + summary: the genome-scale metabolic model test suite + license: Apache-2.0 + license_file: LICENSE + + +extra: + recipe-maintainers: + - Midnighter From 437418e591785b88a356135d1b0cc5c04ef753cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 10:57:14 -0500 Subject: [PATCH 0103/1813] Update wfmash to 0.12.5 (#45404) --- recipes/wfmash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wfmash/meta.yaml b/recipes/wfmash/meta.yaml index 6aa9d544dff40..8ba197d1380e3 100644 --- a/recipes/wfmash/meta.yaml +++ b/recipes/wfmash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "wfmash" %} -{% set version = "0.10.5" %} +{% set version = "0.12.5" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/waveygang/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 04c779f3e378c64543deefaa14ede67f16d1207d15e21128c9714012a0b55bcb + sha256: 797e2f968c85c631f60835ec63268fed2aba39858e7e3b30f29613b8defc40c1 build: skip: True # [osx] From b32c06295aaf74a427e9761b89fe1d2d60fe62f1 Mon Sep 17 00:00:00 2001 From: Andrea Telatin <15690844+telatin@users.noreply.github.com> Date: Wed, 24 Jan 2024 16:46:32 +0000 Subject: [PATCH 0104/1813] add rtk2 (#45390) * add rtk2 * run_exports max_pin * Update meta.yaml * Create build.sh * Update build.sh --- recipes/rtk2/build.sh | 15 +++++++++++++++ recipes/rtk2/meta.yaml | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 recipes/rtk2/build.sh create mode 100644 recipes/rtk2/meta.yaml diff --git a/recipes/rtk2/build.sh b/recipes/rtk2/build.sh new file mode 100644 index 0000000000000..7961fbb423e85 --- /dev/null +++ b/recipes/rtk2/build.sh @@ -0,0 +1,15 @@ +#!/bin/sh + +set -euxo pipefail +mkdir -p "$PREFIX"/bin + +echo " Setting environment variables" +# Fix zlib +export CFLAGS="$CFLAGS -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" +export CPATH=${PREFIX}/include + +echo "RUN MAKE" +make test + +mv rtk2 "$PREFIX"/bin/ diff --git a/recipes/rtk2/meta.yaml b/recipes/rtk2/meta.yaml new file mode 100644 index 0000000000000..0aebea2760f7b --- /dev/null +++ b/recipes/rtk2/meta.yaml @@ -0,0 +1,34 @@ +{% set version="2.10" %} +{% set name="rtk2" %} +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/hildebra/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 310cd4bd124f6d976c1f11fdc6a38da2d362942e3ea82a560c0e64cf3f1a9679 + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + - zlib + run: + - zlib + +test: + commands: + - {{ name }} -h + - {{ name }} --version | grep -w {{ version }} + +about: + home: https://github.com/hildebra/rtk2/ + license: 'GPLv2' + license_file: LICENSE + summary: 'rtk2 - a CLI rarefaction toolkit for OTU tables' From 68c3bfb8b1c7ac08bf69f38ed0439e59433b4b0c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 12:09:09 -0500 Subject: [PATCH 0105/1813] Update thapbi-pict to 1.0.6 (#45400) * Update thapbi-pict to 1.0.6 * Dependency updates --------- Co-authored-by: Peter Cock --- recipes/thapbi-pict/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index d1eca3abad919..319e783d8d6b0 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.5" %} +{% set version = "1.0.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: c7e42668397ac37b869b2c5774e721635e892ebb99eefc014d634b090d9f7c08 + sha256: a80cc24cce224195e5f613353cfe63020daca949defea4511cef392b7a6f30ed build: noarch: python @@ -21,18 +21,18 @@ build: requirements: host: - pip - - python >=3.7 + - python >=3.8 run: # Python - biom-format >=2.1.14 - - biopython >=1.73 + - biopython >=1.82 - cutadapt >=4.0 - matplotlib-base >=3.7 - networkx >=2.4,!=2.8.3,!=2.8.4 - pydot - - python >=3.7 + - python >=3.8 - rapidfuzz >=2.4.0 - - sqlalchemy + - sqlalchemy >=2.0 - xlsxwriter # Command line - blast From b54a0152595b72b70812fcdd7cf64a83a38af73a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 12:50:18 -0500 Subject: [PATCH 0106/1813] Update fibertools-rs to 0.3.8 (#45407) --- recipes/fibertools-rs/build.sh | 2 ++ recipes/fibertools-rs/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/fibertools-rs/build.sh b/recipes/fibertools-rs/build.sh index 6a4023caabe45..e5418801f8fdf 100644 --- a/recipes/fibertools-rs/build.sh +++ b/recipes/fibertools-rs/build.sh @@ -16,6 +16,8 @@ export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${LIBTORCH}/lib # # download pytorch libraries # +# unfortunetally newish size limits on bioconda packages prevent me from including this. +# keeping this code block here in case the size limits change, or bioconda/conda-forge allow the pytorch channel to be accessed. if [[ "x" == "y" ]]; then export TORCH_VERSION="2.0.1" diff --git a/recipes/fibertools-rs/meta.yaml b/recipes/fibertools-rs/meta.yaml index 078fd91c3b47d..112fffa6d7bc4 100644 --- a/recipes/fibertools-rs/meta.yaml +++ b/recipes/fibertools-rs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.7" %} +{% set version = "0.3.8" %} {% set name = "fibertools-rs" %} {% set build_number = "0" %} @@ -9,7 +9,7 @@ package: source: url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz - sha256: 395615d051a322fa08b1d1453691c7d8ece8ca7cc77b91e5c78d3274e1d15498 + sha256: 7e244ceafa5371d21de45a9e6ea5dd66e4922283142bc9a332c1114d5118fa02 build: From d778f7d5e40349474b1d653622a98ef5ba57b48d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 13:03:01 -0500 Subject: [PATCH 0107/1813] Update mitos to 2.1.7 (#45406) --- recipes/mitos/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index 7523ada0fc540..65d99c42a65c6 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "2.1.6" %} +{% set version = "2.1.7" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 66d6ca1138bdda459d4ed6271a946ff86ea6298dcf7e3bb6f63c283213f77284 + sha256: b6c6e5173f37a6ff9e5c2b7ac3f45645f0db3093371a7804e3e336e203c5abe4 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " noarch: python run_exports: From 71a9cdc052645896bf65f9c45b6e629797bf2dd8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 13:38:02 -0500 Subject: [PATCH 0108/1813] Update samtools to 1.19.2 (#45393) --- recipes/samtools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index 3d45b94379193..cd24c1020f76f 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.19.1" %} +{% set version = "1.19.2" %} package: name: samtools @@ -11,7 +11,7 @@ build: source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - sha256: 1f94915cc32dcb6095049ed57560d99b409ba9297f4316bab551d05bb57ff355 + sha256: 71f60499668e4c08e7d745fbff24c15cc8a0977abab1acd5d2bb419bdb065e96 requirements: build: From 46dae9fc0212016d62c0ec9e54b36d2699bea3c8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 13:48:08 -0500 Subject: [PATCH 0109/1813] Update varvamp to 1.1 (#45403) --- recipes/varvamp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index efbed07b77dd9..3c6d6d606e4a2 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "1.0.1" %} +{% set version = "1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 422a4a9dc8d5377242731e3027bba4510939e0dc91555d57636d7b45961261ab + sha256: 186b5fd4ca9670c05f977440976348587a5c79d4b79bc4370390fdabb6715d84 build: entry_points: From ff1628eb372c8cc20fc8b91988394388a11613bb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 14:02:27 -0500 Subject: [PATCH 0110/1813] Update dnoise to 1.4.1 (#45388) --- recipes/dnoise/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnoise/meta.yaml b/recipes/dnoise/meta.yaml index b706edda05cf0..e8aa73687be78 100644 --- a/recipes/dnoise/meta.yaml +++ b/recipes/dnoise/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DnoisE" %} -{% set version = "1.4.0" %} -{% set sha256 = "bee24dbe42fb884810788bb4ac874d6b664e24a3820e6706406fd8a90b6ac328" %} +{% set version = "1.4.1" %} +{% set sha256 = "39c728faea03732df906cb90bf541efdb8d7ebf4858c9bf2717fa8a75e9157b1" %} package: name: {{ name|lower }} From d78bbd9824ecfacc18b71c6f03cd68f38df5ab1b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 14:48:28 -0500 Subject: [PATCH 0111/1813] Update virusrecom to 1.1.3.1 (#45398) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/virusrecom/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/virusrecom/meta.yaml b/recipes/virusrecom/meta.yaml index bafd8ea722121..6e9352ffa5415 100644 --- a/recipes/virusrecom/meta.yaml +++ b/recipes/virusrecom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virusrecom" %} -{% set version = "1.1.3" %} +{% set version = "1.1.3.1" %} package: name: "{{ name }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1950537ea6f2cf83dcfc44dd31b5c524a8e5b6988ca284c1ed291a2234d692c7 + sha256: 3fda39fc84b7a0ffccdfcdb309c2f8bb5e617d7dfc0c5b0cb0fc4a3d245c43b4 build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage('virusrecom', max_pin="x") }} From d89c3e2ffc5f98162012ffbfe3f0f133d2edbb0f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 14:48:52 -0500 Subject: [PATCH 0112/1813] Update last to 1526 (#45394) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 673ba234ef336..c8a7c15ea12ff 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1522" %} +{% set version = "1526" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 0cc27dce53693c4d97864c012f9b9b34e4c02ebd0c38db23c5c5d978dbfd4d4e + sha256: e1db7307005218cbed0c924d583e4bb7bdee96044cb94867cf73d18249058463 build: number: 0 From 5c10dee3e1def4c36082ac6a3a0684ea134726f9 Mon Sep 17 00:00:00 2001 From: Bob <55469084+yhhan19@users.noreply.github.com> Date: Wed, 24 Jan 2024 12:28:37 -0800 Subject: [PATCH 0113/1813] Add TREE-QMC package (#43224) * tqmc * build.sh fixed * "folder_and_package_name_must_match" fixed * missing_run_exports fixed * g++ not found fix * build error fixed * build error fix * build.sh fix * osx compilation fix * made the name and version number consistent * minor --- recipes/tree-qmc/build.sh | 9 +++++++ recipes/tree-qmc/conda_build_config.yaml | 5 ++++ recipes/tree-qmc/meta.yaml | 31 ++++++++++++++++++++++++ recipes/treeqmc/build.sh | 9 +++++++ recipes/treeqmc/conda_build_config.yaml | 5 ++++ recipes/treeqmc/meta.yaml | 31 ++++++++++++++++++++++++ 6 files changed, 90 insertions(+) create mode 100644 recipes/tree-qmc/build.sh create mode 100644 recipes/tree-qmc/conda_build_config.yaml create mode 100644 recipes/tree-qmc/meta.yaml create mode 100644 recipes/treeqmc/build.sh create mode 100644 recipes/treeqmc/conda_build_config.yaml create mode 100644 recipes/treeqmc/meta.yaml diff --git a/recipes/tree-qmc/build.sh b/recipes/tree-qmc/build.sh new file mode 100644 index 0000000000000..afeec38073355 --- /dev/null +++ b/recipes/tree-qmc/build.sh @@ -0,0 +1,9 @@ +cd MQLib +make \ + GXX="${CXX}" \ + AR="${AR}" +cd .. +$CXX -std=c++11 -O2 -I MQLib/include -o TREE-QMC src/*.cpp MQLib/bin/MQLib.a +mkdir -p $PREFIX/bin +cp TREE-QMC $PREFIX/bin/ +chmod a+x $PREFIX/bin/TREE-QMC diff --git a/recipes/tree-qmc/conda_build_config.yaml b/recipes/tree-qmc/conda_build_config.yaml new file mode 100644 index 0000000000000..7fe2892e9edfa --- /dev/null +++ b/recipes/tree-qmc/conda_build_config.yaml @@ -0,0 +1,5 @@ +c_compiler_version: # [unix] + - 9.3.0 # [linux] + +cxx_compiler_version: + - 9.3.0 # [linux] diff --git a/recipes/tree-qmc/meta.yaml b/recipes/tree-qmc/meta.yaml new file mode 100644 index 0000000000000..66298530a9cb3 --- /dev/null +++ b/recipes/tree-qmc/meta.yaml @@ -0,0 +1,31 @@ +{% set name = "TREE-QMC" %} +{% set version = "2.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/molloy-lab/{{ name|upper }}/releases/download/{{ version }}/{{ name|upper }}-{{ version }}.zip + sha256: f8530dd6d106c63ffde0d728eeef835b8bded16e69620e78bd45f562129f86a9 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('tree-qmc', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + run: + +test: + commands: + - TREE-QMC -h + +about: + home: https://github.com/molloy-lab/TREE-QMC + license: MIT + summary: TREE-QMC is a quartet-based method for estimating species trees from gene trees. diff --git a/recipes/treeqmc/build.sh b/recipes/treeqmc/build.sh new file mode 100644 index 0000000000000..afeec38073355 --- /dev/null +++ b/recipes/treeqmc/build.sh @@ -0,0 +1,9 @@ +cd MQLib +make \ + GXX="${CXX}" \ + AR="${AR}" +cd .. +$CXX -std=c++11 -O2 -I MQLib/include -o TREE-QMC src/*.cpp MQLib/bin/MQLib.a +mkdir -p $PREFIX/bin +cp TREE-QMC $PREFIX/bin/ +chmod a+x $PREFIX/bin/TREE-QMC diff --git a/recipes/treeqmc/conda_build_config.yaml b/recipes/treeqmc/conda_build_config.yaml new file mode 100644 index 0000000000000..7fe2892e9edfa --- /dev/null +++ b/recipes/treeqmc/conda_build_config.yaml @@ -0,0 +1,5 @@ +c_compiler_version: # [unix] + - 9.3.0 # [linux] + +cxx_compiler_version: + - 9.3.0 # [linux] diff --git a/recipes/treeqmc/meta.yaml b/recipes/treeqmc/meta.yaml new file mode 100644 index 0000000000000..2af0d99783ba1 --- /dev/null +++ b/recipes/treeqmc/meta.yaml @@ -0,0 +1,31 @@ +{% set name = "TREEQMC" %} +{% set version = "2.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/molloy-lab/TREE-QMC/releases/download/2.0.0/TREE-QMC-2.0.0.zip + sha256: f8530dd6d106c63ffde0d728eeef835b8bded16e69620e78bd45f562129f86a9 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('treeqmc', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + run: + +test: + commands: + - TREE-QMC -h + +about: + home: https://github.com/molloy-lab/TREE-QMC + license: MIT + summary: TREE-QMC is a quartet-based method for estimating species trees from gene trees. From 431a903c6c89942bd1567db96352639632f4e155 Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Wed, 24 Jan 2024 15:36:37 -0500 Subject: [PATCH 0114/1813] Update gsearch v0.1.8 (#45413) * Update gsearch v0.1.8 * Update BinDash v2.1 --------- Co-authored-by: Jianshu Zhao --- recipes/bindash/meta.yaml | 4 ++-- recipes/gsearch/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/bindash/meta.yaml b/recipes/bindash/meta.yaml index a7667087921b2..47ba2fb182600 100644 --- a/recipes/bindash/meta.yaml +++ b/recipes/bindash/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0" %} +{% set version = "2.1" %} package: name: bindash @@ -6,7 +6,7 @@ package: source: url: https://github.com/jianshu93/bindash/archive/v{{ version }}.tar.gz - sha256: 300fd4709df1d000470feb5af1a7d1ecd95c15f9c35f7535ae9c40dce4a540a8 + sha256: 185903149a2a14a4506f0a60d0f9fc0c03bace6705fb5eca8df4048d1b03592b build: skip: True # [osx] diff --git a/recipes/gsearch/meta.yaml b/recipes/gsearch/meta.yaml index 8e51a1a1372fd..b378ec2e3aee7 100644 --- a/recipes/gsearch/meta.yaml +++ b/recipes/gsearch/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.7" %} +{% set version = "0.1.8" %} package: name: gsearch @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/gsearch/archive/v{{ version }}.tar.gz - sha256: ceec9638cbb2bb8f588375a3c3283ca717ba436e9d550624a1039c9d00a76e8a + sha256: bdb954e52c61baf94f7de574b4a578df19f12508af89996d461aeebb43a39a8f requirements: build: From c957d8fa9553c12cb79ba3c960ae5a78c778168d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 16:04:03 -0500 Subject: [PATCH 0115/1813] Update pyrodigal to 3.3.0 (#45416) --- recipes/pyrodigal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml index 94764527e29ad..944dd7eb5dd58 100644 --- a/recipes/pyrodigal/meta.yaml +++ b/recipes/pyrodigal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal" %} -{% set version = "3.2.2" %} +{% set version = "3.3.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 0e02b2089df29c3c0f1379364664f4a83da12373233bb74d7a95d24a346b02ec + sha256: 68f92cd83f9cd2883b99433847a827dd84ccb27edc51cb3f415664f0f08b0325 build: number: 0 From 7c0e10b5cb8cd0f2052fbc11b02fda1b81d20942 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 16:12:44 -0500 Subject: [PATCH 0116/1813] Update genmod to 3.8.2 (#44620) * Update genmod to 3.8.2 * Update meta.yaml * edit python version pinning * lock pypandoc <1.8 --------- Co-authored-by: Thanh Lee <247862+thanhleviet@users.noreply.github.com> Co-authored-by: joshuazhuang7 Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> --- recipes/genmod/meta.yaml | 24 +++++++++--------------- 1 file changed, 9 insertions(+), 15 deletions(-) diff --git a/recipes/genmod/meta.yaml b/recipes/genmod/meta.yaml index 1cd3b5465f5b2..4b226e225aa97 100644 --- a/recipes/genmod/meta.yaml +++ b/recipes/genmod/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genmod" %} -{% set version = "3.8.1" %} +{% set version = "3.8.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d21f072f6c4a34479bc0f1633bd7a15b04a04c87f63f28457dce58615a0a7f14 + sha256: 72921cce29fd8d6b99eea76921a0a71d3846abcb92bcb02dafd24886ab9264a3 build: number: 0 @@ -16,22 +16,15 @@ build: - {{ pin_subpackage('genmod', max_pin="x") }} entry_points: - genmod = genmod.commands.base:cli - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" requirements: host: - - click <7 - - configobj - - extract_vcf >=0.4.2 - - interval_tree >=0.3.2 - - intervaltree - - ped_parser >=1.6.2 - pip - - pytabix - - pytest - - python + - python 3.8.* + - pypandoc <1.8 run: - - click <7 + - click >=8.1.3 - configobj - extract_vcf >=0.4.2 - interval_tree >=0.3.2 @@ -39,7 +32,8 @@ requirements: - ped_parser >=1.6.2 - pytabix - pytest - - python + - python 3.8.* + - vcftoolbox >=1.5.1 test: imports: @@ -61,7 +55,7 @@ about: home: "http://github.com/moonso/genmod" license: MIT license_family: MIT - license_file: + license_file: LICENSE.txt summary: "Annotate genetic inheritance models in variant files" extra: From 6dd2fc937271d14be51c862cd056144d54112a69 Mon Sep 17 00:00:00 2001 From: Mikko Rautiainen Date: Wed, 24 Jan 2024 23:16:26 +0200 Subject: [PATCH 0117/1813] Update GraphAligner to version 1.0.19 (#45387) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/graphaligner/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/graphaligner/meta.yaml b/recipes/graphaligner/meta.yaml index ff837db9ff3f9..38b34e29495ea 100644 --- a/recipes/graphaligner/meta.yaml +++ b/recipes/graphaligner/meta.yaml @@ -1,13 +1,13 @@ {% set name = "GraphAligner" %} -{% set version = "1.0.18" %} +{% set version = "1.0.19" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/maickrau/{{ name }}/files/13412859/{{ name }}.tar.gz - sha256: 69d248332c1df732b74571f9910d3390bfeb48165fb9d99a892ec0a71ab1291f + url: https://github.com/maickrau/{{ name }}/files/14037134/{{ name }}.tar.gz + sha256: b65d26d415c3fd459bf2fc884b3d48dc0c55f7e9135e700c5c38d62be8ee39fc patches: - version.patch - linux_link.patch # [linux] From 9ac3dcaac482a3a7b8a8bb9ab2728f3f94b015ed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 16:21:11 -0500 Subject: [PATCH 0118/1813] Update cazy_webscraper to 2.3.0.2 (#45389) * Update cazy_webscraper to 2.3.0.2 * add run_exports --------- Co-authored-by: mencian --- recipes/cazy_webscraper/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/cazy_webscraper/meta.yaml b/recipes/cazy_webscraper/meta.yaml index f5c23370c9ad7..4e856fcf1d133 100644 --- a/recipes/cazy_webscraper/meta.yaml +++ b/recipes/cazy_webscraper/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cazy_webscraper" %} -{% set version = "2.3.0" %} -{% set sha256 = "08a12134f124622069d4259c55d0bafc618e4f1d4872992529cd495d782fd21e" %} +{% set version = "2.3.0.2" %} +{% set sha256 = "4edd7f8f121bcab1c85af649c40c497490e8b5d5769e748536ce4c965daf5297" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - cazy_webscraper = cazy_webscraper.cazy_scraper:main - cw_get_genbank_seqs = cazy_webscraper.expand.genbank.sequences.get_genbank_sequences:main @@ -25,6 +25,8 @@ build: - cw_get_pdb_structures = cazy_webscraper.expand.pdb.get_pdb_structures:main - cw_query_database = cazy_webscraper.api.cw_query_database:main - cw_get_db_schema = cazy_webscraper.sql.get_schema:main + run_exports: + - {{ pin_subpackage('cazy_webscraper', max_pin="x") }} requirements: host: @@ -57,6 +59,7 @@ about: dev_url: "https://github.com/HobnobMancer/cazy_webscraper" summary: "A tool to automate retrieving data from CAZy, build a local CAZyme SQL database, and throughly interrogating the data. Also, automate retrieving protein data, sequences, EC numbers and structure files for specific datasets in the CAZyme database from UniProt, GenBank and PDB." license: MIT + license_family: MIT license_file: LICENSE extra: From e06b74b36d5dfa7667e9f1aa0cf50f882c7c7e07 Mon Sep 17 00:00:00 2001 From: llegregam <75795040+llegregam@users.noreply.github.com> Date: Wed, 24 Jan 2024 22:32:11 +0100 Subject: [PATCH 0119/1813] Added recipe for skyline2isocor v0.1.0 (#45408) * Added recipe for skyline2isocor v0.1.0 * add run_exports --------- Co-authored-by: mencian --- recipes/skyline2isocor/meta.yaml | 45 ++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 recipes/skyline2isocor/meta.yaml diff --git a/recipes/skyline2isocor/meta.yaml b/recipes/skyline2isocor/meta.yaml new file mode 100644 index 0000000000000..3abfb9f8be2a4 --- /dev/null +++ b/recipes/skyline2isocor/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "skyline2isocor" %} +{% set version = "0.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/skyline2isocor-{{ version }}.tar.gz + sha256: 9bf2b6a8c381ced3a5a24838d944bfff016a12c7da6f3627ff31467918e609bc + +build: + entry_points: + - skyline2isocor = skyline2isocor.cli:start_cli + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('skyline2isocor', max_pin="x.x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - pandas >=2.1.4,<3.0.0 + +test: + imports: + - skyline2isocor + commands: + - skyline2isocor --help + +about: + home: https://pypi.org/project/skyline2isocor/ + summary: Convert skyline output to IsoCor input format + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + +extra: + recipe-maintainers: + - llegregam From e07b1754495f765e62c460047d3690c69b1bb303 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 24 Jan 2024 23:07:08 +0100 Subject: [PATCH 0120/1813] Update sativa (#44990) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Updated sativa build, incl. test case * Update meta.yaml with new Sativa release * Linting * Update keggcharter to 1.0.2 (#44992) * Update keggcharter to 1.0.2 * Update meta.yaml Now put all TXTs and TSVs from "resources" folder into "share" folder. --------- Co-authored-by: João Sequeira * Update hictk to v0.0.5 (#44988) * Update conanfile.txt.patch * Bump version * Update perl-minion to 10.28 (#44495) * bugfix: strand deprecated and removed in BioPython 1.82 (#44987) - see: https://github.com/chapmanb/bcbb/issues/138 * bugfix: breaking API change between ruamel.yaml 0.17.x and 0.18 (#44989) * Update tsebra to 1.1.2.2 (#45000) * Update sylph to 0.5.1 (#45001) * add r-misha 3.7.0 (history version) (#44981) * add misha version 3.7.0 (history version) * fix hash * fix compiler settings * use template variable to specify name * add run_export to lock version * add r-misha 3.7.1 (history version) (#44984) * add r-misha 3.7.1 (history version) * fix: incorrect commit and hash * Update viguno to 0.2.0 (#44996) * Update viguno to 0.2.0 * run_exports --------- Co-authored-by: Thanh Lee * Update annonars to 0.32.0 (#45013) * Fix recognizer (#45012) * Update recognizer to 1.10.0 * Update meta.yaml No more build.sh file * Update meta.yaml Forgot about the other TSV files * Removed build.sh --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> * Update last to 1522 (#45011) * Update pcaone to 0.4.1 (#45009) * genoflu version 1.02 (#44995) * genoflu version 1.02 * Update meta.yaml * Update meta.yaml * https://spdx.org/licenses/GPL-3.0-or-later.html --------- Co-authored-by: Thanh Lee * Update chromhmm to 1.25 (#45016) * Update chromhmm to 1.25 * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer * Update ColabFold to 1.5.5 (#45008) * Update ColabFold to 1.5.4 * Use 1.5.5 instead, 1.5.4 had a bug * OpenMM 8.1 causes issues * Update expam to 1.2.2.4 (#45007) * Update expam to 1.2.2.4 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update upimapi to 1.13.1 (#45019) Co-authored-by: João Sequeira * Update raptor (#44952) multiple binaries and a wrapper scripts depending on available instruction sets. * add AnnoSINE2 recipes (#44980) * add strainscan recipes * add annosine2 recipes * Delete recipes/strainscan/meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Bulk (#45014) * a round of fixes and build-skips * add some build failures * correct version for bioconductor-data-packages * add build failure for STdeconvolve * [ci run] trigger bulk run * run_exports on bioconductor-data-packages * [ci run] trigger bulk run * build failure for omnipathr * [ci run] trigger bulk run * Build important packages first * [ci run] trigger bulk run * revert to full build * [ci run] trigger bulk run * build failure files * skip iclusterplus * skip bioconductor-lpsymphony * bump bioconda-repodata-patches build number * [ci run] * build failures * next round of high priority packages * [ci run] trigger bulk run * [ci run] add dependency * [ci run] finish priority packages * re-enable full bulk * [ci run] trigger bulk run * build failures * [ci run] trigger bulk run * next round of high priority packages * [ci run] trigger bulk run * build more high priority packages * [ci run] test local channel fix * [ci run] increase workers * Try building bioconductor-geoquery (#44726) * Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml * Update meta.yaml * try fixing parsing error * [ci run] try rebuilding bioconductor-coregx (#44727) * try rebuilding bioconductor-coregx * Update meta.yaml * add opencl loading libraries - will this work * [ci run] remove a few build failure files * [ci run] Bioconductor graph (#44733) * remove build failure file * trigger build * Update meta.yaml * add patch back [ci run] * build failures * [ci run] high priority packages * bulk wiki page * [ci run] add missing packges * build failure for bioconductor-sictools * [ci run] missed one * [ci run] full run * Update build.sh * [ci run] fix dexseq * [ci run] next round of high priority packages * [ci run] missing packages * [ci run] high priority package * [ci run] build all bioconductor-bsgenome * [ci run] remove failures associated with bioconductor-bsgenome dependency * full build * use bioconda-common version * build failures: test dev version of utils * escape characters correctly * build failure for bioconductor-pics * use branch * build failure for bioconductor-inspect * try to fix build failure git range * build failure for bioconductor-distinct * use head branch * trigger build failure wf * [ci run] trigger bulk run * build failures fetch depth * build failure for biconductor-benchdamic * build failures * build failures with log * don't run build failures if last commit has ci skip * [ci skip] test build failure wiki * test build failure wiki job * [ci run] reenable record-build-failures * re-add token for build failure updates * build failures add category column * trigger wiki update * fix libsbml version for bioconductor-rsbml * build failure updates * fix bioconductor-glad * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-wppi * [ci skip] add build failure record for recipe recipes/bioconductor-gars * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-metascope * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader * [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r * [ci skip] add build failure record for recipe recipes/bioconductor-gesper * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-seqcna * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-inpas * [ci skip] add build failure record for recipe recipes/bioconductor-factr * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble * [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile * [ci skip] add build failure record for recipe recipes/bioconductor-extrachips * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc * [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats * [ci skip] add build failure record for recipe recipes/bioconductor-chipqc * [ci skip] add build failure record for recipe recipes/bioconductor-outsplice * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk * [ci skip] add build failure record for recipe recipes/bioconductor-ritan * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-vulcan * [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk * [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-deconvr * [ci skip] add build failure record for recipe recipes/bioconductor-ideal * [ci skip] add build failure record for recipe recipes/bioconductor-esatac * [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr * [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate * [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps * [ci skip] add build failure record for recipe recipes/bioconductor-lemur * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-regionreport * [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-cageminer * [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-scpipe * Rbowtie2 (#44856) [ci run] fix rbowtie2 builds * [ci run] remove build file * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * failure for bioconda-multirnaflow * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * bioconductor-lpsymphony fix from master * remove build failures for finished dependencies * restore skip osx-64 * fix bioconductor-rawrr * high priority packages * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] remove build failure record for recipe recipes/bioconductor-proloc * fix bioconductor-chemmineob * [ci run] remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * remove easy build failures * [ci run] next round of dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-pigengene * [ci skip] add build failure record for recipe recipes/bioconductor-repitools * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * build failure updates * [ci run] next batch of fixes * [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2 * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run]remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-gatom * [ci run] set failures to skip * [ci run] reduce resources that are wasted * [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1 * fix accidental reverts * add GSL to bioconductor-pics * add back fix from master for omnipathr * remove build failure * [ci run] skip root nodes to spread out builds * [ci run] include more root nodes in blacklist * update build failures * [ci run] add more blacklist items and do osx build * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * [ci skip] add build failure record for recipe recipes/bioconductor-mumosa * [ci skip] add build failure record for recipe recipes/bioconductor-chromscape * [ci skip] add build failure record for recipe recipes/bioconductor-scmerge * [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare * fix build errors * [ci run] more skipped builds * [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay * [ci run] reduce workers * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler * [ci run] manually distribute packages * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-condiments * [ci skip] add build failure record for recipe recipes/bioconductor-scclassify * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-gcapc * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-traviz * remove build failures * remove colon that breaks yaml parsing * remove temporary bioconductor bulk skips * [ci run] remaining packages * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-promise * [ci skip] add build failure record for recipe recipes/bioconductor-otubase * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * retry http error * [ci run] full bulk build * [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer * [ci skip] remove build failure record for recipe recipes/bioconductor-meb * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci run] categorize failures * add bioconductor-cdi * remove old failure files * update bioconductor-reusedata to 3.18 * remove failures for dependencies that have been built * [ci run] build certain packages * bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (#44986) * update bioconductor-ccfindr with gsl * update bioconductor-rjmcmcnucleosomes with gsl * [ci run] build updated recipes * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-reusedata * remove temporary changes from workflows * build got bumped in merge * remove temp files --------- Co-authored-by: Ryan Dale Co-authored-by: Björn Grüning Co-authored-by: Bjoern Gruening Co-authored-by: BiocondaBot * Update deeplc to 2.2.26 (#44238) * Update deeplc to 2.2.23 * Update deeplc to 2.2.24 * add pyopenms * Update deeplc to 2.2.25 * Update deeplc to 2.2.26 * try extended base * revert extended base --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add recipe for CellBender v0.3.0 (#45024) * Add recipe for CellBender v0.3.0 * add run_exports * Fix nrpys to build on python 3.8+ (#45025) * Update oakvar to 2.9.83 (#45026) * Update foldcomp to 0.0.6 (#45018) * Update foldcomp to 0.0.6 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update antismash-lite to 7.1.0 (#45027) * Update jcvi to 1.3.9 (#45029) * Update jcvi to 1.3.9 * Update meta.yaml --------- Co-authored-by: Christian Brueffer * Update recognizer to 1.10.1 (#45031) Co-authored-by: João Sequeira * Update midsv to 0.11.0 (#45028) * Update midsv to 0.11.0 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer * Update meta.yaml (#45041) Snakemake refactored in newer version. * Rebuild unitig caller for new bifrost version (#45035) * Rebuild unitig caller for new bifrost version * Add run_exports * Fix string interpolation in pinning * Update annosine2 build (#45033) * Update meta.yaml * Update meta.yaml * Update rasusa to 0.8.0 (#45042) * Update rasusa to 0.8.0 * add run_export * bump msrv --------- Co-authored-by: Michael Hall * Update annonars to 0.33.0 (#45043) * patch viroconstrictor snakemake requirements to not use version 8.x (#45036) * Add Deepmei version 1.0.0 recipes (#45005) * Update keggcharter to 1.1.0 (#45046) * Update mosca to 2.2.0 (#45054) * Update mosca to 2.2.0 * Update meta.yaml Added run_exports Added pandas as dependency Fixed python version to <3.12 Fixed snakemake version to <8 --------- Co-authored-by: João Sequeira * Update fgbio to 2.2.1 (#45050) * Update fgbio-minimal to 2.2.1 (#45051) * Update viralmsa to 1.1.41 (#45047) * Update ndex2 to 3.7.0 (#45049) * Update expam to 1.2.2.5 (#45053) * Update bustools to 0.43.2 (#45055) * Update kb-python to 0.28.1 (#45056) * Update xengsort to 2.0.5 (#44888) * Update xengsort to 2.0.4 * pin python to 3.11 * Update xengsort to 2.0.5 --------- Co-authored-by: joshuazhuang7 * Update ena-webin-cli to 6.8.0 (#45059) * Update zol to 1.3.17 (#45067) * Update pybiolib to 1.1.1673 (#45057) * Update pybiolib to 1.1.1682 (#45072) * Update adam to 1.0.1 (#45069) * Update adam to 1.0.1 * add pin_subpackage * Update cannoli to 1.0.1 (#45070) * Update cannoli to 1.0.1. * add pin_subpackage * Update keggcharter to 1.1.1 (#45079) * Update galaxy-objectstore to 23.1.4 (#45061) * Update galaxy-files to 23.1.4 (#45062) * Update mashmap to 3.1.3 (#45064) * Update rosella to 0.5.3 (#45075) * Update snakemake-executor-plugin-googlebatch to 0.2.0 (#45039) * Update snakemake-executor-plugin-googlebatch to 0.2.0 * add summary --------- Co-authored-by: mencian * Update hifihla to 0.2.3 (#45066) * Update micom to 0.33.1 (#45071) * Update flight-genome to 1.6.3 (#45073) * Update bioframe to 0.6.0 (#45076) * Update metdatamodel to 0.5.5 (#45082) * Update odgi to 0.8.4 (#45077) * Update odgi to 0.8.4 * run_exports --------- Co-authored-by: Thanh Lee * Update nanovar to 1.5.1 (#45084) * Update r-ldweaver to 1.4 (#45058) * Update r-ldweaver to 1.4 * drop genbankr dependency * it seems genbankr is still needed --------- Co-authored-by: mencian * Update ncbi-datasets-pylib to 16.1.1 (#45090) * Update dbcan to 4.1.0 (#45088) * Update dbcan to 4.1.0 * fix bug * add hatchling and other fixes * edit sha256 --------- Co-authored-by: mencian * Update perl-math-bigint to 2.003002 (#45096) * Update nf-test to 0.8.3 (#45098) * Update foldcomp to 0.0.7 (#45097) * Update meta.yaml (#45086) * Update ltr_retriever to 2.9.8 (#45006) * Update ltr_retriever to 2.9.8 * add run_exports * revert channel specifications * remove channels section --------- Co-authored-by: joshuazhuang7 * prodigal: include upstream patches fixing critical bugs (#45091) * prodigal: freshen up * prodigal: include patches for critical bugs fixed upstream but unreleased The developer has accepted these changes, but no new release has been made in over a year. * Add vcfphasesets (#45092) * Add vcfphasesets. * Change meta.yaml for run exports. * Complexcgr (#45089) * Add complexcgr v0.8.0 * Add complexcgr v0.8.0 * Add complexcgr v0.8.0 * Update ribowaltz to 2.0 (#45065) * Update ribowaltz to 2.0 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update vcf2variants (#45083) * Update to version 1.0. * Add run_exports. * Extra dependency. * Bump version. * Bump version and test import. * Fix import test. * Add additional requirement. --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update snapatac2 to 2.5.2 (#45078) * Update snapatac2 to 2.5.2 * add typing_extensions to run section --------- Co-authored-by: joshuazhuang7 * Update breseq to 0.38.2 (#45103) * Update breseq to 0.38.2 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update mitos to 2.1.6 (#45104) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update harmony-pytorch to 0.1.8 (#45106) * Update harmony-pytorch to 0.1.8 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update snakemake to 8.1.0 (#45108) * Update ltr_retriever to 2.9.9 (#45107) * Update tn93 to 1.0.13 (#45109) * Update hyphy to 2.5.59 (#45111) * Update pyfaidx to 0.8.0 (#45113) * Depend on gcc; new sha256 * Finally a sativa recipe that puts sativa.py in PATH * Update mitgard to 1.1 (#45101) * Update mitgard to 1.1 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update bioframe to 0.6.1 (#45120) * Add virusrecom (#45099) * add virusrecom recipes * add virusrecom recipes xx * Update meta.yaml * add python to run section and use SPDX identifier --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * bump mitos1 (#45112) * bump mitos1 * repin blast-legacy .. add tests first * Update pybiolib to 1.1.1685 (#45119) * Update ncbi-datasets-pylib to 16.1.2 (#45124) * Update das_tool to 1.1.7 (#45123) * Update das_tool to 1.1.7 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update virusrecom to 1.1.3 (#45122) * Update severus to 0.1.2 (#45135) * Update virusrecom (#45130) * add virusrecom recipes * Update meta.yaml * edit recipe-maintainer --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update hybracter to 0.5.0 (#45128) * Update dnaapler to 0.5.1 (#45129) * Update recentrifuge to 1.13.1 (#45132) * Update tissuumaps to 3.2.0.3 (#45137) * mitos: add tests for R packages (#44971) * mitos: add tests for R packages In test with the container I got: Exception: b"Warning message:\npackage \xe2\x80\x98ggplot2\xe2\x80\x99 was built under R version 3.6.3 \nError: package or namespace load failed for \xe2\x80\x98reshape2\xe2\x80\x99 in dyn.load(file, DLLpath = DLLpath, ...):\n unable to load shared object '/usr/local/lib/R/library/stringi/libs/stringi.so':\n libicui18n.so.64: cannot open shared object file: No such file or directory\nIn addition: Warning message:\npackage \xe2\x80\x98reshape2\xe2\x80\x99 was built under R version 3.6.3 \nExecution halted\n" * try to use R directly in tests * try R > 3 * bump and unpin vienna * retry R>3 * another try * try to pin r-stringi * bump * cnt * unpin some more requirements * remove stringi * repin infernal * repin hmmer * repin blast * Revert "repin blast" This reverts commit 6a5717a86f8231c1ced5ca58e21f97f01c264e2f. * Update kb-python to 0.28.2 (#45138) * Update ena-webin-cli to 6.9.0 (#45139) * Update r-seqmagick to 0.1.7 (#45131) * Update r-seqmagick to 0.1.7 * Update meta.yaml --------- Co-authored-by: Christian Brueffer * Update snakefmt to 0.9.0 (#45134) * remove static compilation (#45141) * Update dajin2 to 0.3.6 (#45143) * Update jbrowse2 to 2.10.1 (#45145) * Update ncbi-datasets-pylib to 16.2.0 (#45144) * Add ACI (#45121) * adding aci recipe * fixed entry point typo * fix typo * matplotlib-base * url * revert url * underscore * version --------- Co-authored-by: Thanh Lee * Update ngs-chew to 0.9.0 (#45140) * Update vcfpy to 0.13.7 (#45150) * Avoid building on OS X --------- Co-authored-by: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Co-authored-by: João Sequeira Co-authored-by: Roberto Rossini <71787608+robomics@users.noreply.github.com> Co-authored-by: DrYak Co-authored-by: TPOB <19909103+TTTPOB@users.noreply.github.com> Co-authored-by: Thanh Lee Co-authored-by: stuber Co-authored-by: Christian Brueffer Co-authored-by: Milot Mirdita Co-authored-by: joshuazhuang7 Co-authored-by: Enrico Seiler Co-authored-by: Ray <851836818@qq.com> Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com> Co-authored-by: Ryan Dale Co-authored-by: Björn Grüning Co-authored-by: Bjoern Gruening Co-authored-by: BiocondaBot Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Carl Mathias Kobel Co-authored-by: John Lees Co-authored-by: Michael Hall Co-authored-by: Florian Zwagemaker <49153065+florianzwagemaker@users.noreply.github.com> Co-authored-by: Kanglu123 <64641114+Kanglu123@users.noreply.github.com> Co-authored-by: Michael L Heuer Co-authored-by: Le (Lena) Huang Co-authored-by: Jens Luebeck Co-authored-by: Afif Elghraoui Co-authored-by: Mark Santcroos Co-authored-by: Koke <49822617+jorgeavilacartes@users.noreply.github.com> Co-authored-by: Zhou ZJ <43747306+ZhijianZhou01@users.noreply.github.com> Co-authored-by: M Bernt Co-authored-by: boukn Co-authored-by: Young Co-authored-by: Alexander Peltzer --- recipes/sativa/build.sh | 31 +- recipes/sativa/gpl_license | 674 ++++++++++++++++++++++++++++++++ recipes/sativa/meta.yaml | 18 +- recipes/sativa/sequences.alnfna | 230 +++++++++++ recipes/sativa/taxonomy.tsv | 5 + 5 files changed, 925 insertions(+), 33 deletions(-) create mode 100644 recipes/sativa/gpl_license create mode 100644 recipes/sativa/sequences.alnfna create mode 100644 recipes/sativa/taxonomy.tsv diff --git a/recipes/sativa/build.sh b/recipes/sativa/build.sh index 4c880d868a6ea..9f821444e5974 100644 --- a/recipes/sativa/build.sh +++ b/recipes/sativa/build.sh @@ -3,30 +3,9 @@ export USE_AVX=yes export USE_AVX2=yes -case `uname` in -Darwin) export DARWIN=1;; -Linux) export DARWIN=0;; -*) echo "Unknown architecture"; exit 1;; -esac - -make -C ./raxml CC="$CC" - -install -d ${PREFIX}/tmp -install -d ${PREFIX}/bin - -if [ $DARWIN -eq 1 ]; then - install sativa.cfg *.py ${PREFIX} -else - install -t ${PREFIX} *.py sativa.cfg -fi - -# Place a symlink to sativa.py in bin/ -( cd ${PREFIX}/bin; ln -s ../sativa.py . ) - -mkdir ${PREFIX}/raxml -cp ./raxml/raxmlHPC8* ./raxml/*.sh ${PREFIX}/raxml - -cp -r ./epac ${PREFIX} -cp -r ./tests ${PREFIX} -cp -r ./example ${PREFIX} +make -C raxml +cp -r raxml ${PREFIX}/bin +cp -r epac ${PREFIX}/bin +cp *.py ${PREFIX}/bin +cp sativa.cfg ${PREFIX}/bin diff --git a/recipes/sativa/gpl_license b/recipes/sativa/gpl_license new file mode 100644 index 0000000000000..818433ecc0e09 --- /dev/null +++ b/recipes/sativa/gpl_license @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/sativa/meta.yaml b/recipes/sativa/meta.yaml index 600f238ce24c5..7fa6e1aee16b4 100644 --- a/recipes/sativa/meta.yaml +++ b/recipes/sativa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sativa" %} -{% set version = "0.9.1" %} +{% set version = "0.9.3" %} package: name: {{ name|lower }} @@ -7,10 +7,13 @@ package: source: url: https://github.com/amkozlov/sativa/archive/refs/tags/v{{ version }}.zip - sha256: 14b772c7e1bc242655e1876e7492fd8d50d363058236bdf513aa5afca7d94841 + sha256: 0d0ae82f0f9608f51301ecadc367f85653fe9954855d9ebbbef8f889eef586b8 build: - number: 1 + number: 0 + skip: true # [osx] + run_exports: + - {{ pin_subpackage('sativa', max_pin="x.x") }} requirements: build: @@ -23,16 +26,17 @@ requirements: - python >=3.0.0 test: - imports: - - unittest + files: + - sequences.alnfna + - taxonomy.tsv commands: -# - python sativa.py -h - - python -m unittest discover -v + - sativa.py -s sequences.alnfna -t taxonomy.tsv -x bac -debug about: home: https://github.com/amkozlov/sativa license: GPL-3 license_family: GPL + license_file: gpl_license summary: "SATIVA Semi-Automatic Taxonomy Improvement and Validation Algorithm" extra: diff --git a/recipes/sativa/sequences.alnfna b/recipes/sativa/sequences.alnfna new file mode 100644 index 0000000000000..7e0aa83c9190c --- /dev/null +++ b/recipes/sativa/sequences.alnfna @@ -0,0 +1,230 @@ +>RS_GCF_000019605.1~NC_010482.1 +---GGTTGATCCTGCCGGAGGGAAC-----CCCTATCGGGCTCGCACTAAGCCATGCGAG +TCTGCTGGGGG------------------------------------------------- +------------------------------------CCCCTGCCCCTGGCGGCGCACGGC +TCCGTAATACACGGTCAACCTGTCCTGGGGACCGGGATAA-------------------- +CCTCGGGAAACTGAGGTTAAT---ACCGGATAGGGGTGGATTCCTGGAATGGGTCCACCC +CTAAAGTAGGCGGGGGGACG-GCC-----CCGCTGAGGCCCCAGGGTGGGACCGTGGCCT +AT-CAGG----TAGTAGGTGGGGTA---------ACGGCCCACCTAGCCTAAGACGGGTA +CGGG------CTCTGAGAG-GAGG-AGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGC +C-CTACGGGGCGCAGCAG--------GCGGGAAACTTCCCCAATG-----CGCGCAAGCG +TGAGGGAGTGAGCCCGAGTGCCGCCCGCTGAGGG------CGGCTGTTCCCCTGTGTAA- +--------A-AAG-------CAGGGGGTAGGAAG-GGGAG-------GGTAAGGCTGGTG +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------CCAGCCGCCGCGGTAAAACCAGC---------TCC-CCGA-- +-GGG--GTTCCCACGCATACTGGGCCTAAAGCGTCCGTAGCCGGCCCCGTAAGTCCTCGG +TT---AAATCCGC--CTGAAGACAGG--CGGACCGCCGAGGAT------A--CTGCGGGG +C-TAGGGAGC--GGGAGGGGCCGAGGGTATTCCGGGGGGAGCGGTAAAATGCGT------ +------------------------------------------AGATCCCCGGAGGACC-- +-ACCAGTGGCGAAGGCGCTCGGCTGGAACGCGTCCGACGGTGAGGG--------ACGAAA +GCTGGG-GGAG------------------CAAACCGGATTAGATACCCGGGTAGTCCCAG +CCGTAAACGATGCCGG---CTAGGTGCCG---GCTGAGG---------TTTCGGCCTCAG +CCGGTGTCGA---------------------AGCGAAGGCATTAAGCCGGCCGC-CTGAG +GAGTACAGCCGCAAGGCCGAAA----------CTTAAAGGAATTG-ACGGGGGGGC---- +------------------------------------------------------------ +--------------------------ACCACAAGGGGTGAATGCCTGCGGCTCAATTGGA +CTCAACGCCGGGAATC-TTACCGGGGGCGACAGCAGGATGAAGGTCAGG----------- +------------------------------------------------------------ +--------------------------------------CTG-------AA---------- +-------GACCTTACCTGAC----GCGCTGAG--GG-GTGGTGCATGGC---------CG +TCGCCAGCTCGTGCCGTGAGGTGT--CCTGTTAAGTCAGGC-------AACGAGCGAGAC +-CCCCGCCCTC-AGTTGCCAGCGGGGCCTT-ACGGCTGG-C-CG-GGCAAACTGGGGGGA +CTGCCGGCGAAGA---GCCGGAGGAAGGAGGGGGCTACGGCAGGTCAGTATGCCCCTAAT +C---CCCCGGGCCGCACGCGGGCTGCAATGGGCGGGACA---GCGG---------G-ATG +CGAC-CCCGAGAGGGGGAGCAAATCCCTGAAACCCGCCCGT-G--GTTGGGATCGAGGGT +TGCAACTCGCCCTCGTGA-ACCCGGAATCCCTAGTAACCGCGGTTCTCC-ATAC------ +----------------------------CGCGGTGAATACGTCCCTGCCCCTTGTACACA +CCGCCCGTCAACCCACCCGAGTGGACTTGGGGCGAGGCCCAGCTCAA------------- +-------------------TGGCTGGGTCGAGCTTTGGGTCCGCGAGGGGGGGTAAGTCG +TAACAAGGTAGCCGTAG---GGGAACCTGCGGCTGGATCACCTCCC-------------- +------------------------------------------------------------ +------------------- +>RS_GCF_000092465.1~NC_014205.1 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------AGGTGATCCA----GCCGCAGGTTCCCCTACGGCTACC +TTGTTACGACTTCTCCCCCCTTGGGAGGGGGGAGTTCGACCTGGCCCCC----CGGGTTT +CCCCGGGAGACCAGGCCTCAC---TCCCCCCTCCCTCGGGTGGAGCGACGGGCGGTGTGT +GCAAGGAGCAGGGA--CG---TATTC--ACCGC-GCGATGATGACGCGCGGTTACTAGGG +ATTCCACGTTCACGAGGG-CGAGTT------------------GCAGCCCTCGATCCCAA +CTGCGGCGGGGTTTGAGGGATTGCCTCCCCCTTAC-GGGGTCGGATCCCGCTGTCCCCGC +CATTGTAGCCC---------------GCGTGTAGCCCGGGGGATT-----CGGGGCATGC +TGAC-------------------------------------------------------- +---------------------------------------------CTGCCGTGGCCCCCT +CCTTCCTCCGCCTTATACGGCGGCAGTCCCCCTAGTGTG-CCCC-GG--AGCCGGAGCTC +CGGGTAGCAACTAGGGGCGGGGGT-CTCGCTCGTTGC------------CGGACTTAACC +GGACACCTCACGG----CACGAGCTGGCGACGGCCATGCACCTCCTCTCAGCGCG----- +-TCGGGCAA--------------------------------------------------- +------------------------------------------------------------ +---------------------------GGCCGTTAGCCTGGCCGTCATC-CTGCTG---- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------TCGCCCCCGGTGAGG------------TTCCCGG +CGTTGACTCCAATTAAACCG--CAGGCTCCACC---CCTTGTGGTGCTCCCCCGC----- +-------------------CAATTCCTTTAAGTTTCAGCCTTGCGGCCGTACTCCCCAG- +-GCGGCGGGCTTAACGGCTTCCCTGCGGCACTGGGCGGGCTCT-AA-G-CCCGCCCAACA +CCTAGCCCGCATCGT---------------TTACAGCCGGGACTACCCGGGTATCTAATC +CGGTTCGCTCCCCC------------------GGCTTTCGCCCCTCACCGTCG------- +----------------GGCGCGTTCCAGCCGAGCGCCTTCGCCACTGGTGGTCCTCCCGG +GATTATAGGATTTCGCCCCTAC-----------C------------------CCGGGAGT +ACCCTCGGCCTCTCCCGCCCCCTAGCCTGGCAGTTTCCCCTCCAGTC-C-CCGGGTTGAG +CCCGGGGATTTAGGAGGGGACTTG-CCAGGCCGGCTACGG------GCGCTTTAGGCCCA +ATAATCGTCCCGA----CCACTCGCGGGGCTGGTATTACCGCGGCGGCTGACACCAGTCT +TGCCCCCCGCTTATTCCCCC---------------------------------------- +------------------------------------------------------------ +-----GCCTTCTTACAGCGG-GGAAAAGCCCC------CT-AATTAGGGGGCACTCGGGG +TGACCCCGTCACGGTTGCCCGCAT--TGCGGAGGTTTCGCGCCTGGTGCACCCCGTAGGG +CCTGGGCCCTTGTCT--CAGTGCCCATCTG----GGGGC-----TCCCGCTCTCA-CGGC +CCCTACCCGTTATCGGCTTGGCGGGCCGTTACCCCGCCAACTACCTG-ATGGGCCGCAGC +CCCATCCTCGGGCTGCGCGGCGGCGATAACCCCCGCCGCA--CCC--TTTCGGGGAGGAA +CCCTTCCAGGCGTCCT---CCCCTATGG-GGGATTAGCACC-A--GTTTCCC---GG-TG +TTATCCCCCTCCCGAGGGTAGGTTAGCCACGTGTTACTCAGCCGTCCGCCACGCTCCGCA +GCGG----------CGGAGCGTACGACTCCCATGGCTTAGCCCCACCCCGATAGCGGTCG +GGTCCGGCAGGATCAACCGGAGTT------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------- +>RS_GCF_000970205.1~NZ_CP009512.1-#2 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------GAGGTGATCCA----GCCGCAGATTCCCCTACGGCTACC +TTGTTACGACTTAACCCCCCTTGCAAAGCACAGGTTCGAACACGGCAC-G---------- +----A-AGTCCGTGCCCTCAC---CCATACCTCACTCGGGTGGTTTGACGGGCGGTGTGT +GCAAGGAGCAGGGA--CG---TATTC--ACCGC-GCTATATTGAAACGCGATTACTACGG +ATTCCAGCTTCACGA-GGGCGAGTT------------------ACAGCCCTCGATCCGAA +CTACGAATGGGTTTGTGAGATTAC-CAGCCCTTTTCAGGGGAGGGACCCATTGTCCCATC +CATTGTAGCCC---------------GCGTGTAGCCCGGGAGATT-----CGGGGCATAC +TGAC-------------------------------------------------------- +---------------------------------------------CTACCGTGGCCCGCA +CCTTCCTCCGATTTAACATCGGCGGTCCCCACAGAGTACCCATCGTCCC----GGAGGAC +ATGCTGGTAACAGTGGGCACGGGT-CTCGCTCGTTGC------------CTGACTTAACA +GGATGCTTCACAG----TACGAACTGGCGACGGCCATGCACCTCCTCTCAGCGAT----- +-TCAGGCAA--------------------------------------------------- +------------------------------------------------------------ +---------------------------AGTCTTCAGCTTGGCCTACATA-TTGCTG---- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------TCGCCCCCGGTGAGT------------TGTCCGG +CGTTGAGTCCAATTAAACCG--CAGGCTCCACC---CGTTGTTGTGCTCCCCCGC----- +-------------------CAATTCCTTTAAGTTTCAGCCTTGCGGCCGTACTTCCCAG- +-GTGGCTCGCTTCACGGCTTCCCTGCGGCACCAGACACGGTCG-CG-C-CATGCCTGACA +CCTAGCGAGCATCGT---------------TTACGGCTGGGACTACCCGGGTATCTAATC +CGGTTCGTGCCCCC------------------AGCTTTCGTCCCTCACCGTCG------- +----------------AACCCGTTCTGGTAAGACGCCTTCGCCACAGGTGGTCCCACAGG +GATTACAAGATTTCACTCCTAC-----------C------------------CCTGTAGT +ACCTCTTACCTCTCCCGGTTCCAAGTCTGGCAGTATCCCCCGAAAGCCT-AATAGTTGAG +CTATCAGATTTCCCGGAGGACTGA-CCAAACCGGCTACGG------ACCCTTTAGACCCA +ATAATCACGATCA----CCACTCGGGCCGCCGGTGTTACCGCGGCGGCTGGCACCGGTCT +TGCCCGGCCCTTGCTAACGG---------------------------------------- +------------------------------------------------------------ +-----ATGTATTTTACACATCCGGACAGCCA------GCATATGATGCTGGCACTCGGTG +TCCCCTTATCACGGTTTCCCGCAT--TGTAAAGTTTTCGCGCCTGCTGCGCCCCGTAGGG +CCTGGATTCATGTCT--CAGAATCCATCTC----CGGGC-----TCTTGCTCTCA-CAAC +CCGTACCCGTCGCTGGCTAGTAGGTACATTACACCCACTACTAC-CTGATAGGCCGCAGA +CCCATCCTTGGGCAGACGAATCCTT-------------------T--T--GACGCATAAA +GCATTCCAGCAAATAT---GCGTTATCC-GGAATTATCCCC-A--GTTTCCC---GG-GG +TTATGCCGGTCCCAAGGGCAGGTTATCCACGTGTTACTGAGCAGTACGCCATGTATT--- +---------------GCTACATATGACTCGCATGGCTTAGGCGAACACCGATAGCAGTAA +CCTCTGGCAGGATCAACCAGAATT------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------- +>RS_GCF_000302455.1~NZ_AMPO01000020.1 +-CCGTTTGATCCTGGCGGAGGCCAC-----TGCTATTGGGTTTCGATTAAGCCATGCAAG +TCGTACGATCCT------------------------------------------------ +-----------------------------------TTC----GGGGTCGTGGCATACGGC +TCAGTAACACGTGGATAACCTACCCTTAGGACTGGGATAA-------------------- +CCCCGGGAAACTGGGGACAAT---ACCGGATATGTAGAGTTGCCTGGAATTGGTACTCTA +TTGAAA-------------------T-GTATTCGTGCGCCTAAGGATGGATCTGCGGCAG +AT-TAGG----TAGTTGGCGGGGTA---------AATGCCCACCAAGCCAGTAATCTGTA +CGGG------TTGTGAGAG-CAAG-AGCCCGGAGATGGAACCTGAGACAAGGTTCCAGGC +C-CTACGGGGCGCAGCAG--------GCGCGAAACCTCCGCAATG-----CACGAAAGTG +CGACGGGGGAAACCCAAGTGCCACTCTTAACG--GG----GTGGCTTTTCTTAAGTGTA- +--------AAAAG-------CTTTTGGAATAAGA-GCTGG-------GC-AAGACCGGTG +C----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------CAGCCGCCGCGGTAACACCGGC---------AGC-TCAA-- +-GTG--GTGGCCATTTTTATTGGGCCTAAAGCGTTCGTAGCCGGTTTGATAAGTCTCTGG +TG---AAATCTCA--CGGCTTAACCGTGAGAATTGCTGGAGAT------A--CTATTAGG +C-TTGAGGCC--GGGAGAGGTTAGCGGTACTCCCAGGGTAGGGGTGAAATCCTA------ +------------------------------------------TAATCCTGGGAGGACC-- +-ACCTGTGGCGAAGGCGGCTAACTGGAACGGACCTGACGGTGAGTA--------ACGAAA +GCCAGG-GGCG------------------CGAACCGGATTAGATACCCGGGTAGTCCTGG +CCGTAAACGATGTGGA---CTTGGTGTTG---GGATGGC--------------------- +------------------------------------------------------------ +---------------------------------TCCGAGCTGCCC-CAGTGCCGAAGGGA +AGCTGTTAAGTCCACC-------GCCTGGGAAGTACG-GTCGCAAGACTGAAACTTAAAG +G------AATTGGCGGGGGAG----CACCACAACGCGTGGAGCCT-GCGGTTTAATTGGA +TTCAACGCCGGACATC-TCACCAGGGGCGACAGCAGAATGATAGCCAGG----------- +------------------------------------------------------------ +--------------------------------------TTG-------AT---------- +-------GACCTTGCTTGAC----AAGCTGAG--AG-GAGGTGCATGGC---------CG +CCGTCAGCTCGTACCGTGAGGCGT--CCTGTTAAGTCAGGC-------AACGAGCGAGAC +-CCACGCCCTT-AGTTACCAGCGGATCCTT-T--GGGAT-G-CCGGGCACACTAAGGGGA +CCGCCAGTGATAA---ACTGGAGGAAGGAGTGGACGACGGTAGGTCCGTATGCCCCGAAT +C---CCCTGGGCTACACGCGGGCTACAATGGCTAGGACA---ATGG---------G-TTC +CGACACTGAA-AAGTGAAGGTAATCTCCTAAACCTAGCCTT-A--GTTCGGATTGAGGGC +TGTAACTCGCCCTCATGA-AGCTGGAATGCGTAGTAATCGCGTGTCATA-ACCG------ +----------------------------CGCGGTGAATACGTCCCTGCTCCTTGCACACA +CCGCCCGTCACGCCACCCAAAAAGGGTTTGGATGAGGCCATAGTCTTT------------ +--G--------------TTGGTTATGGTCGAATCTGGGTTCTTTGAGGAGGGCGAAGTCG +TAACAAGGTAGCCGTAG---GGGAACCTGCGGCTGGATCACCTCCTT------------- +------------------------------------------------------------ +------------------- +>RS_GCF_000993805.1~NZ_CP009961.1 +TCCGGTTGATCCTGCCGGACCCGAC-----TGCTATCAGGGTGGGGCTAACCCATGGAAG +TCTAGGAGCCGGG----------------------------------------------- +---------------------------------GC--TACGGCCGGCTCCGGCGGACGGC +TCAGTAGCACGTGGCTAACCTACCCTCGGGAGGGGGATAA-------------------- +CCCCGGGAAACTGGGGCTAAT---CCCCCATAGGCGCAGACTCCTGGAATGGGTCCGCGC +CGAAAAGGCTGCAACGCCAT-GCCCG---TTGCAGCCGCCCGAGGATGGGGCTGCGCCCC +AT-CAGG----TAGTTGGCGGGGTA---------ACGGCCCGCCAAGCCGATAACGGGTG +GGGG------CCGTGAGAG-CGGG-AGCCCCGAGATGGGCACTGAGACAAGGGCCCAGGC +C-CTACGGGGCGCACCAG--------GGGCGAAACTTCCGCAATG-----CGGGAAACCG +TGACGGAGCCACCCTGAGTGCCACCCGATGAGGG------TGGCTTTTGCCCGGTCTAA- +--------A-AAG-------CCGGGCGAATAAGC-GGGG--------GGCAAGCCTGGTG +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------TCAGCCGCCGCGGTAATACCAGC---------CCC-GCGA-- +-GTG--GTCGGGACGATTATTGGGCCTAAAGCGTCCGTAGCCGGCCCGGCAAGTCCCCCT +TT---AAAGCCCA--CGGCTCAACCG--TGGGAGCGGGGGGAT------A--CTGTCGGG +C-TAGGGGGC--GGGAGAGGCCGGGGGTACTCCTGGGGTAGGGGCGAAATCCTA------ +------------------------------------------TAATCCCAGGAGGACC-- +-ACCAGTGGCGAAGGCGCCCGGCTGGAACGCGCCCGACGGTGAGGG--------ACGAAA +GCTGGG-GGAG------------------CAAAGGGGATTAGATACCCCCGTAGTCCCAG +CTGTAAACGATGCGGG---CTAGGTGTTG---GGTGGG----------CCTCGAGCCCGC +CCAGTGTCGT---------------------AGGGAAGCCGTTAAGCCCGCCGC-CTGGG +GAGTACGGCCGCAAGGCTGAAA----------CTTAAAGGAATTG-GCGGGGGAGC---- +------------------------------------------------------------ +--------------------------ACCACAAGGGGTGAAGCTT-GCGGTTTAATTGGA +GTCAACGCCGGAAACC-TCACCGGGGGCGACAGCAGGATGAAGGCCAGG----------- +------------------------------------------------------------ +--------------------------------------CTA-------AC---------- +-------GACCTTGCCAGAC----GAGCTGAG--AG-GAGGTGCATGGC---------CG +TCGCCGGCTCGTGCCGTGAGGTGT--CCTGTTAAGTCAGGG-------AACGAGCGAGAC +-CCCCGCCCCT-AGTTGCAACCCAGCCTTT-CGGGGCTG-G-GG--CACTCTAGGGGGAC +TGCCGGCGA-TAA---GCCGGAGGAAGGTGGGGGCTACGGCAGGTCAGTATGCCCCGAAA +C---CCCCGGGCTACACGCGAGCTGCAATGGCGGGGACA---GCGG---------G-CTC +CG-ACCCCGAAAGGGGAAGGAAATCCCGTAAACCCCGCCTC-A--GTAGGAATCGAGGGC +TGCAACTCGCCCTCGTGA-ACGTGGAATCCCTAGTAACCGCGTGTCACC-AACG------ +----------------------------CGCGGTGAATACGTCCCTGCTCCTTGCACACA +CCGCCCGTCGCTCCACCCGAGGGAGGCCCAGGTGAGGCCTCTCGCCGAAAG--------- +-------------------GTGGGAGGTCGAATCTGGGCCTCCCAAGGGGGGAGAAGTCG +TAACAAGGTGGCCGTAG---GGGAACCTGCGGCCGGATCACCTCCTT------------- +------------------------------------------------------------ +------------------- diff --git a/recipes/sativa/taxonomy.tsv b/recipes/sativa/taxonomy.tsv new file mode 100644 index 0000000000000..349a7c83c9d8d --- /dev/null +++ b/recipes/sativa/taxonomy.tsv @@ -0,0 +1,5 @@ +RS_GCF_000019605.1~NC_010482.1 d__Archaea;p__Crenarchaeota;c__Korarchaeia;o__Korarchaeales;f__Korarchaeaceae;g__Korarchaeum;s__Korarchaeum +RS_GCF_000092465.1~NC_014205.1 d__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Desulfurococcales;f__Desulfurococcaceae;g__Staphylothermus;s__Staphylothermus +RS_GCF_000970205.1~NZ_CP009512.1-#2 d__Archaea;p__Halobacterota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina;s__Methanosarcina +RS_GCF_000302455.1~NZ_AMPO01000020.1 d__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium;s__Methanobacterium +RS_GCF_000993805.1~NZ_CP009961.1 d__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Thermofilales;f__Thermofilaceae;g__Thermofilum_A;s__Thermofilum_A From 669fe610aa28922bc1cac71b565386cb314c557a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 17:28:10 -0500 Subject: [PATCH 0121/1813] Update yacht to 1.2.1 (#45410) * Update yacht to 1.2.1 * add pandas to host * add scipy to host * add tqdm to host * add biom-format and pytaxonkit to host --------- Co-authored-by: mencian --- recipes/yacht/meta.yaml | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/recipes/yacht/meta.yaml b/recipes/yacht/meta.yaml index c7f12473b7254..c8f57cc59af75 100644 --- a/recipes/yacht/meta.yaml +++ b/recipes/yacht/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.0" %} +{% set version = "1.2.1" %} package: name: yacht @@ -6,13 +6,13 @@ package: source: url: https://github.com/KoslickiLab/YACHT/releases/download/v{{ version }}/yacht-{{ version }}.tar.gz - sha256: 0655301d2ecb949fe75799b8ee67b4032e8a778a03f2edc3572b48066d0e4007 + sha256: 248c85c52e88c576d7afd9842b06fec2a6f89fbb9b1150885486e6adf72ac3ca build: number: 0 noarch: python skip: True # [win or osx] - script: "{{ PYTHON }} -m pip install . --ignore-installed --no-cache-dir -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('yacht', max_pin="x") }} @@ -20,7 +20,14 @@ requirements: host: - python >3.6 - pip - - setuptools + - pandas + - pytaxonkit + - scipy + - sourmash + - loguru + - tqdm + - biom-format + - numpy run: - python >3.6 - sourmash >=4.8.3,<5 @@ -46,6 +53,8 @@ about: home: https://github.com/KoslickiLab/YACHT summary: 'YACHT is a mathematically rigorous hypothesis test for the presence or absence of organisms in a metagenomic sample, based on average nucleotide identity (ANI).' license: MIT + license_family: MIT + license_file: LICENSE.txt dev_url: https://github.com/KoslickiLab/YACHT doc_url: https://github.com/KoslickiLab/YACHT/wiki From a2779b2dd451291d700cc1b1274706298000d9bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 18:57:07 -0500 Subject: [PATCH 0122/1813] Update intarna to 3.4.0 (#45399) * Update intarna to 3.4.0 * run_exports added * disable test build on osx to avoid timeout in package build --------- Co-authored-by: Martin Raden --- recipes/intarna/build.sh | 4 +++- recipes/intarna/meta.yaml | 8 +++++--- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/intarna/build.sh b/recipes/intarna/build.sh index fd174c6efa2cd..5e5ab3a2b0308 100644 --- a/recipes/intarna/build.sh +++ b/recipes/intarna/build.sh @@ -34,5 +34,7 @@ export LDFLAGS=${LDFLAGS} make -j ${CPU_COUNT} -make tests -j ${CPU_COUNT} +if [ `uname` != Darwin ] ; then # skip tests for osx to avoid timeout + make tests -j ${CPU_COUNT} +fi make install diff --git a/recipes/intarna/meta.yaml b/recipes/intarna/meta.yaml index 26009b219a7b8..8177abc6959ae 100644 --- a/recipes/intarna/meta.yaml +++ b/recipes/intarna/meta.yaml @@ -1,5 +1,5 @@ -{% set INTARNA_VERSION = "3.3.2" %} -{% set INTARNA_SHA256 = "57d273fa5bb6b62636e316465240b95089273e7e9e34224ea48c9cd747e88ed1" %} +{% set INTARNA_VERSION = "3.4.0" %} +{% set INTARNA_SHA256 = "4b0c53472dad49f3fbe6f0d3b1613d22d7b438bf650936da6a351a25fa9d535c" %} {% set VRNA_VERSION = "2.4.14" %} package: @@ -12,7 +12,9 @@ about: summary: Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('intarna', max_pin="x.x") }} source: url: "https://github.com/BackofenLab/IntaRNA/releases/download/v{{INTARNA_VERSION}}/intaRNA-{{INTARNA_VERSION}}.tar.gz" From 78454b2d82aaff842a2aa1a4bd924d2352e87296 Mon Sep 17 00:00:00 2001 From: Andrea Telatin <15690844+telatin@users.noreply.github.com> Date: Thu, 25 Jan 2024 02:28:15 +0000 Subject: [PATCH 0123/1813] [seqfu] Re-add macOS support (#45401) * Test OSX * Update build.sh * Update meta.yaml * skip patch on osx --- recipes/seqfu/build.sh | 20 ++++++++++++-------- recipes/seqfu/meta.yaml | 1 - 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/recipes/seqfu/build.sh b/recipes/seqfu/build.sh index 41e15120f4793..3857c7e750166 100644 --- a/recipes/seqfu/build.sh +++ b/recipes/seqfu/build.sh @@ -14,19 +14,23 @@ export CFLAGS="$CFLAGS -I$PREFIX/include" export LDFLAGS="$LDFLAGS -L$PREFIX/lib" export CPATH=${PREFIX}/include -echo "GXX: $GXX" -echo "GCC: $GCC" +echo "GXX: ${GXX:-'not set'}" +echo "GCC: ${GCC:-'not set'}" echo "----------" -echo "Patching makefile" -# Trying to fix build when gcc or g++ are required -sed -i 's/gcc/$(GCC)/g' Makefile -sed -i 's/g++/$(GXX)/g' Makefile -sed -i '1iGCC ?= gcc' Makefile -sed -i '1iGXX ?= g++' Makefile + + if [[ $OSTYPE == "darwin"* ]]; then + echo "OSX" export HOME="/Users/distiller" export HOME=`pwd` +else + # Trying to fix build when gcc or g++ are required + echo "LINUX: Patching makefile" + sed -i 's/gcc/$(GCC)/g' Makefile + sed -i 's/g++/$(GXX)/g' Makefile + sed -i '1iGCC ?= gcc' Makefile + sed -i '1iGXX ?= g++' Makefile fi mkdir -p "$PREFIX"/bin diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml index b8c6278466772..9d494a364ba0b 100644 --- a/recipes/seqfu/meta.yaml +++ b/recipes/seqfu/meta.yaml @@ -12,7 +12,6 @@ source: build: number: 0 - skip: True # Let's skip MacOS until we find out more run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} From 7e9af63238291c294606b357f8001fa92b254c88 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 22:44:29 -0500 Subject: [PATCH 0124/1813] Update aster to 1.16 (#45412) * Update aster to 1.16 * add run_exports * updating the names of the binaries for ASTER since authors changed them --------- Co-authored-by: mencian Co-authored-by: worku005 --- recipes/aster/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/aster/meta.yaml b/recipes/aster/meta.yaml index 74e9391b7ffa2..30d17f22be13c 100644 --- a/recipes/aster/meta.yaml +++ b/recipes/aster/meta.yaml @@ -1,13 +1,15 @@ -{% set version = "1.15" %} +{% set version = "1.16" %} {% set name = "ASTER" %} -{% set sha256 = "71618824a0f39135977709f21f3b6374815407411fb44474442a1a9c88a6c919" %} +{% set sha256 = "c6e80de483a0a59fc0d3a74465b1f793e773b9d79cbd20756c6766136ffbb1a7" %} package: name: "{{ name|lower }}" version: "{{ version }}" build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('aster', max_pin="x") }} source: url: "https://github.com/chaoszhang/ASTER/archive/refs/tags/v{{ version }}.tar.gz" @@ -20,15 +22,17 @@ requirements: test: commands: - - master-site -h &> /dev/null # [linux] - - master-pair -h &> /dev/null # [linux] + - caster-site -h &> /dev/null # [linux] + - caster-pair -h &> /dev/null # [linux] + - waster-site -h &> /dev/null # [linux] - astral -h &> /dev/null - astral-pro -h &> /dev/null - astral-hybrid -h &> /dev/null about: home: https://github.com/chaoszhang/ASTER - license: AGPL-3.0 + license: AGPL-3.0-or-later + license_family: AGPL license_file: LICENSE summary: | Accurate Species Tree EstimatoR series; a family of optimation algorithms From b60fef6911c60e85aefdb16427576c319a1e0ba7 Mon Sep 17 00:00:00 2001 From: John Lees Date: Thu, 25 Jan 2024 11:21:42 +0000 Subject: [PATCH 0125/1813] Add recipe for cgt (#45372) * Add recipe for cgt * Fix license file name * Change executable name --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cgt/meta.yaml | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 recipes/cgt/meta.yaml diff --git a/recipes/cgt/meta.yaml b/recipes/cgt/meta.yaml new file mode 100644 index 0000000000000..9afec628b546a --- /dev/null +++ b/recipes/cgt/meta.yaml @@ -0,0 +1,31 @@ +{% set name = "cgt" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower}} + version: {{ version }} + +source: + url: https://github.com/bacpop/{{ name }}/archive/v{{ version }}.tar.gz + sha256: d79750878e45853e46a3e991e8f7274a2de248bca58476b2be7e527caac3ab2b + +build: + number: 0 + script: "cargo install --no-track --locked --verbose --root \"${PREFIX}\" --path ." + run_exports: + - {{ pin_subpackage("cgt", max_pin="x") }} + +requirements: + build: + - {{ compiler('rust') }} + +test: + commands: + - cgt_bacpop -V + +about: + home: https://github.com/bacpop/cgt + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE.txt + summary: Calculate a core genome threshold (cgt) from metagenome data From bd12bdda9f6c16024f2057b2c8f4b4c211eab195 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 Jan 2024 13:44:29 +0100 Subject: [PATCH 0126/1813] add orthanq 1.1.0 (#44940) * [ci skip] add orthanq draft recipe * fix * fix * add checksum * Update meta.yaml * Update meta.yaml * fixes --- recipes/orthanq/build.sh | 8 ++++++ recipes/orthanq/meta.yaml | 58 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 recipes/orthanq/build.sh create mode 100644 recipes/orthanq/meta.yaml diff --git a/recipes/orthanq/build.sh b/recipes/orthanq/build.sh new file mode 100644 index 0000000000000..9dca7213beca0 --- /dev/null +++ b/recipes/orthanq/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -eu + +# Make sure bindgen passes on our compiler flags. +export BINDGEN_EXTRA_CLANG_ARGS="${CPPFLAGS} ${CFLAGS} ${LDFLAGS}" +export HDF5_DIR=${PREFIX} +export RUSTFLAGS="-C link-args=-Wl,-rpath,$HDF5_DIR/lib" + +cargo install --no-track --locked --verbose --root "${PREFIX}" --path . diff --git a/recipes/orthanq/meta.yaml b/recipes/orthanq/meta.yaml new file mode 100644 index 0000000000000..946b26b7f0fd4 --- /dev/null +++ b/recipes/orthanq/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.1.0" %} + +package: + name: orthanq + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("orthanq", max_pin="x") }} + +source: + url: https://github.com/orthanq/orthanq/archive/v{{ version }}.tar.gz + sha256: 5ce1d2826404c04f1de8e5c543c0e23cc23b693f5d190c2602e654d510375bbd + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ compiler('rust') }} + - rust >=1.54 + - pkg-config + - make + - cmake + - perl-findbin + host: + - gsl + - libcblas + - openssl + - zlib + - bzip2 + - xz + - clangdev + - coincbc + - hdf5 =1.10.5 + - fontconfig + run: + - gsl + - libcblas + - openssl + - zlib + - bzip2 + - xz + - clangdev + - coincbc + - hdf5 =1.10.5 + - fontconfig + +test: + commands: + - orthanq -h + +about: + home: https://github.com/orthanq/orthanq + license: MIT + license_family: MIT + license_file: LICENSE + summary: Uncertainty aware HLA typing and general haplotype quantification From 8da4cc15c4330a83d86aca8da0648bbc86471012 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Thu, 25 Jan 2024 13:49:07 +0100 Subject: [PATCH 0127/1813] bump mitos1 (#45421) --- recipes/mitos/mitos1/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mitos/mitos1/meta.yaml b/recipes/mitos/mitos1/meta.yaml index c1a015275ecc6..0e010a1780797 100644 --- a/recipes/mitos/mitos1/meta.yaml +++ b/recipes/mitos/mitos1/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "1.1.4" %} +{% set version = "1.1.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4f541044977dd3b33628ff780f6435094f1d633a031a88b5bda80342efa05bae + sha256: 1727e5037c679648b4633b4bd811d9f818a2b41d2c8d322bd51ec5b6a94faa02 build: number: 0 From 7f3d2e4cc2c22e56dbedeb86ca96bd87f48ccf5e Mon Sep 17 00:00:00 2001 From: Charlie Date: Thu, 25 Jan 2024 07:51:09 -0500 Subject: [PATCH 0128/1813] Add pycov3 recipe (#45409) --- recipes/pycov3/meta.yaml | 45 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 recipes/pycov3/meta.yaml diff --git a/recipes/pycov3/meta.yaml b/recipes/pycov3/meta.yaml new file mode 100644 index 0000000000000..e9435f67e8e41 --- /dev/null +++ b/recipes/pycov3/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "pycov3" %} +{% set version = "2.0.4b0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 22a3b35bd589e967bf3041356436c652913a64c601efb2af2149375fb095a8e4 + +build: + number: 0 + noarch: python + entry_points: + - pycov3 = pycov3.cli:main + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('pycov3', max_pin="x") }} + +requirements: + host: + - pip + - python + run: + - python + +test: + imports: + - pycov3 + commands: + - pycov3 --help + +about: + home: https://github.com/Ulthran/pycov3 + license: MIT + license_family: MIT + license_file: + summary: "Generate cov3 files used in DEMIC" + doc_url: + dev_url: https://github.com/Ulthran/pycov3 + +extra: + recipe-maintainers: + - Ulthran From 195f893159f3985b84f5ba0d6f0e513d3ac1ac26 Mon Sep 17 00:00:00 2001 From: Eric Kutschera Date: Thu, 25 Jan 2024 08:03:21 -0500 Subject: [PATCH 0129/1813] Update ucsc-twobitinfo to 455 (#45418) --- recipes/ucsc-twobitinfo/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ucsc-twobitinfo/meta.yaml b/recipes/ucsc-twobitinfo/meta.yaml index f3fcd9757c185..782f34538d8c9 100644 --- a/recipes/ucsc-twobitinfo/meta.yaml +++ b/recipes/ucsc-twobitinfo/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-twobitinfo" %} {% set program = "twoBitInfo" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -19,6 +19,8 @@ build: ignore_run_exports: - libpng - libuuid + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: From 9edfa68f507faaa6f84a45a2dbdf6443cf6e78f8 Mon Sep 17 00:00:00 2001 From: Eric Kutschera Date: Thu, 25 Jan 2024 08:04:16 -0500 Subject: [PATCH 0130/1813] Update ucsc-bedgraphtobigwig to 455 (#45419) --- recipes/ucsc-bedgraphtobigwig/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ucsc-bedgraphtobigwig/meta.yaml b/recipes/ucsc-bedgraphtobigwig/meta.yaml index 96ba38c44d3e8..14a8480f5135d 100644 --- a/recipes/ucsc-bedgraphtobigwig/meta.yaml +++ b/recipes/ucsc-bedgraphtobigwig/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedgraphtobigwig" %} {% set program = "bedGraphToBigWig" %} -{% set version = "445" %} -{% set sha256 = "c7abb5db6a5e16a79aefcee849d2b59dbc71ee112ca1e41fea0afb25229cf56c" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -15,6 +15,8 @@ source: build: number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: From 33c3192fd800285d764f81aa5ca1b1b66c1d7579 Mon Sep 17 00:00:00 2001 From: Jeremy Volkening Date: Thu, 25 Jan 2024 07:21:30 -0600 Subject: [PATCH 0131/1813] add run_exports to perl-biox-seq (#45115) --- recipes/perl-biox-seq/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/perl-biox-seq/meta.yaml b/recipes/perl-biox-seq/meta.yaml index 8abda5e2b51b4..3f0b26b9a0481 100644 --- a/recipes/perl-biox-seq/meta.yaml +++ b/recipes/perl-biox-seq/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-biox-seq" %} -{% set version = "0.008008" %} -{% set sha256 = "a301c51f5d58c02ed4d7b1d5e2914666ebb00cc669073242f8d123a8a771a44a" %} +{% set version = "0.008009" %} +{% set sha256 = "93d45421823619317aed195f7f19c486358248d8fe79d3dea7bd91b1fc49e8f5" %} package: name: {{ name }} @@ -13,6 +13,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: From 37158f78846601648701c86159e9ef6a937b69b5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Jan 2024 09:52:09 -0500 Subject: [PATCH 0132/1813] Update snakemake to 8.3.2 (#45366) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake to 8.2.4 * Update snakemake to 8.3.1 * Update meta.yaml * Update snakemake to 8.3.2 --------- Co-authored-by: Johannes Köster Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index e40d63fbdb441..5f0761641c24b 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.2.3" %} +{% set version = "8.3.2" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: d31b7e5ceaa255038475287154b641a973cba9ff7cca6880f109f18ab703351a + sha256: 2959b72891d0c842faa019aba35726090db97f3513b6d78bd668fdbe92056628 build: number: 0 @@ -110,6 +110,7 @@ outputs: - toposort >=1.10 - yte >=1.5.1,<2.0 - wrapt + - dpath >=2.1.6,<3.0.0 test: imports: From 9d57639c2a84d16b3a8c6896b728ffaea6fde080 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Jan 2024 10:17:50 -0500 Subject: [PATCH 0133/1813] Update oakvar to 2.9.85 (#45063) * Update oakvar to 2.9.84 * Update oakvar to 2.9.85 --------- Co-authored-by: Brandon Seah --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 3980d2f261a57..15f40af72b4d6 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.83" %} -{% set sha256 = "b7157f768ee6b631a202ac50a05a6b69c233320c036437f484ebeb2660422f77" %} +{% set version = "2.9.85" %} +{% set sha256 = "ff8f8f8a6ab8cd9c9307edf2cb710a9ccdb9649f3c46ff656f336678419e514b" %} package: name: {{ name|lower }} From 52b49f3d34d6f9217117c7ebc99ed6c1a5ddcfa7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Jan 2024 10:18:11 -0500 Subject: [PATCH 0134/1813] Update mkdesigner to 0.3.4 (#45423) * Update mkdesigner to 0.3.2 * Update mkdesigner to 0.3.3 * Update mkdesigner to 0.3.4 --- recipes/mkdesigner/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mkdesigner/meta.yaml b/recipes/mkdesigner/meta.yaml index 45a3fb5756df4..3585d115b792d 100644 --- a/recipes/mkdesigner/meta.yaml +++ b/recipes/mkdesigner/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mkdesigner" %} -{% set version = "0.3.1" %} +{% set version = "0.3.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mkdesigner-{{ version }}.tar.gz - sha256: db3adaf00bbf6cb906c56ecee29ee233445255c7c7759ae42bd1f0e8262bd7f8 + sha256: 832372167e966e12cc0551cad936ed8049555da474fa3a4ef71574215001bf3a build: entry_points: From 91568ecf9e21feb59e4709ad22cb73c60e38249f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Jan 2024 17:42:10 -0500 Subject: [PATCH 0135/1813] Update hiphase to 1.2.0 (#45428) --- recipes/hiphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index e6d8bad778424..89033d92be5b2 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "1.1.0" %} -{% set hiphase_sha256 = "b5034e3adc53c0314ac9b8b5b205553830e43c65f77169e91635f18559c5be3b" %} +{% set version = "1.2.0" %} +{% set hiphase_sha256 = "e57455275a42a5679895a95f997c132064164343c0ef949946b28cac356c9a3a" %} package: name: {{ name }} From 48b75adc2a57e4b42a8055fb675d262e5f7d7f80 Mon Sep 17 00:00:00 2001 From: Alex Petty Date: Fri, 26 Jan 2024 02:21:36 -0600 Subject: [PATCH 0136/1813] Add recipe r-deconcell (#45426) --- recipes/r-deconcell/build.sh | 4 +++ recipes/r-deconcell/meta.yaml | 53 +++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 recipes/r-deconcell/build.sh create mode 100644 recipes/r-deconcell/meta.yaml diff --git a/recipes/r-deconcell/build.sh b/recipes/r-deconcell/build.sh new file mode 100644 index 0000000000000..6d23e7f876394 --- /dev/null +++ b/recipes/r-deconcell/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +pushd Decon2/DeconCell +$R CMD INSTALL --build . diff --git a/recipes/r-deconcell/meta.yaml b/recipes/r-deconcell/meta.yaml new file mode 100644 index 0000000000000..211669e1ffeda --- /dev/null +++ b/recipes/r-deconcell/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "r-deconcell" %} +{% set version = "0.1.0" %} +{% set vcommit = "335bf320df9c7dd15f636cff2c089d89ba6b786e" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/molgenis/systemsgenetics/archive/{{ vcommit }}.tar.gz + sha256: 9dadbe65cdbe72ca6f7bb6869770f40dc4fcea45945fbfb76ace61e41feb5b14 + + +build: + number: 0 + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + run_exports: + - {{ pin_subpackage('r-deconcell', max_pin="x") }} + +requirements: + host: + - bioconductor-deconrnaseq + - bioconductor-edger + - r-base + - r-data.table + - r-devtools + - r-glmnet + run: + - bioconductor-deconrnaseq + - bioconductor-edger + - r-base + - r-data.table + - r-glmnet + +test: + commands: + - $R -e "library(\"DeconCell\")" + +about: + home: https://github.com/molgenis/systemsgenetics/tree/master/Decon2/DeconCell + license: GPL-3.0-or-later + license_family: GPL3 + summary: DeconCell is an statitsical framework for generating cell proportions predictive models using bulk expresion data. It currently has pre-calculated models + description: | + DeconCell is an statitsical framework for generating cell proportions predictive models using bulk expresion data. It currently has pre-calculated models + dev_url: https://github.com/molgenis/systemsgenetics/tree/master/Decon2/DeconCell + +extra: + recipe-maintainers: + - pettyalex From 5fa73332fe5dc656447b3bffef22f8bbdebe6a76 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Fri, 26 Jan 2024 14:22:14 +0100 Subject: [PATCH 0137/1813] Update seqan3 (#45405) --- recipes/seqan3/fix_glibcxx_debug.patch | 25 +++++++++++++++++++++++++ recipes/seqan3/meta.yaml | 4 +++- 2 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 recipes/seqan3/fix_glibcxx_debug.patch diff --git a/recipes/seqan3/fix_glibcxx_debug.patch b/recipes/seqan3/fix_glibcxx_debug.patch new file mode 100644 index 0000000000000..529cc94d0f3f9 --- /dev/null +++ b/recipes/seqan3/fix_glibcxx_debug.patch @@ -0,0 +1,25 @@ +From 47b77ef92911ff1667f4487edb3961f0c28f407b Mon Sep 17 00:00:00 2001 +From: Simon Gene Gottlieb +Date: Wed, 17 Jan 2024 12:09:11 +0100 +Subject: [PATCH] [FIX] Do not use constexpr vector with _GLIBCXX_DEBUG + +--- + include/seqan3/core/platform.hpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/seqan3/core/platform.hpp b/include/seqan3/core/platform.hpp +index 1fd92faa7..e0c7687fe 100644 +--- a/include/seqan3/core/platform.hpp ++++ b/include/seqan3/core/platform.hpp +@@ -252,7 +252,7 @@ static_assert(sdsl::sdsl_version_major == 3, "Only version 3 of the SDSL is supp + #endif + + //!\brief Our char literals returning std::vector should be constexpr if constexpr std::vector is supported. +-#if defined(__cpp_lib_constexpr_vector) && __cpp_lib_constexpr_vector >= 201907L ++#if __cpp_lib_constexpr_vector >= 201907L && !defined(_GLIBCXX_DEBUG) + # define SEQAN3_WORKAROUND_LITERAL constexpr + #else + # define SEQAN3_WORKAROUND_LITERAL inline +-- +2.43.0 + diff --git a/recipes/seqan3/meta.yaml b/recipes/seqan3/meta.yaml index c5f14a78f7ae3..abb3a201426e9 100644 --- a/recipes/seqan3/meta.yaml +++ b/recipes/seqan3/meta.yaml @@ -8,10 +8,12 @@ package: source: url: https://github.com/seqan/{{ name|lower }}/releases/download/{{ version }}/seqan3-{{ version }}-Source.tar.xz sha256: da2fb621268ebc52b9cc26087e96f4a94109db1f4f28d363d19c7c9cdbd788b1 + patches: + - fix_glibcxx_debug.patch # Fix will be included in 3.4.0 build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('seqan3', max_pin="x") }} From 7f0cd548fae989175204c69aefcd1f7f3dcf36f4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Jan 2024 10:19:21 -0500 Subject: [PATCH 0138/1813] Update varvamp to 1.1.1 (#45435) --- recipes/varvamp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index 3c6d6d606e4a2..98241a40fce99 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "1.1" %} +{% set version = "1.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 186b5fd4ca9670c05f977440976348587a5c79d4b79bc4370390fdabb6715d84 + sha256: 3036bb0b0f9f1453e2978b95c75a5adf3c9f08cec9f3a4a2f38affa28b1fd04b build: entry_points: From 6966c56c54e245565b848aea4d07478ff97dee48 Mon Sep 17 00:00:00 2001 From: Yiming Yang Date: Fri, 26 Jan 2024 07:31:46 -0800 Subject: [PATCH 0139/1813] Update Pegasuspy to 1.9.0 (#45321) * upgrade Pegasuspy to 1.9.0 * resolve issue * Remove unnecessary dependency * try removing git status * remove duplicated 'run_exports' key * simplify --- recipes/pegasuspy/meta.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/recipes/pegasuspy/meta.yaml b/recipes/pegasuspy/meta.yaml index 9b3e42df1b209..f0485e29a84ec 100644 --- a/recipes/pegasuspy/meta.yaml +++ b/recipes/pegasuspy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pegasuspy" %} -{% set version = "1.8.1" %} +{% set version = "1.9.0" %} package: name: {{ name|lower }} @@ -7,17 +7,17 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3897e1048d6ce3547028c0e4220fea7145573e6f62805918c7f7002f683f4105 + sha256: ace00d403d43c91094706a8de85c6c7806e5dce8049c902f6262c808e0089c9f build: number: 0 - skip: True # [py<37] + skip: True # [py<38] entry_points: - pegasus = pegasus.__main__:main - run_exports: - - {{ pin_subpackage(name, max_pin='x') }} script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: @@ -35,8 +35,7 @@ requirements: - loompy >=3 - docopt - scipy >=1.7 - - importlib_metadata >=0.7 - - pegasusio >=0.5.1 + - pegasusio >=0.9.0 - psutil - threadpoolctl - adjusttext @@ -54,12 +53,13 @@ requirements: - python-igraph >=0.8.0 - scikit-learn >=0.23.2 - scikit-misc - - seaborn + - seaborn >=0.13.0 - statsmodels - pyfit-sne >=1.1.1 - umap-learn >=0.5.2 - xlsxwriter - wordcloud + - forceatlas2-python # brought in by numba, trying to ensure it comes from conda-forge rather than defaults - tbb From ba950b4a769ed9bca487c469177158bb9f38487e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Jan 2024 10:37:35 -0500 Subject: [PATCH 0140/1813] Update biocode to 0.11.0 (#44304) * Update biocode to 0.11.0 * run_export * Remove outdated patch --------- Co-authored-by: Thanh Lee Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Brandon Seah Co-authored-by: Brandon Seah --- recipes/biocode/biocode.patch | 23 ----------------------- recipes/biocode/meta.yaml | 8 ++++---- 2 files changed, 4 insertions(+), 27 deletions(-) delete mode 100644 recipes/biocode/biocode.patch diff --git a/recipes/biocode/biocode.patch b/recipes/biocode/biocode.patch deleted file mode 100644 index 2b3d9f2ded9f8..0000000000000 --- a/recipes/biocode/biocode.patch +++ /dev/null @@ -1,23 +0,0 @@ -From 028ea8130db125bcb546bbc90dbdf44c5b5b0d5b Mon Sep 17 00:00:00 2001 -From: Gerry Tonkin-Hill -Date: Mon, 15 Aug 2022 12:26:17 +0100 -Subject: [PATCH] remove old script - ---- - setup.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/setup.py b/setup.py -index 5a96f71..ec9f63d 100644 ---- a/setup.py -+++ b/setup.py -@@ -22,7 +22,7 @@ setup(name='biocode', - license='MIT', - long_description=read('README.rst'), - packages=['biocode'], -- scripts=['bin/append_to_column_9_value.py', 'bin/prepend_to_fasta_header.py', 'bin/download_assemblies_from_genbank.py', 'bin/convert_augustus_to_gff3.py', 'bin/convert_gff3_to_ncbi_tbl.py', 'bin/mark_partial_genes.py', 'bin/filter_fasta_by_abundance.py', 'bin/validate_feature_boundaries_on_molecules.py', 'bin/add_polypeptide_to_gff3_gene_models.py', 'bin/select_training_and_evaluation_transcripts.py', 'bin/filter_fasta_by_type.py', 'bin/filter_uniref_by_taxonomy.py', 'bin/remove_orphaned_features.py', 'bin/convert_blast_btab_to_bed.py', 'bin/replace_gff_type_column_value.py', 'bin/convert_blast_btab_to_gff3.py', 'bin/interleave_fastq.py', 'bin/split_isoforms_into_individual_genes.py', 'bin/make_cufflinks_ids_unique.py', 'bin/convert_gff3_to_gbk.py', 'bin/make_go_slim_index.py', 'bin/eggnog_to_sqlite3.py', 'bin/convert_metagenemark_gff_to_gff3.py', 'bin/append_to_fasta_header.py', 'bin/merge_bam_files.py', 'bin/remove_masked_gene_models.py', 'bin/filter_fastq_by_N_content.py', 'bin/uniref_to_sqlite3.py', 'bin/uniprot_sprot_to_sqlite3.py', 'bin/reverse_misordered_cds_coords.py', 'bin/update_selected_column9_values.py', 'bin/convert_gff3_to_gene_association_format.py', 'bin/interleave_fasta.py', 'bin/make_go_slim.py', 'bin/join_columnar_files.py', 'bin/split_interleaved_sequence_file.py', 'bin/merge_masked_fasta_files.py', 'bin/hmmlib_to_sqlite3.py', 'bin/fasta_size_distribution_plot.py', 'bin/report_gff3_statistics.py', 'bin/reformat_fasta_residue_lengths.py', 'bin/convert_cufflinks_gtf_to_gff3.py', 'bin/list_biocode.py', 'bin/fasta_simple_stats.py', 'bin/fastq_simple_stats.py', 'bin/convert_prodigal_to_gff3.py', 'bin/convert_scipio_gff_to_gff3.py', 'bin/filter_gff3_by_id_list.py', 'bin/reorient_sequences_by_id.py', 'bin/convert_fastq_to_fasta.py', 'bin/create_rsem_html_table.py', 'bin/convert_glimmerHMM_gff_to_gff3.py', 'bin/convert_genbank_to_gff3.py', 'bin/replace_homopolymeric_repeats_with_Ns.py', 'bin/split_fasta_into_even_files.py', 'bin/get_mpilup_from_id_list.py', 'bin/convert_gff_to_ncbi_gff3.py', 'bin/create_taxonomic_profile_from_blast.py', 'bin/convert_fasta_contigs_to_gff3.py', 'bin/merge_fasta_files_and_uniquify_ids.py', 'bin/merge_predicted_gff3.py', 'bin/filter_fasta_by_header_regex.py', 'bin/convert_pasa_gff_to_models.py', 'bin/extract_fasta_regions.py', 'bin/set_source_column.py', 'bin/tigrfam_info_to_sqlite3.py', 'bin/add_gff3_locus_tags.py', 'bin/fasta_base_content.py', 'bin/subsample_fasta.py', 'bin/convert_gff3_to_bed.py', 'bin/compare_gene_structures.py', 'bin/validate_fasta.py', 'bin/randomly_subsample_fastq.py', 'bin/append_to_fastq_read_header.py', 'bin/convert_aat_btab_to_gff3.py', 'bin/check_for_embedded_fasta_headers.py', 'bin/convert_htab_to_bed.py', 'bin/correct_gff3_CDS_phase_column.py', 'bin/report_coverage_gaps.py', 'bin/detect_inverted_repeats.py', 'bin/convert_cegma_gff_to_gff3.py', 'bin/remove_duplicate_features.py', 'bin/remove_duplicate_sequences.py', 'bin/create_taxonomy_db.py', 'bin/calculate_query_coverage_by_blast.py', 'bin/report_or_replace_nonstandard_residues.py', 'bin/write_fasta_from_gff.py', 'bin/filter_uniref_by_repid.py', 'bin/check_gff_for_internal_stops.py', 'bin/report_basic_gff_model_agreement.py', 'bin/calculate_gene_coverage_from_assembly.py', 'bin/report_gff_intron_and_intergenic_stats.py', 'bin/extend_genes_to_stops.py', 'bin/report_go_slim_counts.py', 'bin/make_go_index.py', 'bin/split_molecules_on_gaps.py'], -+ scripts=['bin/append_to_column_9_value.py', 'bin/prepend_to_fasta_header.py', 'bin/download_assemblies_from_genbank.py', 'bin/convert_augustus_to_gff3.py', 'bin/convert_gff3_to_ncbi_tbl.py', 'bin/mark_partial_genes.py', 'bin/filter_fasta_by_abundance.py', 'bin/validate_feature_boundaries_on_molecules.py', 'bin/add_polypeptide_to_gff3_gene_models.py', 'bin/select_training_and_evaluation_transcripts.py', 'bin/filter_fasta_by_type.py', 'bin/filter_uniref_by_taxonomy.py', 'bin/remove_orphaned_features.py', 'bin/convert_blast_btab_to_bed.py', 'bin/replace_gff_type_column_value.py', 'bin/convert_blast_btab_to_gff3.py', 'bin/interleave_fastq.py', 'bin/split_isoforms_into_individual_genes.py', 'bin/make_cufflinks_ids_unique.py', 'bin/convert_gff3_to_gbk.py', 'bin/make_go_slim_index.py', 'bin/eggnog_to_sqlite3.py', 'bin/convert_metagenemark_gff_to_gff3.py', 'bin/append_to_fasta_header.py', 'bin/merge_bam_files.py', 'bin/remove_masked_gene_models.py', 'bin/filter_fastq_by_N_content.py', 'bin/uniref_to_sqlite3.py', 'bin/uniprot_sprot_to_sqlite3.py', 'bin/reverse_misordered_cds_coords.py', 'bin/update_selected_column9_values.py', 'bin/convert_gff3_to_gene_association_format.py', 'bin/make_go_slim.py', 'bin/join_columnar_files.py', 'bin/split_interleaved_sequence_file.py', 'bin/merge_masked_fasta_files.py', 'bin/hmmlib_to_sqlite3.py', 'bin/fasta_size_distribution_plot.py', 'bin/report_gff3_statistics.py', 'bin/reformat_fasta_residue_lengths.py', 'bin/convert_cufflinks_gtf_to_gff3.py', 'bin/list_biocode.py', 'bin/fasta_simple_stats.py', 'bin/fastq_simple_stats.py', 'bin/convert_prodigal_to_gff3.py', 'bin/convert_scipio_gff_to_gff3.py', 'bin/filter_gff3_by_id_list.py', 'bin/reorient_sequences_by_id.py', 'bin/convert_fastq_to_fasta.py', 'bin/create_rsem_html_table.py', 'bin/convert_glimmerHMM_gff_to_gff3.py', 'bin/convert_genbank_to_gff3.py', 'bin/replace_homopolymeric_repeats_with_Ns.py', 'bin/split_fasta_into_even_files.py', 'bin/get_mpilup_from_id_list.py', 'bin/convert_gff_to_ncbi_gff3.py', 'bin/create_taxonomic_profile_from_blast.py', 'bin/convert_fasta_contigs_to_gff3.py', 'bin/merge_fasta_files_and_uniquify_ids.py', 'bin/merge_predicted_gff3.py', 'bin/filter_fasta_by_header_regex.py', 'bin/convert_pasa_gff_to_models.py', 'bin/extract_fasta_regions.py', 'bin/set_source_column.py', 'bin/tigrfam_info_to_sqlite3.py', 'bin/add_gff3_locus_tags.py', 'bin/fasta_base_content.py', 'bin/subsample_fasta.py', 'bin/convert_gff3_to_bed.py', 'bin/compare_gene_structures.py', 'bin/validate_fasta.py', 'bin/randomly_subsample_fastq.py', 'bin/append_to_fastq_read_header.py', 'bin/convert_aat_btab_to_gff3.py', 'bin/check_for_embedded_fasta_headers.py', 'bin/convert_htab_to_bed.py', 'bin/correct_gff3_CDS_phase_column.py', 'bin/report_coverage_gaps.py', 'bin/detect_inverted_repeats.py', 'bin/convert_cegma_gff_to_gff3.py', 'bin/remove_duplicate_features.py', 'bin/remove_duplicate_sequences.py', 'bin/create_taxonomy_db.py', 'bin/calculate_query_coverage_by_blast.py', 'bin/report_or_replace_nonstandard_residues.py', 'bin/write_fasta_from_gff.py', 'bin/filter_uniref_by_repid.py', 'bin/check_gff_for_internal_stops.py', 'bin/report_basic_gff_model_agreement.py', 'bin/calculate_gene_coverage_from_assembly.py', 'bin/report_gff_intron_and_intergenic_stats.py', 'bin/extend_genes_to_stops.py', 'bin/report_go_slim_counts.py', 'bin/make_go_index.py', 'bin/split_molecules_on_gaps.py'], - url='http://github.com/jorvis/biocode', - version='0.10.0', - zip_safe=False) --- diff --git a/recipes/biocode/meta.yaml b/recipes/biocode/meta.yaml index 2d3c8dc8fe5d8..42ff93ce5a92a 100644 --- a/recipes/biocode/meta.yaml +++ b/recipes/biocode/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biocode" %} -{% set version = "0.10.0" %} +{% set version = "0.11.0" %} package: name: "{{ name|lower }}" @@ -7,14 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ab48e0ea92f52c7fe48c6c947d4d5aa43437f16cd42a804546c71ef0e5ba2265 - patches: biocode.patch + sha256: 5c0df506d07e6b073b56da360bba4dad8e0b90e4ceb6f62009ae51c56a83b162 build: noarch: python number: 0 script: "{{ PYTHON }} -m pip install . --no-deps -vv" - + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: - pip From d4454836e2b5f834d6c5bc35eaa2b1f9ee5c7e8a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Jan 2024 11:09:17 -0500 Subject: [PATCH 0141/1813] Update whatshap to 2.2 (#45436) --- recipes/whatshap/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index 7c3aeef9ad35c..f8554c9bb5021 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -1,10 +1,10 @@ package: name: whatshap - version: "2.1" + version: "2.2" source: - url: https://files.pythonhosted.org/packages/35/1a/d6fedb787eac8d616ec598f6a42cf2289bcc11dbbfdeae65afdf1dcb7bfc/whatshap-2.1.tar.gz - sha256: 9b61812eda1dd5251ba8d02db16d7ddda152ccc813cb3db6a1ec796f1865fe8d + url: https://files.pythonhosted.org/packages/00/f3/2e2c850755629a151c2027b636f253745bbbfeee052870f03e99f94a4996/whatshap-2.2.tar.gz + sha256: 4cd34e9b82930c4f42e9e6b7dce2e321e4c81f934fdb980b6093ad91a06ae30a build: number: 0 From 32b6ac35af7b4344e945e7df7730df0726114e4f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Jan 2024 14:51:07 -0500 Subject: [PATCH 0142/1813] Update hiphase to 1.2.1 (#45443) --- recipes/hiphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index 89033d92be5b2..5f949dfe8a40b 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "1.2.0" %} -{% set hiphase_sha256 = "e57455275a42a5679895a95f997c132064164343c0ef949946b28cac356c9a3a" %} +{% set version = "1.2.1" %} +{% set hiphase_sha256 = "a5bd4926bb57f934fae5d72859d530991ce804ca7127fc134ca7e4c8245fe9f0" %} package: name: {{ name }} From 0bd57d546ba59144c4be7d9a7dabcc7346655f5a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Jan 2024 15:50:54 -0500 Subject: [PATCH 0143/1813] Update viralmsa to 1.1.42 (#45422) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 78d60f0913045..51aad2edd4c70 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.41" %} +{% set version = "1.1.42" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: 1475eb3497823fd85febd5bb983c919b830b1e367aa7cf21af19fb33d437404b + sha256: dd4ba1779681479f86c3fa38c486ee36ee8f2ca5d66301e583125dc9767d1171 requirements: run: From 9cd4df5287873e7920bb76b24e2f178657a069c2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 05:56:18 -0500 Subject: [PATCH 0144/1813] Update ncbi-datasets-pylib to 16.4.3 (#45424) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 150d6075f3184..cc7f56893916a 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.3.0" %} -{% set sha256 = "9dafbff2b355d0b28f3621cdab580e5cadc8299d2ceeb845bb474d8413d14b85" %} +{% set version = "16.4.3" %} +{% set sha256 = "3155f0ebc388c30208315f253e0e36ea3df1bf83c89c97ea9765386fd3829d5d" %} package: name: {{ name|lower }} From 520a384532612f49ced8939cd4827676bebe0c31 Mon Sep 17 00:00:00 2001 From: Bryce Kille Date: Sat, 27 Jan 2024 12:45:57 -0600 Subject: [PATCH 0145/1813] Enable macos build for parsnp (#45444) * Enable macos build * update build number * Add patch for osx cpu count --- recipes/parsnp/cpu_count.patch | 52 ++++++++++++++++++++++++++++++++++ recipes/parsnp/meta.yaml | 7 +++-- 2 files changed, 56 insertions(+), 3 deletions(-) create mode 100644 recipes/parsnp/cpu_count.patch diff --git a/recipes/parsnp/cpu_count.patch b/recipes/parsnp/cpu_count.patch new file mode 100644 index 0000000000000..eac0bdea42d0f --- /dev/null +++ b/recipes/parsnp/cpu_count.patch @@ -0,0 +1,52 @@ +diff --git a/parsnp b/parsnp +index 85fd9c9..9501ab8 100755 +--- a/parsnp ++++ b/parsnp +@@ -8,6 +8,7 @@ + import os, sys, string, random, subprocess, time, operator, math, datetime, numpy #pysam + from collections import defaultdict + import shutil ++import multiprocessing + import shlex + from tempfile import TemporaryDirectory + import re +@@ -1210,8 +1211,13 @@ SETTINGS: + (len(outputDir)+17)*"*")) + + # If we requested more threads than available, give a warning. +- if len(os.sched_getaffinity(0)) < threads: +- logger.warning("You have asked to use more threads than you have available on your machine. This may lead to serious performance degredation with RAxML.") ++ try: ++ if len(os.sched_getaffinity(0)) < threads: ++ logger.warning("You have asked to use more threads than you have available on your machine. This may lead to serious performance degredation with RAxML.") ++ except AttributeError: ++ if multiprocessing.cpu_count() < threads: ++ logger.warning("You have asked to use more threads than you have available on your machine. This may lead to serious performance degredation with RAxML.") ++ + logger.info("<>") + + #1)read fasta files (contigs/scaffolds/finished/DBs/dirs) +@@ -1614,19 +1620,16 @@ SETTINGS: + else: + import partition + +- full_query_list_path = f"{outputDir}/config/input-list.txt" +- with open(full_query_list_path, 'w') as input_list_handle: +- random_seeded.shuffle(finalfiles) +- for qf in finalfiles: +- input_list_handle.write(qf + "\n") +- + if len(finalfiles) % args.partition_size == 1: + logger.warning("Incrementing partition size by 1 to avoid having a remainder partition of size 1") + args.partition_size += 1 + partition_output_dir = f"{outputDir}/partition" + partition_list_dir = f"{partition_output_dir}/input-lists" + os.makedirs(partition_list_dir, exist_ok=True) +- run_command(f"split -l {args.partition_size} -a 5 --additional-suffix '.txt' {full_query_list_path} {partition_list_dir}/{partition.CHUNK_PREFIX}-") ++ for partition_idx in range(math.ceil(len(finalfiles) / args.partition_size)): ++ with open(f"{partition_list_dir}/{partition.CHUNK_PREFIX}-{partition_idx:010}.txt", 'w') as part_out: ++ for qf in finalfiles[partition_idx*args.partition_size : (partition_idx+1)*args.partition_size]: ++ part_out.write(f"{qf}\n") + + chunk_label_parser = re.compile(f'{partition.CHUNK_PREFIX}-(.*).txt') + chunk_labels = [] diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index 5591dab327142..4d0c7af0086ec 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -7,10 +7,11 @@ package: source: url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" sha256: 1d9a4c6e5b414511ebc0052e3c9e6e32984b545ef8816086ed1d74af69c27c8f + patches: + - cpu_count.patch build: - skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('parsnp', max_pin="x") }} @@ -35,7 +36,7 @@ requirements: - phipack - raxml - fasttree - - fastani # [linux] + - fastani - mash - harvesttools - pyspoa From 5f2bd011c9c4802641092fd2b4d464b9969db874 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:08:12 -0500 Subject: [PATCH 0146/1813] Update dimet to 0.2.1 (#45442) --- recipes/dimet/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dimet/meta.yaml b/recipes/dimet/meta.yaml index fd7147d1ce9d8..8a230316e2d32 100644 --- a/recipes/dimet/meta.yaml +++ b/recipes/dimet/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dimet" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dimet-{{ version }}.tar.gz - sha256: 40d5dee29232deb5722392c745a70f757c78128829b372ce0093fe2fbaf9411e + sha256: e5ad617a5f45072bfd4257cc09b965cf27341a252de979864462c3a8e0ba94dc build: noarch: python From afa1e2080022ae08bedfdb9d715dfdecbf21c006 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:08:29 -0500 Subject: [PATCH 0147/1813] Update annembed to 0.1.3 (#45441) --- recipes/annembed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml index 5a2b606fcd0b3..44ad55f01bd75 100644 --- a/recipes/annembed/meta.yaml +++ b/recipes/annembed/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: annembed @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/annembed/archive/v{{ version }}.tar.gz - sha256: 68d08b42f06d873a3b301cb609530cb1072cd97cd8ccefa8d0331d857f692352 + sha256: 9a9175f728bb46ada240989060d7687e551c387288151186ae327b51965e4945 requirements: build: From 29afd249c058a998c1788d5ac54a2cffa85fc1c6 Mon Sep 17 00:00:00 2001 From: stuber Date: Sat, 27 Jan 2024 13:09:56 -0700 Subject: [PATCH 0148/1813] vsnp3 version 3.19 (#45440) --- recipes/vsnp3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsnp3/meta.yaml b/recipes/vsnp3/meta.yaml index 9fe286418fdbe..7daba8dea3820 100644 --- a/recipes/vsnp3/meta.yaml +++ b/recipes/vsnp3/meta.yaml @@ -1,7 +1,7 @@ {% set user = "USDA-VS" %} {% set name = "vsnp3" %} -{% set version = "3.18" %} -{% set sha256 = "46c6d760d4e7ad6e437bbd1096cd9ae681a33c90c1be7c410439b0a1a0ba7769" %} +{% set version = "3.19" %} +{% set sha256 = "cc1c282094fc4cfcf8fdf865a954807eabe5f45a9cd1218041bd03ce2e13648d" %} package: name: {{ name|lower }} From 45e55767c450650b489e862e7416e53b973c0e80 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:11:58 -0500 Subject: [PATCH 0149/1813] Update sirius-csifingerid to 5.8.6 (#45451) --- recipes/sirius-csifingerid/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sirius-csifingerid/meta.yaml b/recipes/sirius-csifingerid/meta.yaml index ef47cac572991..818c2dd93a169 100644 --- a/recipes/sirius-csifingerid/meta.yaml +++ b/recipes/sirius-csifingerid/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "5.8.5" %} +{% set version = "5.8.6" %} {% set siriusDistDir = "sirius_gui_dist" %} package: @@ -15,7 +15,7 @@ build: source: - url: https://github.com/boecker-lab/sirius/archive/refs/tags/v{{ version }}.zip - sha256: 72bf7762f143740c6f2be06a268149e85787c97064586791348b8a27f9e9f5c8 + sha256: f769a474140d6e28168d6d1526afc9e923e66eaeb0ace400e6c2ae77aa7f9202 requirements: build: From 55e142a5f927bc910467cc8b19c65d689875f9c2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:13:08 -0500 Subject: [PATCH 0150/1813] Update comebin to 1.0.4 (#45439) --- recipes/comebin/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/comebin/meta.yaml b/recipes/comebin/meta.yaml index 655515c4b5f9f..3b95de96aefd5 100644 --- a/recipes/comebin/meta.yaml +++ b/recipes/comebin/meta.yaml @@ -1,10 +1,10 @@ package: name: comebin - version: "1.0.3" + version: "1.0.4" source: - url: https://github.com/ziyewang/COMEBin/archive/refs/tags/1.0.3.tar.gz - sha256: 27001cff1029ddf492da18ba8f4db18c055f48e062237bb9e17ad65ed7602930 + url: https://github.com/ziyewang/COMEBin/archive/refs/tags/1.0.4.tar.gz + sha256: 63726b4ae450c0ca366845d46f2065326a83454b2c7f87cec5b53adc9527be22 build: number: 0 From 33d7e6b751c0b90f4dbba80fad30c72349ee2fef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:13:29 -0500 Subject: [PATCH 0151/1813] Update zdb to 1.2.3 (#45434) --- recipes/zdb/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/zdb/meta.yaml b/recipes/zdb/meta.yaml index d410159bdd9f4..508c74054ba0c 100644 --- a/recipes/zdb/meta.yaml +++ b/recipes/zdb/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.1" %} +{% set version = "1.2.3" %} package: name: zdb @@ -6,13 +6,13 @@ package: build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage('zdb', max_pin="x.x") }} source: - url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.2.1.tar.gz - sha256: 621146aa73de7bf04dd05da4e226eb558d07eb1f79e04760456c84e00ae9be0c + url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.2.3.tar.gz + sha256: b73a72cce424c1db28ccb0f1be20cbf61855260bb957e2829a6d9f991a20c029 requirements: run: From 5e07f0e0dcd2d64bdc296f0fa54c57a97e5c447e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:13:44 -0500 Subject: [PATCH 0152/1813] Update sneep to 0.9 (#45437) --- recipes/sneep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sneep/meta.yaml b/recipes/sneep/meta.yaml index 97578dcf17ba2..6158e18019de4 100644 --- a/recipes/sneep/meta.yaml +++ b/recipes/sneep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SNEEP" %} -{% set version = "0.8" %} +{% set version = "0.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/SchulzLab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 147e10e6f64056f6fde4fec609f7019d0a765a5b4b14ead954e1ef3071d95d49 + sha256: 3d1f0a20f4d54ae91dd555d0fb8f9d25e980be9399bf6cbec5a5ddeedf47961d build: skip: True # [py2k] From a237bef7fc88bb80d41329e236c8e1c8d708937c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:14:34 -0500 Subject: [PATCH 0153/1813] Update tides-ml to 1.1.4 (#45427) Co-authored-by: Brandon Seah --- recipes/tides-ml/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tides-ml/meta.yaml b/recipes/tides-ml/meta.yaml index 8700a6649354a..ff653618f6ed2 100644 --- a/recipes/tides-ml/meta.yaml +++ b/recipes/tides-ml/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tides-ml" %} -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/TIdeS-ML-{{ version }}.tar.gz - sha256: a2a872ac26c24705a6f538823b53081ae456a313fa587520997418fbda8e612e + sha256: 393f24ce18a58f40b2387e2a2fc2d45eb0088c8231c3d533f647deaf4b38c6ee build: entry_points: From 7359e098d1dee0c92942353fee591bab09d3d5e1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Jan 2024 12:02:21 -0500 Subject: [PATCH 0154/1813] Update r-oncopharmadb to 1.5.1 (#45452) * Update r-oncopharmadb to 1.5.1 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-oncopharmadb/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/r-oncopharmadb/meta.yaml b/recipes/r-oncopharmadb/meta.yaml index 58e8fc471ae38..bbfbdc7933bbf 100644 --- a/recipes/r-oncopharmadb/meta.yaml +++ b/recipes/r-oncopharmadb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "r-oncopharmadb" %} -{% set version = "1.4.6" %} +{% set version = "1.5.1" %} {% set github = "https://github.com/sigven/oncoPharmaDB" %} package: @@ -8,7 +8,7 @@ package: source: url: https://github.com/sigven/pharmOncoX/archive/refs/tags/{{ version }}.tar.gz - sha256: 5c0c708828cc91f032018e5ff2c42a391a9f98bb411038b1fa431ef6992d3095 + sha256: 7765b9122063aeacd96db0c536141ab2e23a116a84e313b7264d707a09c92316 build: number: 0 @@ -24,6 +24,7 @@ requirements: - r-stringr - r-lgr - r-tidyr + - r-ggplot2 - r-googledrive - r-rlang - r-assertthat @@ -35,6 +36,7 @@ requirements: - r-stringr - r-lgr - r-tidyr + - r-ggplot2 - r-googledrive - r-rlang - r-assertthat From a7af6e0bbea3b48f0a4a220aec1c9ddb31a6e420 Mon Sep 17 00:00:00 2001 From: Mingfu Shao Date: Sun, 28 Jan 2024 15:48:36 -0500 Subject: [PATCH 0155/1813] aletsch 1.1.0 (#45454) * init for coral * update meta * Update meta.yaml * add recipes for aletsch * Update meta.yaml * update meta.yaml --------- Co-authored-by: Devon Ryan --- recipes/aletsch/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/aletsch/meta.yaml b/recipes/aletsch/meta.yaml index d456e3db645dd..f97373d1f61d4 100644 --- a/recipes/aletsch/meta.yaml +++ b/recipes/aletsch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "aletsch" %} -{% set version = "1.0.3" %} +{% set version = "1.1.0" %} package: name: "{{ name }}" @@ -7,10 +7,12 @@ package: source: url: "https://github.com/Shao-Group/aletsch/releases/download/v{{ version }}/aletsch-{{ version }}.tar.gz" - sha256: "1eae28ae32f40097320ef14c8dd65e30319cae5f1cb11533905b4330b5b76478" + sha256: "075e514da0b8e264fb7822d065061f406d5f73bea95c60ab31f08d2c498010a2" build: - number: 6 + number: 0 + run_exports: + - {{ pin_subpackage('aletsch', max_pin="x") }} requirements: build: @@ -32,7 +34,7 @@ about: home: "https://github.com/Shao-Group/aletsch" license: BSD-3-Clause license_file: LICENSE - summary: "Aletsch is a scalable, accurate, and versatile assembler for multiple RNA-seq samples." + summary: "Aletsch is an accurate, versatile assembler for multiple RNA-seq samples." extra: recipe-maintainers: From 9ab2508e883a0fd721e6650559b1567a928e72e1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Jan 2024 15:59:37 -0500 Subject: [PATCH 0156/1813] Update cpat to 3.0.5 (#45425) * Update cpat to 3.0.5 * Add run_exports; use SPDX abbrev for license * Link executables to old names with .py suffix --------- Co-authored-by: Brandon Seah Co-authored-by: Brandon Seah --- recipes/cpat/build.sh | 9 +++++++++ recipes/cpat/meta.yaml | 11 ++++++----- 2 files changed, 15 insertions(+), 5 deletions(-) create mode 100644 recipes/cpat/build.sh diff --git a/recipes/cpat/build.sh b/recipes/cpat/build.sh new file mode 100644 index 0000000000000..ea41484c36517 --- /dev/null +++ b/recipes/cpat/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +${PYTHON} -m pip install . --no-deps --ignore-installed -vv + +# Prefix '.py' has been removed from v3.0.5 +# symlinking for reverse compatibility, as suggested in release notes +ln -s ${PREFIX}/bin/cpat ${PREFIX}/bin/cpat.py +ln -s ${PREFIX}/bin/make_hexamer_tab ${PREFIX}/bin/make_hexamer_tab.py +ln -s ${PREFIX}/bin/make_logitModel ${PREFIX}/bin/make_logitModel.py diff --git a/recipes/cpat/meta.yaml b/recipes/cpat/meta.yaml index 7303729af7f68..749a4451c6ab6 100644 --- a/recipes/cpat/meta.yaml +++ b/recipes/cpat/meta.yaml @@ -1,18 +1,19 @@ {% set name = "CPAT" %} -{% set version = "3.0.4" %} +{% set version = "3.0.5" %} package: name: "{{ name|lower }}" version: "{{ version }}" build: - number: 2 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + number: 0 skip: True # [py2k or py > 39] + run_exports: + - {{ pin_subpackage('cpat', max_pin="x") }} source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 6d832f20729f8fc814384a27a4fcebcf81b11c0e6d80a404b4c4860d17e7d935 + sha256: ea7c9216208221f68055f962073622939ff90bbe52ebe36c305ead9f91ed24bc requirements: build: @@ -40,6 +41,6 @@ test: about: home: https://cpat.readthedocs.io/en/latest/ - license: GNU General Public v2 or later (GPLv2+) + license: GPL-2.0-or-later license_file: LICENSE.txt summary: Coding Potential Assessment Tool From d8a2720b6380af0061a8e5f24170a7b4cd231733 Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 29 Jan 2024 09:12:41 +1000 Subject: [PATCH 0157/1813] Update syri (#45284) * add mummer to run dependencies * add run_exports * try different install method * Update meta.yaml * add patch for missing sys * try old install method * adjust pinnings to match upstream * remove test skip * attempt custon config * try pinning numpy * shot in the dark * pin cython based on open PR * remove custom config, make note on cython * trigger CI, mac test was stuck --------- Co-authored-by: Robert A. Petit III --- recipes/syri/import-sys.patch | 12 ++++++++++++ recipes/syri/meta.yaml | 30 ++++++++++++++++++------------ 2 files changed, 30 insertions(+), 12 deletions(-) create mode 100644 recipes/syri/import-sys.patch diff --git a/recipes/syri/import-sys.patch b/recipes/syri/import-sys.patch new file mode 100644 index 0000000000000..001ae2d87f0e3 --- /dev/null +++ b/recipes/syri/import-sys.patch @@ -0,0 +1,12 @@ +diff --git a/syri/pyxFiles/findshv.pyx b/syri/pyxFiles/findshv.pyx +index b23bd33..4bc3372 100644 +--- a/syri/pyxFiles/findshv.pyx ++++ b/syri/pyxFiles/findshv.pyx +@@ -9,6 +9,7 @@ from collections import defaultdict + import pandas as pd + from functools import partial + import os ++import sys + import logging + from re import findall + \ No newline at end of file diff --git a/recipes/syri/meta.yaml b/recipes/syri/meta.yaml index 583b8c738ccee..3ab1f4198571e 100755 --- a/recipes/syri/meta.yaml +++ b/recipes/syri/meta.yaml @@ -8,31 +8,37 @@ package: source: url: https://github.com/schneebergerlab/syri/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} + patches: + - import-sys.patch build: - number: 1 - skip: True # [py < 38 or py > 39] + number: 2 script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt" + run_exports: + - {{ pin_subpackage('syri', max_pin="x") }} requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} host: - - python + - python 3.8 - setuptools - - numpy >=1.20 - - cython + - numpy >=1.21.2 + # Please review cython pinning on future releases + # see: https://github.com/schneebergerlab/syri/pull/217 + - cython <=0.29.36 run: - - python - - numpy >=1.20 - - pandas - - scipy - - psutil - - python-igraph - - pysam + - python 3.8 + - numpy >=1.21.2 + - pandas >=1.2.4 + - scipy >=1.6.2 + - psutil >=5.8 + - python-igraph >=0.9.1 + - pysam >=0.16.0.1 - longestrunsubsequence - pulp + - mummer4 test: commands: From ac4d63453ef69e392d41ca883785d94f753e694a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 03:22:13 -0500 Subject: [PATCH 0158/1813] Update annembed to 0.1.4 (#45459) --- recipes/annembed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml index 44ad55f01bd75..5b9b7bcc27166 100644 --- a/recipes/annembed/meta.yaml +++ b/recipes/annembed/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: annembed @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/annembed/archive/v{{ version }}.tar.gz - sha256: 9a9175f728bb46ada240989060d7687e551c387288151186ae327b51965e4945 + sha256: 0f923798db3843aac0352eba5d2b169673ee087fce2cc37981bd19a1ecb878d0 requirements: build: From f3b34c5ac2d4ac8a283579312c84d8de6b16fce1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 03:22:36 -0500 Subject: [PATCH 0159/1813] Update pycov3 to 2.1.0 (#45456) --- recipes/pycov3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pycov3/meta.yaml b/recipes/pycov3/meta.yaml index e9435f67e8e41..f5ac7f49a1a19 100644 --- a/recipes/pycov3/meta.yaml +++ b/recipes/pycov3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pycov3" %} -{% set version = "2.0.4b0" %} +{% set version = "2.1.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 22a3b35bd589e967bf3041356436c652913a64c601efb2af2149375fb095a8e4 + sha256: 7fcd34f840fb93b0e951eca51f23b4df7548412577d9bc4a6e1fbf855b97329a build: number: 0 From abd9ac697f2b4d890b0d2aeec75f22a9eb803038 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 05:27:51 -0500 Subject: [PATCH 0160/1813] Update ppanggolin to 2.0.2 (#45460) --- recipes/ppanggolin/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ppanggolin/meta.yaml b/recipes/ppanggolin/meta.yaml index fe77191e7d636..16e09e9ca169c 100644 --- a/recipes/ppanggolin/meta.yaml +++ b/recipes/ppanggolin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: ppanggolin @@ -6,7 +6,7 @@ package: source: url: https://github.com/labgem/PPanGGOLiN/archive/{{ version }}.tar.gz - sha256: 0e13410a03f825894ceccb7c7a85f8acee060cd98c720486fbb90df71cbd5275 + sha256: a655b378b05da41c5d2b7e8e8269af722681854c5d6c7c9589d01bea636035a1 build: number: 0 From 99d0e1e46652e5726d1277c1d9af07887918f9c9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 07:00:11 -0500 Subject: [PATCH 0161/1813] Update snakemake to 8.4.0 (#45461) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 5f0761641c24b..2bd9541d59cd1 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.3.2" %} +{% set version = "8.4.0" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 2959b72891d0c842faa019aba35726090db97f3513b6d78bd668fdbe92056628 + sha256: c875e88c561370c5b545622fe7397cc0d7d2399c285044c83d1309816d0d224f build: number: 0 From 7804e1c6bb56cbc6bbde12448b4f3f013e461c69 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 09:49:32 -0500 Subject: [PATCH 0162/1813] Update bcbio-gff to 0.7.1 (#45464) --- recipes/bcbio-gff/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bcbio-gff/meta.yaml b/recipes/bcbio-gff/meta.yaml index ff55d1753cf3b..173e1c0c2cda6 100644 --- a/recipes/bcbio-gff/meta.yaml +++ b/recipes/bcbio-gff/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bcbio-gff" %} -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/b/{{ name|lower }}/{{ name }}-{{ version }}.tar.gz - sha256: f7b3922ee274106f8716703f41f05a1795aa9d73e903f4e481995ed8f5f65d2d + sha256: d1dc3294147b95baced6033f6386a0fed45c43767ef02d1223df5ef497e9cca6 build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} From 444628a5b632e09e0709cc6528b9a04220369f39 Mon Sep 17 00:00:00 2001 From: Jose Figueroa Date: Mon, 29 Jan 2024 11:18:52 -0500 Subject: [PATCH 0163/1813] Update metacerberus (#45448) * Update metacerberus * Update metacerberus * Update metacerberus --- recipes/metacerberus/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/metacerberus/meta.yaml b/recipes/metacerberus/meta.yaml index 5983b3673b124..79300581b533d 100644 --- a/recipes/metacerberus/meta.yaml +++ b/recipes/metacerberus/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MetaCerberus" %} -{% set version = "1.1" %} +{% set version = "1.2" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 65610ac32ca00ad7917cb5fa49fc2282db66590fc5310115c32e0090600eff90 + sha256: 6103002803d448df349f770a38e0da9a261a688993b5d33afbf1a9024ecbba07 build: - number: 1 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_compatible('MetaCerberus', max_pin="x") }} requirements: host: @@ -54,7 +56,7 @@ about: home: "https://github.com/raw-lab/metacerberus" license: BSD-3-Clause license_family: BSD - license_file: + license_file: LICENSE.txt summary: "Versatile Functional Ontology Assignments for Metagenomes via Hidden Markov Model (HMM) searching with environmental focus of shotgun meta'omics data" doc_url: dev_url: From 39faa7d849fcfb4b8a9d041809e30e67d5d603e5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 11:43:05 -0500 Subject: [PATCH 0164/1813] Update thapbi-pict to 1.0.7 (#45467) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 319e783d8d6b0..176bda0e09969 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.6" %} +{% set version = "1.0.7" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: a80cc24cce224195e5f613353cfe63020daca949defea4511cef392b7a6f30ed + sha256: 30381e97d0af98fd4d0924130f4efaa722e8e5a3cc7a4719c7bc597d87d9e5fa build: noarch: python From 85dc8e7167062e7d663fbaa906325e5f71ecd89b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 14:16:53 -0500 Subject: [PATCH 0165/1813] Update simpleaf to 0.16.0 (#45471) * Update simpleaf to 0.16.0 * Update meta.yaml requires piscem unless we're on osx-arm64 --------- Co-authored-by: Rob Patro --- recipes/simpleaf/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index 689fa08030ddc..fa26b7bab51b4 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.15.1" %} +{% set version = "0.16.0" %} package: name: simpleaf @@ -12,7 +12,7 @@ build: source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: 888ebb199a27ef4f009fa890fce221da3ed8b08420269faee3169e48d754932a + sha256: 1939d27ca19e7e01b951b619aa16d564935227e6f1ea14c8b730dee1faafe26b requirements: build: @@ -25,6 +25,7 @@ requirements: run: - alevin-fry >=0.8.1 - salmon >=1.10.1 + - piscem >=0.7.0 # [not osx-arm64] test: commands: From 506851c405f946aa8c51d851810fae3941235fb7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 14:17:08 -0500 Subject: [PATCH 0166/1813] Update parsnp to 2.0.3 (#45466) * Update parsnp to 2.0.3 * Remove osx patch --------- Co-authored-by: Bryce Kille --- recipes/parsnp/meta.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index 4d0c7af0086ec..80b3d3aff5598 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.2" %} +{% set version = "2.0.3" %} package: name: parsnp @@ -6,12 +6,10 @@ package: source: url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" - sha256: 1d9a4c6e5b414511ebc0052e3c9e6e32984b545ef8816086ed1d74af69c27c8f - patches: - - cpu_count.patch + sha256: 8e0c71662f69fc77eeb10a8c4687ff75dfb9d37daf7fca1a4ca410b1c1b1f7cb build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('parsnp', max_pin="x") }} From 21cb9be34bd574382eab3bbd81ba00cba491e261 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 14:37:43 -0500 Subject: [PATCH 0167/1813] Update star to 2.7.11b (#45429) * Update star to 2.7.11b * Include gzip * Include zlib * Include zlib --------- Co-authored-by: Michael Steinbaugh --- recipes/star/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/star/meta.yaml b/recipes/star/meta.yaml index 08e21507fba8d..fd2d21ffee404 100644 --- a/recipes/star/meta.yaml +++ b/recipes/star/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.7.11a" %} -{% set sha256 = "542457b1a4fee73f27a581b1776e9f73ad2b4d7e790388b6dc71147bd039f99a" %} +{% set version = "2.7.11b" %} +{% set sha256 = "3f65305e4112bd154c7e22b333dcdaafc681f4a895048fa30fa7ae56cac408e7" %} package: name: star @@ -27,8 +27,10 @@ requirements: - vim host: - htslib + - zlib run: - htslib + - zlib test: commands: @@ -46,3 +48,5 @@ extra: - biotools:star - usegalaxy-eu:rna_starsolo - usegalaxy-eu:rna_star + recipe-maintainers: + - mjsteinbaugh From 6b6fd4949c19f444345cba13964f232442ece5d6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 15:05:06 -0500 Subject: [PATCH 0168/1813] Update last to 1540 (#45462) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index c8a7c15ea12ff..0bb421e9f8b58 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1526" %} +{% set version = "1540" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: e1db7307005218cbed0c924d583e4bb7bdee96044cb94867cf73d18249058463 + sha256: 047d5ec2f3745f14e29de72c606fa9e74393723ebac9286584435650201de0cf build: number: 0 From 42a59f02753f51656bf279efeda39d97cee0f2a2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 15:05:15 -0500 Subject: [PATCH 0169/1813] Update pyfamsa to 0.3.2 (#45450) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pyfamsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyfamsa/meta.yaml b/recipes/pyfamsa/meta.yaml index 14d799d24909a..587c9a9ee11d7 100644 --- a/recipes/pyfamsa/meta.yaml +++ b/recipes/pyfamsa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyfamsa" %} -{% set version = "0.3.1" %} +{% set version = "0.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 1122a8b06bbbe1045a185d7671e87be0030e3db8e2dd0cb885ff21744c9d24a6 + sha256: c926d6fe00029d712dd277a1544e632c2b20546da322e13bd92780ea3f756dae build: number: 0 From e46ff0dbd9410d7e537b8fa358974b4b9bee7086 Mon Sep 17 00:00:00 2001 From: Jean Mainguy Date: Mon, 29 Jan 2024 22:41:13 +0100 Subject: [PATCH 0170/1813] Update Binette to v0.1.7 (#45469) * update binette recipe to v0.1.7 * add run_exports * update sha256 --- recipes/binette/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/binette/meta.yaml b/recipes/binette/meta.yaml index dbeca042db483..ff3604957f999 100644 --- a/recipes/binette/meta.yaml +++ b/recipes/binette/meta.yaml @@ -1,16 +1,20 @@ {% set name = "Binette" %} -{% set version = "0.1.6" %} +{% set version = "0.1.7" %} package: name: {{ name|lower }} version: {{ version }} source: url: https://github.com/genotoul-bioinfo/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 97f2bb4f9d8e0c06fadb4b1bc4097cc3bfeb80fe84d3c63424ae080b8ac4086d + sha256: a3ede9f274e8eec53401ee92727922ff08a8d89116bed411391b5671616e1d1e + build: noarch: python number: 0 script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + requirements: host: @@ -23,14 +27,13 @@ requirements: - numpy =1.19.2 - diamond =2.0.4 - pandas =1.4.0 - - prodigal =2.6.3 - checkm2 - requests - packaging - tqdm - - networkx + - networkx >=3 - pyfastx - - pyrodigal + - pyrodigal >=2 test: imports: @@ -40,7 +43,8 @@ test: about: home: https://github.com/genotoul-bioinfo/{{ name|lower }} + doc_url: https://binette.readthedocs.io license: MIT license_family: MIT license_file: LICENSE - summary: A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. + summary: "A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools." From 6b1951fb852020441b4d58522267f20895293877 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 17:21:05 -0500 Subject: [PATCH 0171/1813] Update nf-core to 2.12 (#45465) * Update nf-core to 2.12 * add trogon depends * add pillow depend --------- Co-authored-by: Robert A. Petit III --- recipes/nf-core/meta.yaml | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index df210d833f8d2..c5f20958f1b84 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nf-core" %} -{% set version = "2.11.1" %} -{% set sha256 = "f81e411a66a417b9355657eec4337e8d004b166d8690e39f337994763b0ecc63" %} +{% set version = "2.12" %} +{% set sha256 = "a1af4ad7407cc7b65097b066e2593bdfc302b4c61301dd7476c2203924e92e46" %} package: name: {{ name|lower }} @@ -27,26 +27,28 @@ requirements: run: - python >=3.8 - click + - filetype + - galaxy-tool-util - git - - pyyaml - - requests - - requests-cache - - tabulate - gitpython - - markdown >=3.3 - - jsonschema >=3.0 - jinja2 - - rich >=13.3.1 - - rich-click >=1.6.1 + - jsonschema >=3.0 + - markdown >=3.3 + - packaging + - pillow - pre-commit - prompt_toolkit >=3.0.3 - pytest >=7.0.0 - pytest-workflow >=1.6.0 + - pyyaml - questionary >=1.8.0 - - packaging - - galaxy-tool-util - refgenie - - filetype + - requests + - requests-cache + - rich >=13.3.1 + - rich-click >=1.6.1 + - tabulate + - trogon test: commands: From 7060996c4b0e41468fffdce307e25bd3284e1fae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 17:49:49 -0500 Subject: [PATCH 0172/1813] Update tksm to 0.5.0 (#44839) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update tksm to 0.4.0 * add run_exports * add make * add lld to build reqs * Update tksm to 0.5.0 * remove python pinning * Update TKSM to v0.5 (#45473) Fix python build + add more tests --------- Co-authored-by: joshuazhuang7 Co-authored-by: Fatih Karaoglanoglu Co-authored-by: Baraa Orabi /baraːʔ ʕraːbi/ --- recipes/tksm/meta.yaml | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/recipes/tksm/meta.yaml b/recipes/tksm/meta.yaml index 1d3bc532de1b6..df1add61a6a93 100644 --- a/recipes/tksm/meta.yaml +++ b/recipes/tksm/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.2" %} -{% set sha256 = "e965a8e932698570b6bc7c2ea15ebecaf7e0a50985c26cf87ece7869eaf44c83" %} +{% set version = "0.5.0" %} +{% set sha256 = "d2e0abc0ca378945fc2165d489dbe189c71fe0fc7d50bf8fb3be1bd9ce1e7bf3" %} package: name: tksm @@ -11,23 +11,24 @@ source: build: number: 0 - skip: True # [py<3.8 or osx] + skip: True # [py < 3.8 or osx] + run_exports: + - {{ pin_subpackage('tksm', max_pin="x.x") }} requirements: build: + - python - {{ compiler('cxx') }} - - python {{ python }} - - zlib - make - vim - lld host: - - python {{ python }} + - python - zlib - cxxopts >=3.1.0 - fmt >=9.1.0 run: - - python {{ python }} + - python - zlib - python-edlib - numpy @@ -37,11 +38,14 @@ requirements: test: commands: + - tksm list - tksm sequence --help - + - tksm abundance --help + - tksm model-truncation --help about: home: https://github.com/vpc-ccg/tksm license: MIT + license_family: MIT license_file: LICENSE summary: Very modular, very cool long-read transcriptomic simulator From f2d545b2709983ca4c7e2e615d2e65576321fdb3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 17:58:19 -0500 Subject: [PATCH 0173/1813] Update koverage to 0.1.9 (#45475) --- recipes/koverage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/koverage/meta.yaml b/recipes/koverage/meta.yaml index e9a66d5265d47..a05f96e6afbb5 100644 --- a/recipes/koverage/meta.yaml +++ b/recipes/koverage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "koverage" %} -{% set version = "0.1.8" %} +{% set version = "0.1.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0680e72916022fbedbf14c9dc5daa0e159e41196f81da15b5e9367d93af0832a + sha256: 45e3e3ae21669f0c7a45f023ee130d4494ebc2637c0aa4529e95a3867c4b488a build: noarch: python From fedee050624eef56fc019087d51b9cc3c248e4ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 17:58:39 -0500 Subject: [PATCH 0174/1813] Update ena-webin-cli to 6.10.0 (#45468) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index 98bc27a785056..aa7f4b8f4abec 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.9.0" %} -{% set sha256 = "13218491e3d0dce8b28360606e23ffd54bd491452449c996e7f05944bf352217" %} +{% set version = "6.10.0" %} +{% set sha256 = "3fd887d5fc5a1fbb28060f55e3903051aa9b15cc85cafd5bedb6e2c2645df1c4" %} package: name: ena-webin-cli From 4931809534b56fba3268878f860646f0f3169cf6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 17:59:44 -0500 Subject: [PATCH 0175/1813] Update protgraph to 0.3.10 (#45457) * Update protgraph to 0.3.10 * Add run_exports statement --------- Co-authored-by: Brandon Seah --- recipes/protgraph/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/protgraph/meta.yaml b/recipes/protgraph/meta.yaml index 1837064bfc1d0..49cc0bb70b774 100644 --- a/recipes/protgraph/meta.yaml +++ b/recipes/protgraph/meta.yaml @@ -1,5 +1,5 @@ {% set name = "protgraph" %} -{% set version = "0.3.9" %} +{% set version = "0.3.10" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a1e69aed7dc57c8dcde2a70605a7ed0b39e36bcb03800f0dfecad476cbce143d + sha256: 52d0449eea53c8f113d1287fd5f40e837bf3bd6ed13193974fbd0c3bd358f800 build: number: 0 @@ -15,6 +15,8 @@ build: script: {{ PYTHON }} -m pip install . -vv entry_points: - protgraph=protgraph.protgraph:main + run_exports: + - {{ pin_subpackage('protgraph', max_pin="x.x") }} requirements: host: From 72470362f52c967c817f88aa503d0097c5be73f8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 18:01:00 -0500 Subject: [PATCH 0176/1813] Update nextstrain-cli to 8.0.1 (#45472) --- recipes/nextstrain-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml index ea7189f07bb13..e0bbbca25862b 100644 --- a/recipes/nextstrain-cli/meta.yaml +++ b/recipes/nextstrain-cli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.0.0" %} +{% set version = "8.0.1" %} package: name: nextstrain-cli @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain-cli-{{ version }}.tar.gz - sha256: 515fb4be3c013a9a30ef8cc28d8e7430d20e2edd840a9a3aa3419764b57e8268 + sha256: b552463d4c4195c9b2e57cf20bfc72e9e6927231715d88ebaec13481328fb080 build: number: 0 From 6c8a1789d6f595fb7765e7811d8d878a72b61e5d Mon Sep 17 00:00:00 2001 From: Zak <52193148+zclaas@users.noreply.github.com> Date: Tue, 30 Jan 2024 01:01:28 +0200 Subject: [PATCH 0177/1813] Update bbmap to 39.06 (#45449) * Update bbmap to 39.06 * Copy resources to path without version number for consistency * Added run_exports --- recipes/bbmap/build.sh | 4 ++++ recipes/bbmap/meta.yaml | 12 +++++++----- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/recipes/bbmap/build.sh b/recipes/bbmap/build.sh index e1f2e8a16fe49..3cad42d6b4a27 100755 --- a/recipes/bbmap/build.sh +++ b/recipes/bbmap/build.sh @@ -4,12 +4,16 @@ set -x -e -o pipefail BINARY_HOME=$PREFIX/bin BBMAP_HOME=$PREFIX/opt/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +DATA_HOME=$PREFIX/share/$PKG_NAME mkdir -p $BINARY_HOME mkdir -p $BBMAP_HOME +mkdir -p $DATA_HOME chmod a+x *.sh cp -R * $BBMAP_HOME/ find *.sh -type f -exec ln -s $BBMAP_HOME/{} $BINARY_HOME/{} \; + +cp -R $BBMAP_HOME/resources $DATA_HOME diff --git a/recipes/bbmap/meta.yaml b/recipes/bbmap/meta.yaml index 68499749c3bf0..0ddc96a75784f 100644 --- a/recipes/bbmap/meta.yaml +++ b/recipes/bbmap/meta.yaml @@ -1,9 +1,6 @@ {% set name = "BBMap" %} -{% set version = "39.01" %} -{% set sha256 = "98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6" %} - -build: - number: 1 +{% set version = "39.06" %} +{% set sha256 = "61d45bd59a543b90a143c5c7dbfec0ff6163dce54194b8c4b648fb6aac67d42e" %} package: name: {{ name|lower }} @@ -13,6 +10,11 @@ source: url: http://downloads.sourceforge.net/project/{{ name|lower }}/{{ name }}_{{ version }}.tar.gz sha256: {{ sha256 }} +build: + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + requirements: build: - {{ compiler('c') }} From 1ac8dd7266e005852b2c500859b04c0d179ed221 Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Tue, 30 Jan 2024 00:04:11 +0100 Subject: [PATCH 0178/1813] Update nextclade to 3.0.1 (#45474) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index 1a01d3d0d15c5..2bf851ea44aee 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.0.0" %} +{% set version = "3.0.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: b5f40f1ef809ad17bdb1fe31661b965c861115325ea2d73beadc86550ffccf16 # [linux64] + sha256: 181d0ff48fe09e67f3a1e186ec0f89b15aa08eba779089f7837fc15c7b6501b1 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: a5763a28d4b1da627aac358156923650b3ea21dae1b1c3bbfb5f5e617c2ed3a4 # [osx and x86_64] + sha256: bd21bfb9ae40be1e4a839519718b7127f146b2f8bc831771359844e27ae649f0 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: ce156efb5f5a9ead01ac140d6f701f4b780b224cc64c27cb15a4dcfd13dbdc7a # [arm64] + sha256: 20cebf5b8494645f915dddb24b87540634df31bf321c20ff97a091f85c06932d # [arm64] build: number: 0 From 1a28a6d847e19ac970385090f3953418687e093a Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Mon, 29 Jan 2024 18:07:41 -0500 Subject: [PATCH 0179/1813] Update annembed v0.1.4 (#45458) --- recipes/annembed/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml index 5b9b7bcc27166..8b87e6aa37968 100644 --- a/recipes/annembed/meta.yaml +++ b/recipes/annembed/meta.yaml @@ -26,7 +26,7 @@ test: - annembed -h about: - home: https://github.com/jean-pierreBoth/gsearch + home: https://github.com/jianshu93/annembed license: MIT summary: annembed is an ultra-fast and scalable non-linear dimension reduction algorithm (similar to UMAP or t-SNE) for large-scale biological data From 86d1f45fa2731bb8a3fbdb6ef157b38a04254885 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Tue, 30 Jan 2024 00:12:09 +0100 Subject: [PATCH 0180/1813] Update hictk to v0.0.7 (#45433) * Bump hictk to v0.0.7 * Try to reduce the level of parallelism during build * Update URL * Update checksum * Update patch * Bugfix * Bugfix --- recipes/hictk/build.sh | 2 +- recipes/hictk/conanfile.txt.patch | 14 ++++++++------ recipes/hictk/meta.yaml | 12 +++++++++--- recipes/hictk/run_test.sh | 12 ++++-------- 4 files changed, 22 insertions(+), 18 deletions(-) diff --git a/recipes/hictk/build.sh b/recipes/hictk/build.sh index 81e494d834d06..237a19ba2e1ad 100755 --- a/recipes/hictk/build.sh +++ b/recipes/hictk/build.sh @@ -2,7 +2,7 @@ export CONAN_NON_INTERACTIVE=1 -export CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT} +export CMAKE_BUILD_PARALLEL_LEVEL=1 # ${CPU_COUNT} export CTEST_PARALLEL_LEVEL=${CPU_COUNT} if [[ ${DEBUG_C} == yes ]]; then diff --git a/recipes/hictk/conanfile.txt.patch b/recipes/hictk/conanfile.txt.patch index 05ea419f8ae85..7925b911e0e70 100644 --- a/recipes/hictk/conanfile.txt.patch +++ b/recipes/hictk/conanfile.txt.patch @@ -1,29 +1,31 @@ diff --git a/conanfile.txt b/conanfile.txt -index 0ea6184..eb94f2c 100644 +index c3cfb89..163ff31 100644 --- a/conanfile.txt +++ b/conanfile.txt -@@ -3,72 +3,11 @@ +@@ -3,74 +3,11 @@ # SPDX-License-Identifier: MIT [requires] --boost/1.83.0#7825569cd0622461dec7bc87dfdf47ae +-boost/1.83.0#39551a6ba03b4fe2c7a86b9a6d80cd67 bshoshany-thread-pool/3.5.0#5aaea7ccf37107d3c1ba9ca9ab246e42 +-catch2/3.5.2#9554dc3c4ffcab50daf8f2cac4b79308 -cli11/2.3.2#1424b9b1d9e3682a7122f415b078b4d7 + concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502 -eigen/3.4.0#2e192482a8acff96fe34766adca2b24c -fast_float/6.0.0#6c8a953c57879453982a6ce69c0ba87c --fmt/10.1.1#cd63809a79574a2f9eb73ca35f16a243 +-fmt/10.2.1#9199a7a0611866dea5c8849a77467b25 -hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1 -highfive/2.8.0#b1de99f678ff5699cce6fb5fcac44d2d -libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602 parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7 readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83 span-lite/0.10.3#1967d71abb32b314387c2ab9c558dd22 --spdlog/1.12.0#0e390a2f5c3e96671d0857bc734e4731 +-spdlog/1.13.0#2775cc949e26b339029a852785b6b276 -zstd/1.5.5#b87dc3b185caa4b122979ac4ae8ef7e8 [generators] CMakeDeps - +- -[options] -boost*:system_no_deprecated=True -boost*:asio_no_deprecated=True diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index aaa53c1d48491..2efb3189fdfa5 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.6" %} -{% set sha256 = "5913792f858304ff82996c9e9720442736b443d56c53aa8eb2a1ac2ae8ccc88f" %} +{% set version = "0.0.7" %} +{% set sha256 = "f3aaa80a399074f29747d99f5779d5a8221947044ef6946de3d7b9425d29d415" %} package: name: {{ name|lower }} @@ -22,6 +22,7 @@ requirements: - cmake >=3.25 - conan >=2 - make + - catch2 >=3.5 - cli11 >=2.3 - eigen >=3.4 - fast_float >=5 @@ -53,11 +54,13 @@ test: requires: - curl - cooler>=0.9.3 - - openjdk>=11 - perl-digest-sha1 - xz source_files: - cmake/FetchTestDataset.cmake + - test/scripts/check_test_files_exist.sh + - test/scripts/compare_matrix_files.sh + - test/scripts/compare_plain_files.sh - test/scripts/hictk_balance.sh - test/scripts/hictk_convert_hic2cool.sh - test/scripts/hictk_convert_cool2hic.sh @@ -78,6 +81,9 @@ test: - test/scripts/hictk_rename_chromosomes.sh - test/scripts/hictk_validate.sh - test/scripts/hictk_zoomify.sh + - test/scripts/nproc.sh + - test/scripts/readlink.sh + - test/scripts/shuffle.sh commands: - hictk --help - hictk --version diff --git a/recipes/hictk/run_test.sh b/recipes/hictk/run_test.sh index 045b9c4db17c7..9d039acef9489 100755 --- a/recipes/hictk/run_test.sh +++ b/recipes/hictk/run_test.sh @@ -16,16 +16,12 @@ shasum -c checksum.sha256 tar -xf hictk_test_dataset.tar.xz -# Download hictools -hictools_url='https://github.com/aidenlab/HiCTools/releases/download/v3.30.00/hic_tools.3.30.00.jar' -hictools_sha256='2b09b0642a826ca5730fde74e022461a708caf62ed292bc5baaa841946721867' -curl -L "$hictools_url" -o hic_tools.jar -echo "$hictools_sha256 hic_tools.jar" | tee checksum.sha256 -shasum -c checksum.sha256 - hictk="$(which hictk)" # Run integration tests + +test/scripts/hictk_balance.sh "$hictk" + test/scripts/hictk_dump_chroms.sh "$hictk" test/scripts/hictk_dump_bins.sh "$hictk" test/scripts/hictk_dump_gw.sh "$hictk" @@ -34,7 +30,7 @@ test/scripts/hictk_dump_trans.sh "$hictk" test/scripts/hictk_dump_balanced.sh "$hictk" test/scripts/hictk_convert_hic2cool.sh "$hictk" -test/scripts/hictk_convert_cool2hic.sh "$hictk" hic_tools.jar +test/scripts/hictk_convert_cool2hic.sh "$hictk" test/scripts/hictk_load_coo.sh "$hictk" sorted test/scripts/hictk_load_coo.sh "$hictk" unsorted From 157805204a502139df7018b6efda01d03d7fca84 Mon Sep 17 00:00:00 2001 From: Jody Phelan Date: Tue, 30 Jan 2024 02:31:50 +0000 Subject: [PATCH 0181/1813] add itol-config (#45476) --- recipes/itol-config/meta.yaml | 46 +++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/itol-config/meta.yaml diff --git a/recipes/itol-config/meta.yaml b/recipes/itol-config/meta.yaml new file mode 100644 index 0000000000000..069a6ee5a623a --- /dev/null +++ b/recipes/itol-config/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "itol-config" %} +{% set version = "0.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/jodyphelan/itol-config/archive/v{{ version }}.tar.gz + sha256: e4fb28eb6c434a7a2c823f0d34b86a483c67a7f139e2c18832d564b9b4555bb6 + +build: + number: 0 + noarch: python + entry_points: + - itol-config = itol_config.cli:cli + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('itol-config', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - flit-core >=3.2,<4 + - pip + run: + - python >=3.8 + - tomli + +test: + imports: + - itol_config + commands: + - itol-config --help + +about: + home: https://github.com/jodyphelan/itol-config + license: MIT + license_family: MIT + license_file: LICENSE + doc_url: https://jodyphelan.github.io/itol-config/ + summary: Package to create iTOL config files + +extra: + recipe-maintainers: + - jodyphelan From a175bb82c05bbf3dd2a88c6d6922151b8727ad7a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 03:36:35 -0500 Subject: [PATCH 0182/1813] Update simpleaf to 0.16.1 (#45478) --- recipes/simpleaf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index fa26b7bab51b4..2a135224532ca 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.16.0" %} +{% set version = "0.16.1" %} package: name: simpleaf @@ -12,7 +12,7 @@ build: source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: 1939d27ca19e7e01b951b619aa16d564935227e6f1ea14c8b730dee1faafe26b + sha256: f6204577500063f89c55de9d496c6aeb58ef9048fb5ef8904efaa4f2850b31cc requirements: build: From 241c54998384a2a66fe931786cd621b7cf45c7d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 06:02:32 -0500 Subject: [PATCH 0183/1813] Update snakemake to 8.4.1 (#45483) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 2bd9541d59cd1..5a553102e641a 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.0" %} +{% set version = "8.4.1" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: c875e88c561370c5b545622fe7397cc0d7d2399c285044c83d1309816d0d224f + sha256: 476f1f979b98dc2cd10d774e7e5319262dc2559a4f36013459e94d03e076ab4a build: number: 0 From a159d5692c8e291e328f61ad6f78eea1caa2ff49 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 07:15:19 -0500 Subject: [PATCH 0184/1813] Update varlociraptor to 8.4.4 (#45486) --- recipes/varlociraptor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index a499dd821034d..98b3bb7d447fc 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.3" %} +{% set version = "8.4.4" %} package: name: varlociraptor @@ -11,7 +11,7 @@ build: source: url: https://github.com/varlociraptor/varlociraptor/archive/v{{ version }}.tar.gz - sha256: bbb192ea88f22a85a95273ef425425f2d60686d58ae104c2d182effbd3d61ae9 + sha256: e95294fb7dcefc1f61e26fac3fceedb8355138ff386e5ffd76236f3aea083cb3 requirements: build: From dfb93edd13729c39d3850bfea12bd9bac76a22d0 Mon Sep 17 00:00:00 2001 From: Martin Raden Date: Tue, 30 Jan 2024 13:50:18 +0100 Subject: [PATCH 0185/1813] rebuild locarna 2.0 (#45432) using recent viennarna package --- recipes/locarna/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/locarna/meta.yaml b/recipes/locarna/meta.yaml index 6575d3c121e45..8b20692981d04 100644 --- a/recipes/locarna/meta.yaml +++ b/recipes/locarna/meta.yaml @@ -13,7 +13,9 @@ about: summary: Multiple alignment of RNAs build: - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage('locarna', max_pin="x.x") }} source: url: "https://github.com/s-will/LocARNA/releases/download/v{{ version }}/locarna-{{ version }}.tar.gz" @@ -27,9 +29,9 @@ requirements: - make - {{ compiler('cxx') }} host: - - viennarna =={{ vrnaversion }} + - viennarna >={{ vrnaversion }},<3 run: - - viennarna =={{ vrnaversion }} + - viennarna >={{ vrnaversion }},<3 - perl test: From 92a564b9f9ce6498dbed2e144b97a3fe89b45684 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 09:11:16 -0500 Subject: [PATCH 0186/1813] Update ccsmeth to 0.5.0 (#45490) * Update ccsmeth to 0.5.0 * Update meta.yaml * add run_exports --------- Co-authored-by: Peng Ni <543943952@qq.com> --- recipes/ccsmeth/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/ccsmeth/meta.yaml b/recipes/ccsmeth/meta.yaml index 2d8d97c2f3349..b31d55381a2a0 100644 --- a/recipes/ccsmeth/meta.yaml +++ b/recipes/ccsmeth/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ccsmeth" %} -{% set version = "0.4.1" %} -{% set hash = "783382fc3f3a108d7b1f4de8f60c06a45c049d8de797251d14cadb1ae69b6aa7" %} +{% set version = "0.5.0" %} +{% set hash = "9f6bd61ebf1e7e7a4b6d0690658ccf0a70936faf3229db7998ef3ad6ef3e3a54" %} package: name: "{{ name|lower }}" @@ -16,6 +16,8 @@ build: entry_points: - ccsmeth=ccsmeth.ccsmeth:main script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage("ccsmeth", max_pin="x.x") }} requirements: host: @@ -28,7 +30,7 @@ requirements: - numpy >=1.20.0 - scikit-learn >=1.0.2 - statsmodels >=0.13.2 - - pytorch >=1.2.0,<=1.12.1 + - pytorch >=1.2.0,<=2.1.0 - pysam >=0.19.0 - tqdm >=4.64.0 - bedtools =2.30.0 From f4edfa4bd29d145f44266cff0a0dd7debe69f234 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 11:48:31 -0500 Subject: [PATCH 0187/1813] Update nf-test to 0.8.4 (#45494) --- recipes/nf-test/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-test/meta.yaml b/recipes/nf-test/meta.yaml index 21bcaf9fe3c08..280a8e4979ddd 100644 --- a/recipes/nf-test/meta.yaml +++ b/recipes/nf-test/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.3" %} +{% set version = "0.8.4" %} package: @@ -13,7 +13,7 @@ build: source: url: https://github.com/askimed/nf-test/releases/download/v{{version}}/nf-test-{{version}}.tar.gz - sha256: af48883e8d0cd2d65b0846b3f60a476a5ec28a3799ba9374e0cb307a2a2d634d + sha256: 8023bbe6e354294fba514493f423f80e75869e5daf7e51f4cb808877fdc84381 requirements: host: From f12869924ca32d6be067a6b031c9f3de0e9cfd0c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 11:52:37 -0500 Subject: [PATCH 0188/1813] Update hictk to 0.0.8 (#45479) --- recipes/hictk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index 2efb3189fdfa5..8045e185b4dd9 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.7" %} -{% set sha256 = "f3aaa80a399074f29747d99f5779d5a8221947044ef6946de3d7b9425d29d415" %} +{% set version = "0.0.8" %} +{% set sha256 = "4bdadf49cb053731ea31f50312c9e4fcbcdcbaf94c39715f7b325641629bed4b" %} package: name: {{ name|lower }} From 1189e7ee35e8f86bc186af06b35acd2c15aa7dc4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=A3o=20Sequeira?= Date: Tue, 30 Jan 2024 20:20:29 +0000 Subject: [PATCH 0189/1813] Update mosca (#45485) * Update mosca to 2.3.0 * Add txt files from resources * build.sh removed * Update meta.yaml Updated license name --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> --- recipes/mosca/build.sh | 5 ----- recipes/mosca/meta.yaml | 11 ++++++++--- 2 files changed, 8 insertions(+), 8 deletions(-) delete mode 100644 recipes/mosca/build.sh diff --git a/recipes/mosca/build.sh b/recipes/mosca/build.sh deleted file mode 100644 index 4582f8c0c8704..0000000000000 --- a/recipes/mosca/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -echo "Storing MOSCA's files in the Conda environment at: ${PREFIX}" -mkdir -p "${PREFIX}/share/MOSCA" "${PREFIX}/bin" -cp -r workflow/* resources/*.json "${PREFIX}/share/MOSCA" -chmod +x "${PREFIX}/share/MOSCA/mosca.py" -ln -s "${PREFIX}/share/MOSCA/mosca.py" "${PREFIX}/bin/mosca" diff --git a/recipes/mosca/meta.yaml b/recipes/mosca/meta.yaml index d4ec74195aabd..d5f6fa74f4ac4 100644 --- a/recipes/mosca/meta.yaml +++ b/recipes/mosca/meta.yaml @@ -1,6 +1,6 @@ {% set name = "mosca" %} -{% set version = "2.2.1" %} -{% set sha256 = "c2b66c9cb0d55edf1c452fd23e31965ce9fb45793007521b372a1229ab5ed254" %} +{% set version = "2.3.0" %} +{% set sha256 = "1eba9c082273dd46badd2d5ff8df56aabdc496214e337331d000f54399893a94" %} package: name: {{ name|lower }} @@ -15,6 +15,11 @@ build: number: 0 run_exports: - {{ pin_subpackage("mosca", max_pin="x.x") }} + script: > + mkdir -p $PREFIX/share/MOSCA $PREFIX/bin && + cp -r workflow/* resources/*.json resources/*.txt $PREFIX/share/MOSCA && + chmod +x $PREFIX/share/MOSCA/mosca.py && + ln -s $PREFIX/share/MOSCA/mosca.py $PREFIX/bin/mosca requirements: run: @@ -28,7 +33,7 @@ test: about: home: https://github.com/iquasere/MOSCA - license: GNU General Public License v3 (GPL-3.0) + license: GPL-3.0-or-later license_family: GPL license_file: LICENSE summary: 'MOSCA - Meta-Omics Software for Community Analysis' From 8874e579a5e037f0889346dcd28978ca2ad3da98 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Tue, 30 Jan 2024 16:25:08 -0500 Subject: [PATCH 0190/1813] Update meta.yaml (#45500) Bump piscem to 0.7.1 --- recipes/piscem/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/piscem/meta.yaml b/recipes/piscem/meta.yaml index c8a3c44e6338e..d1158ff26aa29 100644 --- a/recipes/piscem/meta.yaml +++ b/recipes/piscem/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.0" %} -{% set git_commit = "c2b7489018f5b146d7206b3f080ca949cc6427fc" %} +{% set version = "0.7.1" %} +{% set git_commit = "db091893716b1709d97cdf4a8659607e99f5b534" %} {% set sha256 = "a72af2ab728e95aa6766a3bb4520af6273a9ea3be44a6a8dc260cd97615877df" %} package: From a7f487792e5de5acdac2a670db86c7fe181c20e7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 16:25:28 -0500 Subject: [PATCH 0191/1813] Update cyvcf2 to 0.30.28 (#45499) --- recipes/cyvcf2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cyvcf2/meta.yaml b/recipes/cyvcf2/meta.yaml index 26df81e5b90b8..2ebb65713d6f9 100644 --- a/recipes/cyvcf2/meta.yaml +++ b/recipes/cyvcf2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cyvcf2" %} -{% set version = "0.30.27" %} -{% set sha256 = "f1b12c1fb78bd039c5d94b0ff2d838edfa0716c0e4902ad3ecec3d48da3d4ff9" %} +{% set version = "0.30.28" %} +{% set sha256 = "dde7771570e210df9ca6d21c171a8aa376f191966826241fdcdf960befb9cc0f" %} package: name: {{ name }} From f740ea96cd78a988a166f2f3c4cc680df9dcaf82 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 16:25:49 -0500 Subject: [PATCH 0192/1813] Update snakemake to 8.4.2 (#45497) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 5a553102e641a..614c8729ad5bc 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.1" %} +{% set version = "8.4.2" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 476f1f979b98dc2cd10d774e7e5319262dc2559a4f36013459e94d03e076ab4a + sha256: ea9273d7a27706b635fafae87bb21100dad02275570e138fdcff125cb3cba4f4 build: number: 0 From 04e3f0ab6cebcfb29c563f73715cd10f00537ef4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 16:26:13 -0500 Subject: [PATCH 0193/1813] Update gubbins to 3.3.3 (#45495) --- recipes/gubbins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml index 8305801f9caa9..34c62e3484b4a 100644 --- a/recipes/gubbins/meta.yaml +++ b/recipes/gubbins/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gubbins" %} -{% set version = "3.3.1" %} -{% set sha256 = "1794ba37780f1444131f84fa34fb144e709ec1af239c46f7f18636d8b1b73edf" %} +{% set version = "3.3.3" %} +{% set sha256 = "b1d878130a6f07ff133efa55f0d6ed2ec3bcfa64029352ce5050c6a162b9a0b2" %} package: name: {{ name|lower }} From 0b8f8fbb215078847a9676ba10716991c5d688b2 Mon Sep 17 00:00:00 2001 From: Jean Mainguy Date: Tue, 30 Jan 2024 23:32:57 +0100 Subject: [PATCH 0194/1813] update binette to v1.0.0 (#45482) --- recipes/binette/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/binette/meta.yaml b/recipes/binette/meta.yaml index ff3604957f999..f666ea8f6e0f9 100644 --- a/recipes/binette/meta.yaml +++ b/recipes/binette/meta.yaml @@ -1,12 +1,12 @@ {% set name = "Binette" %} -{% set version = "0.1.7" %} +{% set version = "1.0.0" %} package: name: {{ name|lower }} version: {{ version }} source: url: https://github.com/genotoul-bioinfo/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: a3ede9f274e8eec53401ee92727922ff08a8d89116bed411391b5671616e1d1e + sha256: 121cff275fac2bbec2062863fa074c7f4f2a16eb52cada89bc46c87b7429d63d build: noarch: python From c32d39c52172b45748f255c7b1e6d8e7bef489b4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 17:38:20 -0500 Subject: [PATCH 0195/1813] Update ncbi-datasets-pylib to 16.4.4 (#45503) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index cc7f56893916a..ed48d3f17a024 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.3" %} -{% set sha256 = "3155f0ebc388c30208315f253e0e36ea3df1bf83c89c97ea9765386fd3829d5d" %} +{% set version = "16.4.4" %} +{% set sha256 = "34db22fd526188b0c819c1b9487a183c98c33f65ca940876b52e1debb8a8e450" %} package: name: {{ name|lower }} From be67c10e1eca559202f29bb8ce3bd95a80667aed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 18:22:35 -0500 Subject: [PATCH 0196/1813] Update augur to 24.1.0 (#45502) * Update augur to 24.1.0 * Bump minimum bcbio-gff to 0.7.1, biopython 1.80 --------- Co-authored-by: Cornelius Roemer --- recipes/augur/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index c890f6e104b18..9d585bfd5ce39 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.0.0" %} +{% set version = "24.1.0" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: 6766330e7db7d6ceab8256b1f815882fdf3a9dccdeb224f316266d7983f2a407 + sha256: 22d349581fbbdfdcca0df02ce5d093965c9963931ef42c946a63b87d79a7ab08 build: number: 0 @@ -23,13 +23,13 @@ requirements: - pip run: - python >=3.8 - - bcbio-gff >=0.7.0,<0.8 - - biopython >=1.73,!=1.77,!=1.78,<1.82 + - bcbio-gff >=0.7.1,<0.8 + - biopython >=1.80,<2 - cvxopt >=1.1.9,<2 - importlib_resources >=5.3.0 # [py<311] - isodate >=0.6.0,<0.7 - jsonschema >=3.0.0,<4 - - networkx >=2.5, <3 + - networkx >=2.5,<3 - numpy >=1.0.0,<2 - packaging >=19.2 - pandas >=1.0.0,<2 From 01581ac74332e5fec169ed8dc7f9fdf70dd01698 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 31 Jan 2024 09:23:01 +0100 Subject: [PATCH 0197/1813] adjust GitHub org for annonars (#45504) --- recipes/annonars/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 61ae02aad9578..a7e856b889433 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -5,13 +5,13 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("annonars", max_pin="x.x") }} source: - url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz sha256: 8b0725fc8d7e861bc08c96882f6e9e489b5079c10eb723295b26d2100e6e86f9 requirements: @@ -37,7 +37,7 @@ test: - annonars --help about: - home: https://github.com/bihealth/annonars + home: https://github.com/varfish-org/annonars license: Apache-2.0 license_file: LICENSE.txt summary: 'Genome annotation based on Rust and RocksDB.' From afd3833c04120d6c5d3fd30960f288dea8cc8c2d Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 31 Jan 2024 09:23:30 +0100 Subject: [PATCH 0198/1813] move viguno to other org (#45505) --- recipes/viguno/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/viguno/meta.yaml b/recipes/viguno/meta.yaml index aee151869b737..44a32ed9707e4 100644 --- a/recipes/viguno/meta.yaml +++ b/recipes/viguno/meta.yaml @@ -7,12 +7,12 @@ package: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("viguno", max_pin="x.x") }} source: - url: https://github.com/bihealth/viguno/archive/v{{ version }}.tar.gz + url: https://github.com/varfish-org/viguno/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: @@ -38,6 +38,6 @@ test: - viguno -h about: - home: https://github.com/bihealth/viguno + home: https://github.com/bihealth/varfish-org license: MIT summary: Lookup OMIM genes and HPO terms and compute similarities From a5f174cd13ca252558942b640ff5e10082ab64c6 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 31 Jan 2024 09:23:54 +0100 Subject: [PATCH 0199/1813] adjust GitHub org (#45506) --- recipes/mehari/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index c36b6f1c6475a..a9745e92008b9 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -7,12 +7,12 @@ package: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("mehari", max_pin="x.x") }} source: - url: https://github.com/bihealth/mehari/archive/v{{ version }}.tar.gz + url: https://github.com/varfish-org/mehari/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: @@ -38,6 +38,6 @@ test: - mehari -h about: - home: https://github.com/bihealth/mehari + home: https://github.com/bihealth/varfish-org license: MIT summary: VEP-like tool for sequence ontology and HGVS annotation of VCF files written in Rust. From 141f5fd3a2dfb1aa6e207bd735eece07a35fe739 Mon Sep 17 00:00:00 2001 From: Felix Becker Date: Wed, 31 Jan 2024 11:59:22 +0100 Subject: [PATCH 0200/1813] Update learnMSA to version 1.3.4 (#45493) * added run_exports * changed package name to lower case --- recipes/learnmsa/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/learnmsa/meta.yaml b/recipes/learnmsa/meta.yaml index dacfbf73ca0a2..2ddcc263cfca5 100644 --- a/recipes/learnmsa/meta.yaml +++ b/recipes/learnmsa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "learnMSA" %} -{% set version = "1.3.2" %} +{% set version = "1.3.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: da7ec9b5f89685098cbeb272918e9c89f2e67bd6698dbbc7bfa49a036d06d73c + sha256: b942cc9f2c6835f8a067ad647e542fe1f2b12517a4b1b81ac70e120b0385637d build: number: 0 @@ -15,6 +15,8 @@ build: - learnMSA = learnMSA.run:run_main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv" noarch: python + run_exports: + - {{ pin_subpackage('learnmsa', max_pin="x") }} requirements: host: From 76fb4b89843a172a9dc612057bb1b474d7538f8c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 07:13:48 -0500 Subject: [PATCH 0201/1813] Update cellqc to 0.0.7 (#45501) --- recipes/cellqc/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/cellqc/meta.yaml b/recipes/cellqc/meta.yaml index 898e630900d0c..0582defd01a18 100644 --- a/recipes/cellqc/meta.yaml +++ b/recipes/cellqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cellqc" %} -{% set version = "0.0.6" %} +{% set version = "0.0.7" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3da8ed9e2c275626ab2eb2c779cdb8eacf1429fce212357c0dd29c9753e08764 + sha256: d637e51cf5bbe5dae7b3fd8dc85f32af1e8b9c379882351878673bdd3ff6bf6d build: - number: 1 + number: 0 entry_points: - cellqc=cellqc.cellqc:main run_exports: From 34272b928e8da20b72f41e9f316dac08d55a8fe4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 07:14:18 -0500 Subject: [PATCH 0202/1813] Update massdash to 0.0.8 (#45509) --- recipes/massdash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/massdash/meta.yaml b/recipes/massdash/meta.yaml index b3ae8c95452b5..dcbbef4ea0961 100644 --- a/recipes/massdash/meta.yaml +++ b/recipes/massdash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "massdash" %} -{% set version = "0.0.6" %} +{% set version = "0.0.8" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f2b4160745ddcd96698f92c7d9c86b5a354970ace233924a0e26cba88421a761 + sha256: 9e03e23c7f2f9c84c30ba7aef936d2f26b0284b4fa0dd330618e6fd6fb40cbef build: number: 0 From 2bd040eaaa693dc6d167c278a426570da8d9f104 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 07:14:48 -0500 Subject: [PATCH 0203/1813] Update skyline2isocor to 0.1.1 (#45516) --- recipes/skyline2isocor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skyline2isocor/meta.yaml b/recipes/skyline2isocor/meta.yaml index 3abfb9f8be2a4..cd67bddec37b2 100644 --- a/recipes/skyline2isocor/meta.yaml +++ b/recipes/skyline2isocor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skyline2isocor" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/skyline2isocor-{{ version }}.tar.gz - sha256: 9bf2b6a8c381ced3a5a24838d944bfff016a12c7da6f3627ff31467918e609bc + sha256: 276d9ced9a3f69c9692a7803ec3cd84f16466aac1bbab9ec4c827ea599db7f8e build: entry_points: From dec70b86a40ce20f88f888d04b05e5d995d9f1ac Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 07:16:16 -0500 Subject: [PATCH 0204/1813] Update earlgrey to 4.0.6 (#45515) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index 268616558bed9..19c3246edd5ab 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.5" %} -{% set sha256 = "5fe1341dad3da2bf322415cb048a846173e386b1998be188828f3c905349daa8" %} +{% set version = "4.0.6" %} +{% set sha256 = "bc4ba13a2f7cf10ef6eedec17529bf8e191ecdd81d85d9db8a788467e282d655" %} package: name: {{ name|lower }} From 8725ab727920cbb493231ff105f0a0ec7e34ed22 Mon Sep 17 00:00:00 2001 From: Jesus Garcia Garcia <44952878+garci1294@users.noreply.github.com> Date: Wed, 31 Jan 2024 06:19:32 -0600 Subject: [PATCH 0205/1813] Update bioconductor-infercnv (#45481) * Update meta.yaml `htmltools >=0.5.7' package is required by infercnv. * increased build no --------- Co-authored-by: Thanh Lee --- recipes/bioconductor-infercnv/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-infercnv/meta.yaml b/recipes/bioconductor-infercnv/meta.yaml index 846a226731767..cca8ee52d9314 100644 --- a/recipes/bioconductor-infercnv/meta.yaml +++ b/recipes/bioconductor-infercnv/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d5bce5518c27e86b3fb26b6fedad5d7b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -27,6 +27,7 @@ requirements: - 'bioconductor-edger >=4.0.0,<4.1.0' - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'r-htmltools >=0.5.7' - r-ape - r-argparse - r-base @@ -61,6 +62,7 @@ requirements: - 'bioconductor-edger >=4.0.0,<4.1.0' - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'r-htmltools >=0.5.7' - r-ape - r-argparse - r-base From c28bc3f191ae496792cee82559e7340cf18935f4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 12:15:19 -0500 Subject: [PATCH 0206/1813] Update zol to 1.3.18 (#45519) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index ce26b14a3821b..b2c6b239d2e12 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.17" %} +{% set version = "1.3.18" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 71205d5144d4489d863d63dd0e4eb5b4341e66b71bf4bc7fc186e9bed98fa17b + sha256: 7c5a9693a0ca4225581b8f31da73b154d415067c5619a882a7b1d6b99efdc6f7 build: number: 0 From 92ea1f11a4010802670dcd93313c992eb7173368 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 16:48:45 -0500 Subject: [PATCH 0207/1813] Update gw to 0.9.3 (#45525) --- recipes/gw/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gw/meta.yaml b/recipes/gw/meta.yaml index 7bf6ab483b790..b76079b337bc9 100644 --- a/recipes/gw/meta.yaml +++ b/recipes/gw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.9.1" %} -{% set sha256 = "10a65107717811179a124e8bac5b2f202bdbde6679a9e6eb67ef97c990b7cf9d" %} +{% set version = "0.9.3" %} +{% set sha256 = "43445ef6d96bd8a09a9a45cd18e21481d7fefe7e9ab26aec4abd8d1f4bff3fcd" %} package: name: gw From ecfa9e5f9c719572017ec3b8340e553246ee233a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 16:52:12 -0500 Subject: [PATCH 0208/1813] Update skyline2isocor to 0.1.2 (#45520) --- recipes/skyline2isocor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skyline2isocor/meta.yaml b/recipes/skyline2isocor/meta.yaml index cd67bddec37b2..a888d3d122ba4 100644 --- a/recipes/skyline2isocor/meta.yaml +++ b/recipes/skyline2isocor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skyline2isocor" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/skyline2isocor-{{ version }}.tar.gz - sha256: 276d9ced9a3f69c9692a7803ec3cd84f16466aac1bbab9ec4c827ea599db7f8e + sha256: de1516845912f31ecb84ddd19c28f3ff6f6db2dd11ca834a42424276d795ec74 build: entry_points: From b56b05b25f7110b1c187a5d186308d967f76b898 Mon Sep 17 00:00:00 2001 From: Mingfu Shao Date: Wed, 31 Jan 2024 16:57:17 -0500 Subject: [PATCH 0209/1813] terrace (#45526) * init for coral * update meta * Update meta.yaml * add recipes for aletsch * Update meta.yaml * update meta.yaml * Create build.sh for TERRACE * Create meta.yaml --------- Co-authored-by: Devon Ryan --- recipes/terrace/build.sh | 5 +++++ recipes/terrace/meta.yaml | 41 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/terrace/build.sh create mode 100644 recipes/terrace/meta.yaml diff --git a/recipes/terrace/build.sh b/recipes/terrace/build.sh new file mode 100644 index 0000000000000..7a0d70011ef7a --- /dev/null +++ b/recipes/terrace/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +./configure --prefix=$PREFIX +make LIBS+=-lhts +make install diff --git a/recipes/terrace/meta.yaml b/recipes/terrace/meta.yaml new file mode 100644 index 0000000000000..136afdf510081 --- /dev/null +++ b/recipes/terrace/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "terrace" %} +{% set version = "1.1.1" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: "https://github.com/Shao-Group/TERRACE/releases/download/v{{ version }}/terrace-{{ version }}.tar.gz" + sha256: "2014bce67e6d05cf7c71ba16033f044c7043dc60217ca390741cff8818538664" + +build: + number: 0 + run_exports: + - {{ pin_subpackage('terrace', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - htslib + - boost-cpp + run: + - htslib + - boost-cpp + +test: + commands: + - terrace --help + +about: + home: "https://github.com/Shao-Group/TERRACE" + license: BSD-3-Clause + license_file: LICENSE + summary: "TERRACE is an assembler for circular RNAs." + +extra: + recipe-maintainers: + - shaomingfu From 3a4da82a05bd8f5167475c5b8f4d5f1daf9969a4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 17:15:58 -0500 Subject: [PATCH 0210/1813] Update varcode to 1.2.0 (#45498) * Update varcode to 1.2.0 * add run_exports --------- Co-authored-by: mencian --- recipes/varcode/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/varcode/meta.yaml b/recipes/varcode/meta.yaml index 01e085d867ed8..061bbf466712d 100644 --- a/recipes/varcode/meta.yaml +++ b/recipes/varcode/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varcode" %} -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ed2c81a322e13f4b9fcfc15fc1dba87dbeef8ab4cd808f22188ec67db9159512 + sha256: e3ae050bf772fca49417044f7dfc5f68c373b11ace7afea106d4f35b4721091f build: number: 0 @@ -15,7 +15,9 @@ build: entry_points: - varcode-genes = varcode.cli.genes_script:main - varcode = varcode.cli.effects_script:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('varcode', max_pin="x") }} requirements: host: @@ -44,8 +46,9 @@ test: about: home: "https://github.com/openvax/varcode" - license: Apache Software + license: Apache-2.0 license_family: APACHE + license_file: LICENSE summary: "Variant annotation in Python" extra: From 7077907b2647791ef63abf19fc81867c521609a6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 17:26:02 -0500 Subject: [PATCH 0211/1813] Update diamond to 2.1.9 (#45518) * Update diamond to 2.1.9 * add run_exports --------- Co-authored-by: mencian --- recipes/diamond/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/diamond/meta.yaml b/recipes/diamond/meta.yaml index 0fe8f5553d59f..d35213fa65257 100644 --- a/recipes/diamond/meta.yaml +++ b/recipes/diamond/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.1.8" %} -{% set sha256 = "b6088259f2bc92d1f9dc4add44590cff68321bcbf91eefbc295a3525118b9415" %} +{% set version = "2.1.9" %} +{% set sha256 = "4cde9df78c63e8aef9df1e3265cd06a93ce1b047d6dba513a1437719b70e9d88" %} package: name: diamond @@ -11,6 +11,8 @@ source: build: number: 0 + run_exports: + - {{ pin_subpackage('diamond', max_pin="x") }} requirements: build: @@ -32,10 +34,11 @@ test: about: home: https://github.com/bbuchfink/diamond - license: GPL-3.0 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Accelerated BLAST compatible local sequence aligner + doc_url: https://github.com/bbuchfink/diamond/wiki extra: identifiers: From c6741cea8182caa1d4735fbb7327d47e4f84db3d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 19:32:07 -0500 Subject: [PATCH 0212/1813] Update ephemeris to 0.10.9 (#45523) * Update ephemeris to 0.10.9 * add run_exports * edit tests --------- Co-authored-by: mencian --- recipes/ephemeris/meta.yaml | 51 ++++++++++++++++++++++++------------- 1 file changed, 33 insertions(+), 18 deletions(-) diff --git a/recipes/ephemeris/meta.yaml b/recipes/ephemeris/meta.yaml index 23825c1b8f8f3..7afc256a6fbd3 100644 --- a/recipes/ephemeris/meta.yaml +++ b/recipes/ephemeris/meta.yaml @@ -1,42 +1,53 @@ +{% set name = "ephemeris" %} +{% set version = "0.10.9" %} + package: - name: ephemeris - version: "0.10.8" + name: {{ name }} + version: {{ version }} source: - url: https://files.pythonhosted.org/packages/92/56/0544ef43ecb994e543a81f68bbe65dd0ccaf1a21eaa3706a75190f4ba256/ephemeris-0.10.8.tar.gz - sha256: dd19c739ddb83ffbfa7d23b63e979f26602af2282c21a799cc52ea4342d62d37 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ephemeris-{{ version }}.tar.gz + sha256: fdc09b71f902f638fb74bbb1a4b22fcaf76869c4aa3ec6739c4be25c856e45b7 build: number: 0 noarch: python - preserve_egg_dir: True entry_points: - - get-tool-list=ephemeris.get_tool_list_from_galaxy:main - - shed-tools=ephemeris.shed_tools:main - - workflow-install=ephemeris.workflow_install:main - - run-data-managers=ephemeris.run_data_managers:main - - workflow-to-tools=ephemeris.generate_tool_list_from_ga_workflow_files:main - - setup-data-libraries=ephemeris.setup_data_libraries:main - - galaxy-wait=ephemeris.sleep:main - script: python -m pip install --no-deps --ignore-installed . + - get-tool-list = ephemeris.get_tool_list_from_galaxy:main + - shed-tools = ephemeris.shed_tools:main + - workflow-install = ephemeris.workflow_install:main + - run-data-managers = ephemeris.run_data_managers:main + - workflow-to-tools = ephemeris.generate_tool_list_from_ga_workflow_files:main + - setup-data-libraries = ephemeris.setup_data_libraries:main + - galaxy-wait = ephemeris.sleep:main + - install_tool_deps = ephemeris.install_tool_deps:main + - install-tool-deps = ephemeris.install_tool_deps:main + - set-library-permissions = ephemeris.set_library_permissions:main + - _idc-lint = ephemeris._idc_lint:main + - _idc-split-data-manager-genomes = ephemeris._idc_split_data_manager_genomes:main + - _idc-data-managers-to-tools = ephemeris._idc_data_managers_to_tools:main + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + run_exports: + - {{ pin_subpackage('ephemeris', max_pin="x.x") }} requirements: host: - - python + - python >=3.7 - pip run: - - python + - python >=3.7 - pyyaml - six >=1.9.0 - bioblend >=0.10.0 - jinja2 - - galaxy-tool-util >=20.5.0 - - galaxy-util >=20.5.0 + - galaxy-tool-util >=20.9.1 + - galaxy-util >=20.9.0 + - pysam + - rich test: imports: - ephemeris - commands: - get-tool-list --help - shed-tools --help @@ -45,9 +56,13 @@ test: - workflow-to-tools --help - setup-data-libraries --help - galaxy-wait --help + - install_tool_deps --help + - install-tool-deps --help + - set-library-permissions --help about: home: https://github.com/galaxyproject/ephemeris license: Academic Free License (AFL) summary: 'Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows.' license_family: OTHER + doc_url: https://ephemeris.readthedocs.io/en/latest/ From ed4cdc6e6574d4151f207498c5115ed41b132457 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 22:00:52 -0500 Subject: [PATCH 0213/1813] Update dnaapler to 0.6.0 (#45533) --- recipes/dnaapler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index 699f0fa47dae3..3417697c03deb 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.5.2" %} +{% set version = "0.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 3e0a03afdf00c20943892184062d9b778d3d8b2b549605a69c883a8f5e68e946 + sha256: b68c138bf11285f5f09add09ae44e5342c8809ce349a1bce6446d8e64f06510d build: number: 0 From 41e120f935899d8d5fed945290c904ea4e40c75e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 23:20:27 -0500 Subject: [PATCH 0214/1813] Update snakefmt to 0.10.0 (#45529) * Update snakefmt to 0.10.0 * Update black version --------- Co-authored-by: Michael Hall --- recipes/snakefmt/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/snakefmt/meta.yaml b/recipes/snakefmt/meta.yaml index 399a36ceda420..a86a8e347327b 100644 --- a/recipes/snakefmt/meta.yaml +++ b/recipes/snakefmt/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9.0" %} +{% set version = "0.10.0" %} package: name: snakefmt @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/s/snakefmt/snakefmt-{{ version }}.tar.gz - sha256: 54c78050edead20cea5f87a6c9674ee1b5e4e38faac2852b45d0650faf9cb319 + sha256: 53eae69fc81425e2192684eba76171bd648b05dcba93c9d5f45746d3fadb8617 build: - number: 1 + number: 0 noarch: python entry_points: - snakefmt = snakefmt.snakefmt:main @@ -19,14 +19,14 @@ build: requirements: host: - - black >=23.12.1,<24.0 + - black >=24.1,<25.0 - click >=8.0.0,<9.0.0 - pip - python >=3.8 - toml >=0.10.2,<0.11.0 - poetry >=1.3,<2.0 run: - - black >=23.12.1,<24.0 + - black >=24.1,<25.0 - click >=8.0.0,<9.0.0 - python >=3.8 - toml >=0.10.2,<0.11.0 From 36b3432e1507d90e1bb95753f8b817f3b6fd0442 Mon Sep 17 00:00:00 2001 From: Daniel DW Kim <49298377+endixk@users.noreply.github.com> Date: Thu, 1 Feb 2024 14:09:07 +0900 Subject: [PATCH 0215/1813] Update ezaai to 1.2.3 (#45531) * Update ezaai to 1.2.3 * add run_exports * improve exec command * posix sh * heredoc * heredoc style script writer --- recipes/ezaai/build.sh | 10 +++++++--- recipes/ezaai/meta.yaml | 10 ++++++---- 2 files changed, 13 insertions(+), 7 deletions(-) diff --git a/recipes/ezaai/build.sh b/recipes/ezaai/build.sh index 125996f06d360..1c8fd24997d5c 100644 --- a/recipes/ezaai/build.sh +++ b/recipes/ezaai/build.sh @@ -2,7 +2,8 @@ EZ_AAI_JAR_NAME="EzAAI.jar" EZ_AAI_LICENSE="LICENSE.md" -EZ_AAI_BIN="${PREFIX}/bin/EzAAI" +EZ_AAI_BIN="${PREFIX}/bin/ezaai" +EZ_AAI_BIN_ALT="${PREFIX}/bin/EzAAI" # Copy the JAR to the resource directory TARGET="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}" @@ -12,6 +13,9 @@ cp "${EZ_AAI_LICENSE}" "${TARGET}" # Alias the JAR in the bin directory mkdir -p "${PREFIX}/bin" -echo '#!/usr/bin/env bash' > "${EZ_AAI_BIN}" -echo "java -jar ${TARGET}/${EZ_AAI_JAR_NAME} \$@" >> "${EZ_AAI_BIN}" +cat << EOF > "${EZ_AAI_BIN}" +#!/bin/sh +exec java -jar "${TARGET}/${EZ_AAI_JAR_NAME}" "\${@}" +EOF chmod +x "${EZ_AAI_BIN}" +cp "${EZ_AAI_BIN}" "${EZ_AAI_BIN_ALT}" diff --git a/recipes/ezaai/meta.yaml b/recipes/ezaai/meta.yaml index f2ac8a0971924..c3376bf7614bf 100644 --- a/recipes/ezaai/meta.yaml +++ b/recipes/ezaai/meta.yaml @@ -1,16 +1,18 @@ {% set name = "EzAAI" %} -{% set version = "1.2.2" %} -{% set sha256 = "657f2b131e2564f291ef22417cabcd6615cdf88c59f3c553ceccd3ea3b86e564" %} +{% set version = "1.2.3" %} +{% set sha256 = "dbf2433928edb223f5fb6c105e3a32ae7784bac7f2ab506a5d9470d13d240332" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/endixk/ezaai/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/endixk/ezaai/releases/download/v{{ version }}/ezaai-bin.tar.gz sha256: {{ sha256 }} build: + run_exports: + - {{ pin_subpackage('ezaai', max_pin="x") }} noarch: generic number: 0 @@ -24,7 +26,7 @@ requirements: test: commands: - - EzAAI -h + - ezaai -h about: home: http://leb.snu.ac.kr/ezaai From ef75a1c65b032023a26ae5c9e4c70102489fbe5a Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Thu, 1 Feb 2024 07:54:50 +0000 Subject: [PATCH 0216/1813] Update SeqKit to v2.7.0 (#45527) --- recipes/seqkit/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index 845a461c51f7a..a3be4a4ee909e 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.6.1" %} +{% set version = "2.7.0" %} package: name: seqkit @@ -6,10 +6,10 @@ package: source: url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx] - md5: c3596d65d5fa973a7c65485a97d735ac # [osx] + md5: 2d0bd16060b100c90abd216eaf6c9947 # [osx] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux] - md5: c48e7806a03cb9e3f2c1a091c9113908 # [linux] + md5: 78311f53ecebbcd4acd5455ae46debbe # [linux] build: number: 0 From d374041c96695cd8acb2ac4bbfc62cc6bd2132b2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 1 Feb 2024 09:06:16 +0100 Subject: [PATCH 0217/1813] update chromograph (#45521) --- recipes/chromograph/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/chromograph/meta.yaml b/recipes/chromograph/meta.yaml index 17ef1fb5263cb..559bb6398e177 100644 --- a/recipes/chromograph/meta.yaml +++ b/recipes/chromograph/meta.yaml @@ -7,8 +7,10 @@ package: build: noarch: python - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('chromograph', max_pin="x.x") }} source: url: https://github.com/Clinical-Genomics/chromograph/archive/refs/tags/v{{version}}.tar.gz @@ -16,11 +18,11 @@ source: requirements: host: - - python >=3.7,<3.10 + - python ==3.9 - pip run: - - python >=3.7,<3.10 - - matplotlib-base + - python ==3.9 + - matplotlib-base ==3.5.3 - numpy >=1.15 - pyaml - pandas From 69e0b05bdc83350c4744458013940d9a24d77b42 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 03:08:54 -0500 Subject: [PATCH 0218/1813] Update annonars to 0.34.1 (#45539) --- recipes/annonars/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index a7e856b889433..49388dd1ed49a 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,18 +1,18 @@ -{% set version = "0.34.0" %} +{% set version = "0.34.1" %} package: name: annonars version: {{ version }} build: - number: 1 + number: 0 skip: True # [osx] run_exports: - {{ pin_subpackage("annonars", max_pin="x.x") }} source: url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8b0725fc8d7e861bc08c96882f6e9e489b5079c10eb723295b26d2100e6e86f9 + sha256: 55f4d7fff2f94eaf94e7752a426ee2532f88ffb25a0d2bb0cf0b4127212bf3e1 requirements: build: From ff9bedc4590254bfe279b72fe1dc32ff6b4c3d09 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 03:53:33 -0500 Subject: [PATCH 0219/1813] Update simpleaf to 0.16.2 (#45536) Co-authored-by: Rob Patro --- recipes/simpleaf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index 2a135224532ca..3d1763a882e62 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.16.1" %} +{% set version = "0.16.2" %} package: name: simpleaf @@ -12,7 +12,7 @@ build: source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: f6204577500063f89c55de9d496c6aeb58ef9048fb5ef8904efaa4f2850b31cc + sha256: e35fb2773b3f4f158d23ebc6d0b51aed29ea54206a3c57a56931325e67add720 requirements: build: From 5c684130abd8bff421d387ce00a387b959bde138 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:43:32 -0500 Subject: [PATCH 0220/1813] Update gget to 0.28.4 (#45530) --- recipes/gget/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gget/meta.yaml b/recipes/gget/meta.yaml index fa18fdcf7a298..f47038aae5141 100644 --- a/recipes/gget/meta.yaml +++ b/recipes/gget/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gget" %} -{% set version = "0.28.3" %} -{% set sha256 = "4f9e2f3e445b7e898e1a12fa7460604330e73d917c8e357a91a09c0c005b64b9" %} +{% set version = "0.28.4" %} +{% set sha256 = "bab45530f72b189b233a72be20421176fbc4ca7ed407e36eec758086c2cda7c6" %} package: name: "{{ name|lower }}" From 4fca4ee7760cd186ae5b357d1838f800b0979093 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:44:09 -0500 Subject: [PATCH 0221/1813] Update hecatomb to 1.3.0 (#45537) * Update hecatomb to 1.3.0 * Update meta.yaml lint fix and update run dependencies * Update meta.yaml --------- Co-authored-by: Michael Roach --- recipes/hecatomb/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/hecatomb/meta.yaml b/recipes/hecatomb/meta.yaml index 52fb463a7f9b2..b5783bce3c181 100644 --- a/recipes/hecatomb/meta.yaml +++ b/recipes/hecatomb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "Hecatomb" %} -{% set version = "1.2.0" %} +{% set version = "1.3.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,13 @@ package: source: url: "https://github.com/shandley/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 20da6871131a01222d4374194188f766bfdd3ab164ab4dbdd4307db0b80341a7 + sha256: ad53c9ab16b9db9a8d6bff2874c96727cffd030d3f5f8d7213496248a8f3659e build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('hecatomb', max_pin='x.x') }} script: "{{ PYTHON }} -m pip install . -vv " requirements: @@ -19,12 +21,13 @@ requirements: - python - pip run: - - python >=3.8,<3.11 - - snakemake >=7.14.0 + - python >=3.9,<=3.12 + - snakemake >=7.14.0,<8 + - pulp <2.8 - pyyaml >=6.0 - click >=8.1.3 - - jinja2 >=3.0.2 - - mamba >=0.15.3 + - metasnek >=0.0.7 + - snaketool-utils >=0.0.4 test: commands: From dbdb712172f6a1775d0ab14894f29edb28ee03c2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:45:16 -0500 Subject: [PATCH 0222/1813] Update mehari to 0.21.2 (#45540) --- recipes/mehari/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index a9745e92008b9..91cc370330ddc 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.21.1" %} -{% set sha256 = "6dcdd453ca44a531e4b4903ebf32921707bebe9d51f389a463dc2df3b3042f12" %} +{% set version = "0.21.2" %} +{% set sha256 = "37fc1ef33d8d7f49886312283ac1e4009fba92db40e254cb03356e0e6f643774" %} package: name: mehari @@ -7,7 +7,7 @@ package: build: skip: True # [osx] - number: 1 + number: 0 run_exports: - {{ pin_subpackage("mehari", max_pin="x.x") }} From d9d3ca8e14f29ba21fd9d38f631ad77f678e1b11 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:45:29 -0500 Subject: [PATCH 0223/1813] Update viguno to 0.2.1 (#45538) --- recipes/viguno/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/viguno/meta.yaml b/recipes/viguno/meta.yaml index 44a32ed9707e4..cfeec69d90f06 100644 --- a/recipes/viguno/meta.yaml +++ b/recipes/viguno/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.0" %} -{% set sha256 = "a4217f7ba34d55cda76b392e774be8392c18d550e752eb9db81e6cc3afa53010" %} +{% set version = "0.2.1" %} +{% set sha256 = "00da4730a4dd63b05eeb8e7ae0b58ba829e7145cc41f0f9194470376f367b937" %} package: name: viguno @@ -7,7 +7,7 @@ package: build: skip: True # [osx] - number: 1 + number: 0 run_exports: - {{ pin_subpackage("viguno", max_pin="x.x") }} From baa036827d75cf30ad07aa84397f9cd4fd1d4773 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:46:21 -0500 Subject: [PATCH 0224/1813] Update skyline2isocor to 0.2.0 (#45541) --- recipes/skyline2isocor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skyline2isocor/meta.yaml b/recipes/skyline2isocor/meta.yaml index a888d3d122ba4..ce4c92b00b71e 100644 --- a/recipes/skyline2isocor/meta.yaml +++ b/recipes/skyline2isocor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skyline2isocor" %} -{% set version = "0.1.2" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/skyline2isocor-{{ version }}.tar.gz - sha256: de1516845912f31ecb84ddd19c28f3ff6f6db2dd11ca834a42424276d795ec74 + sha256: 7f8e122e4ffe2cb66d02fe1d5ee06d97846d120ffb4987ed46075f0267784796 build: entry_points: From 43779810e4183436745d24545d3d49999359fd9f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:46:48 -0500 Subject: [PATCH 0225/1813] Update scirpy to 0.16.0 (#45545) --- recipes/scirpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml index 91d97a5982193..fd3cf450186d3 100644 --- a/recipes/scirpy/meta.yaml +++ b/recipes/scirpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scirpy" %} -{% set version = "0.15.0" %} +{% set version = "0.16.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 4b0e5ce9fa8a874f0dd502a9493d9201dd6afc673512ab0287644a98c77b3744 + sha256: 169d71fcb26da1adac33be0e30541eb09ed9ae32d484f16a194c2fa07bf9a4fb folder: "{{ name }}-{{ version }}" build: From 5d3b7b4234476c7e29a1c3f702a8d7ba033078b2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:47:34 -0500 Subject: [PATCH 0226/1813] Update sevenbridges-python to 2.10.2 (#45546) --- recipes/sevenbridges-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index 7bdcd4c93f64a..34b191fef1cfc 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.10.1" %} -{% set sha256 = "5db46a3fce7b0235be9273ec070092775be43e4bb1b2787c349f3598eaa3fd07" %} +{% set version = "2.10.2" %} +{% set sha256 = "4402b7b874f97532c5156a68b45ebb9554a774ffd182ef346876cca83db791a9" %} package: name: sevenbridges-python From 23f0b894e08ea772317e214e8d850fa31978068a Mon Sep 17 00:00:00 2001 From: Kez Cleal <42997789+kcleal@users.noreply.github.com> Date: Thu, 1 Feb 2024 10:48:52 +0000 Subject: [PATCH 0227/1813] GW v0.9.3 (#45524) From de35024a3260408cf5c26835062338040facfc7b Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Thu, 1 Feb 2024 02:50:16 -0800 Subject: [PATCH 0228/1813] Update ntLink build (#45522) --- recipes/ntlink/meta.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/recipes/ntlink/meta.yaml b/recipes/ntlink/meta.yaml index 609bc60ac8087..f67d1d7829657 100644 --- a/recipes/ntlink/meta.yaml +++ b/recipes/ntlink/meta.yaml @@ -9,20 +9,18 @@ source: sha256: 3a6fe7ca9c7a0226cf51b7e55804e235ac2b959e82a30f9bce55b9caea5bb03b build: - number: 2 - skip: True # [py<38 or py > 39] + number: 3 + noarch: generic run_exports: - {{ pin_subpackage('ntlink', max_pin="x") }} requirements: - build: - - {{ compiler('cxx') }} host: - make - python - pip - zlib - - btllib <=1.4.10 + - btllib run: - python - zlib From a5c2cca435217738d5d67c0ae93a9ed8f5ed34af Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 1 Feb 2024 12:36:30 +0100 Subject: [PATCH 0229/1813] Update MALT to 0.62 (#45193) * Update meta.yaml * Update build.sh * Add run_exports * Apply suggestions from code review --- recipes/malt/build.sh | 4 ++-- recipes/malt/meta.yaml | 8 +++++--- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/malt/build.sh b/recipes/malt/build.sh index 49b33d38c0310..61ca8fc5e25e0 100755 --- a/recipes/malt/build.sh +++ b/recipes/malt/build.sh @@ -1,9 +1,9 @@ #!/bin/bash # call installer -chmod u+x MALT_unix_0_6_1.sh +chmod u+x MALT_unix_0_6_2.sh MALT="$PREFIX/opt/$PKG_NAME-$PKG_VERSION" -./MALT_unix_0_6_1.sh -q -dir "$MALT" +./MALT_unix_0_6_2.sh -q -dir "$MALT" ln -s "$MALT"/malt-build "$PREFIX"/bin/malt-build ln -s "$MALT"/malt-run "$PREFIX"/bin/malt-run diff --git a/recipes/malt/meta.yaml b/recipes/malt/meta.yaml index 154885195a594..28c4fe7bffb80 100755 --- a/recipes/malt/meta.yaml +++ b/recipes/malt/meta.yaml @@ -1,12 +1,14 @@ package: name: malt - version: 0.61 # Keep without patch release decimal. Versioning style changed in 0.5 causing latest-version sorting problems when installing from bioconda. + version: 0.62 # Keep without patch release decimal. Versioning style changed in 0.5 causing latest-version sorting problems when installing from bioconda. build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage("malt", max_pin="x.x") }} source: - md5: 41573f8c652fc81f3745729dee2d5e2d - url: https://software-ab.informatik.uni-tuebingen.de/download/malt/MALT_unix_0_6_1.sh + md5: 3e9b7516c722ca959d92722bea209b04 + url: https://maira.cs.uni-tuebingen.de/download/malt/MALT_unix_0_6_2.sh requirements: build: - openjdk From 99ab6d8a9979e5932a2db9fa36e8f2ea4bd94fb2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 06:47:17 -0500 Subject: [PATCH 0230/1813] Update nf-core to 2.12.1 (#45547) --- recipes/nf-core/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index c5f20958f1b84..bdfc0e175394a 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nf-core" %} -{% set version = "2.12" %} -{% set sha256 = "a1af4ad7407cc7b65097b066e2593bdfc302b4c61301dd7476c2203924e92e46" %} +{% set version = "2.12.1" %} +{% set sha256 = "29503365111d5f760fe178cb0db317f9196af5340e649e68e345eb06c95be211" %} package: name: {{ name|lower }} From b6f2803233497d9a3951391fcf24cbc746ede21f Mon Sep 17 00:00:00 2001 From: Marco Matthies <71844+marcom@users.noreply.github.com> Date: Thu, 1 Feb 2024 13:41:08 +0100 Subject: [PATCH 0231/1813] Update linearfold to 1.0.1.dev20220829 (#45470) * Update linearfold to 1.0.1.dev20220829 This is a release from the last commit on github from 2022-08-29, git-sha1 c3ee9bd80c06c2fc39a7bb7ae5e77b9566227cac. Changes since the last release 1.0 (my summary): - driver script works with python3 - fixes for dangles - SHAPE support - other bugfixes There hasn't yet been an upstream release that doesn't require python2 for the driver script, making it difficult to use the package with other packages depending on python3. Upstream issue: https://github.com/LinearFold/LinearFold/issues/14 * Add missing run_exports line * Try and fix linting issues * Simplify version string to try and fix post-build error --- ...IX-command-broken-with-symbolic-link.patch | 22 +++++-------------- recipes/linearfold/meta.yaml | 13 ++++++----- 2 files changed, 13 insertions(+), 22 deletions(-) diff --git a/recipes/linearfold/0001-FIX-command-broken-with-symbolic-link.patch b/recipes/linearfold/0001-FIX-command-broken-with-symbolic-link.patch index 3709632b08a68..2efbe34655620 100644 --- a/recipes/linearfold/0001-FIX-command-broken-with-symbolic-link.patch +++ b/recipes/linearfold/0001-FIX-command-broken-with-symbolic-link.patch @@ -1,25 +1,13 @@ -From bb95a8f98b874fb9061c5ee1b3178f4d40f96416 Mon Sep 17 00:00:00 2001 -From: Fabien Pertuy -Date: Fri, 21 May 2021 09:23:34 +0000 -Subject: [PATCH] FIX command broken with symbolic link - ---- - linearfold | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - diff --git a/linearfold b/linearfold -index f5541d2..2c86b63 100755 +index fca4a30..7e68544 100755 --- a/linearfold +++ b/linearfold -@@ -28,7 +28,7 @@ def main(): - zuker_subopt = '1' if FLAGS.zuker else '0' - delta = str(FLAGS.delta) +@@ -38,7 +38,7 @@ def main(): + + dangles = str(FLAGS.dangles) - path = os.path.dirname(os.path.abspath(__file__)) + path = os.path.dirname(os.path.realpath(__file__)) - cmd = ["%s/%s" % (path, ('bin/linearfold_v' if use_vienna else 'bin/linearfold_c')), beamsize, is_sharpturn, is_verbose, is_eval, is_constraints, zuker_subopt, delta] + cmd = ["%s/%s" % (path, ('bin/linearfold_v' if use_vienna else 'bin/linearfold_c')), beamsize, is_sharpturn, is_verbose, is_eval, is_constraints, zuker_subopt, delta, shape_file_path, is_fasta, dangles] subprocess.call(cmd, stdin=sys.stdin) --- -2.30.2 - diff --git a/recipes/linearfold/meta.yaml b/recipes/linearfold/meta.yaml index 68bd8d83073a7..62e614174d93e 100644 --- a/recipes/linearfold/meta.yaml +++ b/recipes/linearfold/meta.yaml @@ -1,17 +1,20 @@ {% set name = "LinearFold" %} -{% set version = "1.0" %} -{% set sha256 = "2ae56b5f183472c2de96782e770a91e57f82e0ab511dfc0d9d612aa4e6155f60" %} +{% set git_sha1 = "c3ee9bd80c06c2fc39a7bb7ae5e77b9566227cac" %} +{% set version = "1.0.1.dev20220829" %} +{% set sha256 = "cad8b93ba961820ca3701a1d931944bd307b1d1f92d74e1b02d5bd34d4ffe998" %} package: name: {{ name | lower }} version: {{ version }} build: - number: 3 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name | lower, max_pin="x.x.x") }} source: - url: https://github.com/{{ name }}/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/{{ name }}/{{ name }}/archive/{{ git_sha1 }}.tar.gz sha256: {{ sha256 }} patches: - 0001-FIX-command-broken-with-symbolic-link.patch @@ -23,7 +26,7 @@ requirements: run: - python-gflags - - python=2.7 + - python >=3,<4 test: source_files: From 25b8726ab338b7c7c0b1d20a76f774539f410e52 Mon Sep 17 00:00:00 2001 From: Ray <851836818@qq.com> Date: Thu, 1 Feb 2024 21:48:08 +0800 Subject: [PATCH 0232/1813] Update meta.yaml (#45549) * Update meta.yaml * Update meta.yaml --- recipes/strainscan/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/strainscan/meta.yaml b/recipes/strainscan/meta.yaml index e4bb6caf0e437..a16796f4a5b47 100644 --- a/recipes/strainscan/meta.yaml +++ b/recipes/strainscan/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 2d927c5ac4d9b89a166afeca2aabaf4086d49b097e357ed0feb34181295cf243 build: - number: 0 + number: 1 entry_points: - strainscan = StrainScan.StrainScan:main - strainscan_build = StrainScan.StrainScan_build:main @@ -25,7 +25,7 @@ requirements: - python ==3.7.3 run: - python ==3.7.3 - - sibeliaz ==1.2.2 + - sibeliaz ==1.2.3 - r-base ==4.0.2 - numpy ==1.17.3 - pandas ==1.0.1 From 0e7a27cc3375444c5a37c2f9bac04548470dd350 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 1 Feb 2024 14:50:15 +0100 Subject: [PATCH 0233/1813] Update MEGAN to 6.25.9 (#45548) * Update MEGAN to 6.25.9 * Add pin subpackage for linting * Apply suggestions from code review --- recipes/megan/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/megan/meta.yaml b/recipes/megan/meta.yaml index b630ebb5fdfad..d3014d47e4e3c 100644 --- a/recipes/megan/meta.yaml +++ b/recipes/megan/meta.yaml @@ -1,13 +1,13 @@ {% set name = "megan" %} -{% set version = "6.24.20" %} +{% set version = "6.25.9" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://software-ab.cs.uni-tuebingen.de/download/megan6/MEGAN_Community_unix_{{ version|replace(".", "_") }}.sh # [linux] - sha256: 4eaf7797b4a2b9cdc2157b2780810504b9b8b539dd81bb6130f4b69e453f009b # [linux] + url: https://maira.cs.uni-tuebingen.de/download/megan6/MEGAN_Community_unix_{{ version|replace(".", "_") }}.sh # [linux] + sha256: 09975351baff29e620d49f14145bde7840ec5d58828ba9ddf187c9ba54e46b4b # [linux] # url: https://software-ab.informatik.uni-tuebingen.de/download/megan6/MEGAN_Community_macos_{{ version|replace(".", "_") }}.dmg # [osx] # sha256: dd843e823f358f496834a2034e1b638e9602ba83251a5f0542f20b0d22d7dc70 # [osx] @@ -15,6 +15,8 @@ build: # detect_binary_files_with_prefix: true number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage("megan", max_pin="x.x") }} requirements: host: From 60220d4f2eb1602deff84ddc5a3fde277bdaff4c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 09:21:06 -0500 Subject: [PATCH 0234/1813] Update cmat to 3.1.1 (#45550) --- recipes/cmat/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/cmat/meta.yaml b/recipes/cmat/meta.yaml index 69e11aa455e27..22556a626dd0c 100644 --- a/recipes/cmat/meta.yaml +++ b/recipes/cmat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cmat" %} -{% set version = "3.1.0" %} +{% set version = "3.1.1" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/EBIvariation/CMAT/archive/v{{version}}.tar.gz - sha256: 1e46a83d3d7e46a41f9f62ff4af0c151851fbbebc1c6b129255f987d75b64079 + sha256: 0ff44acd1a9c1df9ed76804faf62d49716edcc1376679a19b1ef1b5003cde535 build: number: 0 @@ -61,4 +61,4 @@ about: extra: recipe-maintainers: - - apriltuesday \ No newline at end of file + - apriltuesday From ed476fbfe12cfc7e7a39e11243161fc4663870d5 Mon Sep 17 00:00:00 2001 From: Martin Raden Date: Thu, 1 Feb 2024 16:11:34 +0100 Subject: [PATCH 0235/1813] rebuild pourRNA (#45511) * rebuild pourRNA * name via variable --- recipes/pourrna/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/pourrna/meta.yaml b/recipes/pourrna/meta.yaml index 993b810c88dc6..4313accff6e9c 100644 --- a/recipes/pourrna/meta.yaml +++ b/recipes/pourrna/meta.yaml @@ -11,7 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage( name, max_pin="x.x") }} requirements: build: From 077a81cfa642292fdd2ef2b4a63364f086c6e859 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 10:23:37 -0500 Subject: [PATCH 0236/1813] Update ephemeris to 0.10.10 (#45552) --- recipes/ephemeris/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ephemeris/meta.yaml b/recipes/ephemeris/meta.yaml index 7afc256a6fbd3..e6929208c86a9 100644 --- a/recipes/ephemeris/meta.yaml +++ b/recipes/ephemeris/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ephemeris" %} -{% set version = "0.10.9" %} +{% set version = "0.10.10" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ephemeris-{{ version }}.tar.gz - sha256: fdc09b71f902f638fb74bbb1a4b22fcaf76869c4aa3ec6739c4be25c856e45b7 + sha256: 397599341949e359c5dc1cb6bf8b4be06b14cc3d2e8fb404a3421f37d17c2b44 build: number: 0 From 178f18726f6527d3e122aa9a863589d1897853a4 Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Thu, 1 Feb 2024 18:46:47 +0100 Subject: [PATCH 0237/1813] Update nextclade to 3.1.0 (#45560) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index 2bf851ea44aee..fa81294b44098 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.0.1" %} +{% set version = "3.1.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 181d0ff48fe09e67f3a1e186ec0f89b15aa08eba779089f7837fc15c7b6501b1 # [linux64] + sha256: 949ec8ea1eb9705529425543292347ce7fbf9c799ec9f82fb3a9dab5f9e39450 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: bd21bfb9ae40be1e4a839519718b7127f146b2f8bc831771359844e27ae649f0 # [osx and x86_64] + sha256: 878523f7c278c16bb19c47ab6421c63ccb876bbd2820cc997bcda62dcf3eb4d4 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: 20cebf5b8494645f915dddb24b87540634df31bf321c20ff97a091f85c06932d # [arm64] + sha256: 967ed5de693aa162ba010521d397462c7a73ff9430b2d70af42bc05b52782881 # [arm64] build: number: 0 From 23303b599f11bd56cc5494e1e49cdedef078761a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 15:33:51 -0500 Subject: [PATCH 0238/1813] Update attotree to 0.1.2 (#45559) --- recipes/attotree/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/attotree/meta.yaml b/recipes/attotree/meta.yaml index 3cd8f4c661f08..577c993650692 100644 --- a/recipes/attotree/meta.yaml +++ b/recipes/attotree/meta.yaml @@ -1,5 +1,5 @@ {% set name = "attotree" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: ada454ac2a9392667476816c466c005935d5ffe73f87b2b7bc7960a0ec0753a4 + sha256: 8ae3799fd513595a0d05625e420b17b7745a0fa067e2e100302a2ddefe438ebf build: number: 0 From 2e2c6e74d20cb9b02ba81c1d7887a0f3a666c9bc Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 1 Feb 2024 15:18:35 -0600 Subject: [PATCH 0239/1813] Update kma to 1.4.14 (#45566) --- recipes/kma/build.sh | 4 +++- recipes/kma/meta.yaml | 12 ++++++++---- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/recipes/kma/build.sh b/recipes/kma/build.sh index 202febb333a5e..20626f6691fb4 100755 --- a/recipes/kma/build.sh +++ b/recipes/kma/build.sh @@ -1,5 +1,7 @@ +#!/bin/bash + BINARIES="kma kma_index kma_shm kma_update" -make CFLAGS="-w -O3 -I$PREFIX/include -L$PREFIX/lib" +make CFLAGS="${CFLAGS} -w -O3 -I${PREFIX}/include -L${PREFIX}/lib" mkdir -p ${PREFIX}/bin cp $BINARIES $PREFIX/bin diff --git a/recipes/kma/meta.yaml b/recipes/kma/meta.yaml index 8cfa498075d15..9805f97f9b6e5 100644 --- a/recipes/kma/meta.yaml +++ b/recipes/kma/meta.yaml @@ -1,6 +1,6 @@ {% set name = "kma" %} -{% set version = "1.4.9" %} -{% set sha256 = "6434e6fcc23420edc29922baf289e4a6d923f31949c34d8efd2331f3bb5e8e8b" %} +{% set version = "1.4.14" %} +{% set sha256 = "85971fcb2e806d2ee95d3499cd9b358f313b1635d5d71cb189eabc503be4b10f" %} package: name: {{ name|lower }} @@ -11,7 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('kma', max_pin="x") }} requirements: build: @@ -21,7 +23,7 @@ requirements: - zlib run: - zlib - + test: commands: - kma -h | grep KMA >/dev/null @@ -33,6 +35,8 @@ about: home: https://bitbucket.org/genomicepidemiology/kma summary: 'KMA is mapping a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.' license: Apache-2.0 + license_family: APACHE + extra: identifiers: - doi:10.1186/s12859-018-2336-6 From 396bb5a9ca74e28ed22c3dc939f31ee459e6b55a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 17:00:54 -0500 Subject: [PATCH 0240/1813] Update centrifuge-core to 1.0.4.1 (#45557) * Update centrifuge-core to 1.0.4.1 * Apply suggestions from code review * test if custom build config is still needed * skip osx builds --------- Co-authored-by: James A. Fellows Yates Co-authored-by: Robert A. Petit III --- recipes/centrifuge-core/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/centrifuge-core/meta.yaml b/recipes/centrifuge-core/meta.yaml index dfb689b988214..5381ccdd5d741 100644 --- a/recipes/centrifuge-core/meta.yaml +++ b/recipes/centrifuge-core/meta.yaml @@ -1,16 +1,19 @@ {% set name = "centrifuge-core" %} -{% set version = "1.0.4" %} +{% set version = "1.0.4.1" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 2 + number: 0 + skip: true # [osx] + run_exports: + - {{ pin_subpackage("centrifuge-core", max_pin="x.x") }} source: url: https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v{{ version }}.tar.gz - sha256: 929daed0f84739f7636cc1ea2757527e83373f107107ffeb5937a403ba5201bc + sha256: 638cc6701688bfdf81173d65fa95332139e11b215b2d25c030f8ae873c34e5cc requirements: build: From 2a3152c646450e91e6b77fced0cd004aa7ff2f39 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 18:35:41 -0500 Subject: [PATCH 0241/1813] Update pybiolib to 1.1.1703 (#45563) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index bbcec685a8ceb..9676b29d9dd02 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1691" %} +{% set version = "1.1.1703" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 5f25f9028e05b606a32a452fb065288915d94a010481db935ddc2379812abec6 + sha256: fce4db168dccecd6500d5967d307a3fbd26bd4c4d586668a189f72103b75edbf build: noarch: python From 52fc47dfed25303f0cce1751b2c7211b99059fc6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:05:06 -0500 Subject: [PATCH 0242/1813] Update npstructures to 0.2.16 (#45556) --- recipes/npstructures/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/npstructures/meta.yaml b/recipes/npstructures/meta.yaml index aabf2fa368189..41873871a5cd0 100644 --- a/recipes/npstructures/meta.yaml +++ b/recipes/npstructures/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.15" %} +{% set version = "0.2.16" %} {% set name = "npstructures" %} package: name: {{ name }} @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 6266b74fae8f58d1cdc8967e5a85f557610df4956fae28e6b3eb39ddebb46aae + sha256: 0964520dfb11789635ceae36c9ab477e60cd4fbc99f069656fafbdcb3878a0be build: From 6472b8b458bf992bc9df4efee073778e88b62082 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:05:26 -0500 Subject: [PATCH 0243/1813] Update htsinfer to 0.10.0 (#45555) --- recipes/htsinfer/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/htsinfer/meta.yaml b/recipes/htsinfer/meta.yaml index a88775a875d23..1a4e250b5331b 100644 --- a/recipes/htsinfer/meta.yaml +++ b/recipes/htsinfer/meta.yaml @@ -1,13 +1,13 @@ {% set name = "HTSinfer" %} -{% set version = "0.9.0" %} +{% set version = "0.10.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/zavolanlab/htsinfer/archive/refs/tags/v0.9.0.tar.gz - sha256: f4708d43e56389240752e45ac3f4cdcb620ab3783b57ff068599eec0adbd91f3 + url: https://github.com/zavolanlab/htsinfer/archive/refs/tags/v0.10.0.tar.gz + sha256: a851d00a47ef5a47e9c2540599ff2c16723dfac95c12ac85f7152b0ad4c295a7 build: number: 0 @@ -54,4 +54,4 @@ about: extra: recipe-maintainers: - - balajtimate \ No newline at end of file + - balajtimate From 269ade3109ce5cf36a8a59224ff4568df855012d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:05:39 -0500 Subject: [PATCH 0244/1813] Update bionumpy to 1.0.2 (#45553) --- recipes/bionumpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index 30519b96389e1..e150ab834eebc 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9e00254dc1c2ee2669048b7fd0bb6309e6caa218f8a330b00e3929f1dfeee58c + sha256: 0052120fb3c07a83d5064b680246b2b8ddf251dac526ac60d6d1c18f4ee944eb build: noarch: python From 4af8d975ef28d84f312dd049edebb128ab64fd06 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:05:54 -0500 Subject: [PATCH 0245/1813] Update snakemake-executor-plugin-slurm to 0.3.0 (#45554) * Update snakemake-executor-plugin-slurm to 0.2.2 * Update snakemake-executor-plugin-slurm to 0.3.0 --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index a7cdccccdb508..3d08d331ed1ed 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.2.1" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: dd484fcb136612a3f2bdcccf15ca4ebffc2f5fcdfa7f1fcc14416dd272812999 + sha256: 0200006e4860d4966ed092e0b2d335068a2b0aef33f8938bca435890b790e5fa build: noarch: python From 0108d81db264a741cfdbf4ec42a843f81d00f2f7 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 1 Feb 2024 18:54:55 -0600 Subject: [PATCH 0246/1813] Add recipe for dropkick v1.2.8 (#45569) * Add recipe for dropkick v1.2.8 * add run_exports * skip OSX --- recipes/dropkick/meta.yaml | 51 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 recipes/dropkick/meta.yaml diff --git a/recipes/dropkick/meta.yaml b/recipes/dropkick/meta.yaml new file mode 100644 index 0000000000000..8454489e5b6ba --- /dev/null +++ b/recipes/dropkick/meta.yaml @@ -0,0 +1,51 @@ +{% set name = "dropkick" %} +{% set version = "1.2.8" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dropkick-{{ version }}.tar.gz + sha256: 4bfbd23984ac11669691818f29e1f0033e32dd7c2236b16d8a2f20fe60c923c6 + +build: + number: 0 + # "Failed to find libgfortran.3.dylib" build error on OSX + skip: True # [py < 36 or osx] + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + entry_points: + - dropkick = dropkick.__main__:main + run_exports: + - {{ pin_subpackage('dropkick', max_pin="x") }} + +requirements: + build: + - {{ compiler('fortran') }} + - {{ compiler('c') }} + host: + - python + - pip + - numpy + run: + - python + - scipy >=0.14.1 + - pandas + - scikit-learn >=0.18.0 + - scikit-image + - matplotlib-base >=3.0.3 + - scanpy + - {{ pin_compatible('numpy') }} + +test: + imports: + - dropkick + commands: + - dropkick --help + +about: + home: https://github.com/KenLauLab/dropkick + summary: Automated scRNA-seq filtering + license: MIT + license_family: MIT + license_file: LICENSE From 18221279960989c01fc5c84660cc469f0475e222 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:55:22 -0500 Subject: [PATCH 0247/1813] Update tides-ml to 1.2.0 (#45561) * Update tides-ml to 1.2.0 * pin python to <3.12 --------- Co-authored-by: mencian --- recipes/tides-ml/meta.yaml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/tides-ml/meta.yaml b/recipes/tides-ml/meta.yaml index ff653618f6ed2..75f14a4175336 100644 --- a/recipes/tides-ml/meta.yaml +++ b/recipes/tides-ml/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tides-ml" %} -{% set version = "1.1.4" %} +{% set version = "1.2.0" %} package: name: {{ name|lower }} @@ -7,23 +7,23 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/TIdeS-ML-{{ version }}.tar.gz - sha256: 393f24ce18a58f40b2387e2a2fc2d45eb0088c8231c3d533f647deaf4b38c6ee + sha256: 8c31f4429303e5d34c031b243963fae3eec1f0d9c97e856949a7eac17f82452c build: entry_points: - tides = tides.tides:main noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: - - python >=3.8 + - python <3.12 - pip run: - - python >=3.8 + - python <3.12 - biopython >=1.79 - ete3 >=3.1.2 - optuna >=3.0 @@ -33,7 +33,7 @@ requirements: - diamond >=2.1.3 - cd-hit >=4.8.1 - barrnap >=0.9 - - kraken2 >=2.0.0 + - kraken2 >=2.0.0 test: imports: @@ -44,12 +44,12 @@ test: - (barrnap --help 2>&1; true) | grep -q Options - tides --help - kraken2 --version - about: home: https://github.com/xxmalcala/TIdeS summary: Tool for ORF-calling and ORF-classification using ML approaches license: MIT + license_family: MIT license_file: LICENSE extra: From 8437f1e0483464531f1749da3f3fd631eecbc715 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:55:32 -0500 Subject: [PATCH 0248/1813] Update clonalframeml to 1.13 (#45542) * Update clonalframeml to 1.13 * add run_exports --------- Co-authored-by: mencian --- recipes/clonalframeml/meta.yaml | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/recipes/clonalframeml/meta.yaml b/recipes/clonalframeml/meta.yaml index e90bef289093c..eb47de77ebb1c 100644 --- a/recipes/clonalframeml/meta.yaml +++ b/recipes/clonalframeml/meta.yaml @@ -1,13 +1,18 @@ +{% set name = "clonalframeml" %} +{% set version = "1.13" %} + package: - name: clonalframeml - version: "1.12" + name: {{ name }} + version: {{ version }} build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage('clonalframeml', max_pin="x") }} source: - url: https://github.com/xavierdidelot/ClonalFrameML/archive/v1.12.tar.gz - sha256: ef76705c1a0f1343184f956cd0bdc96c2cfdbb998177330b09b6df84c74c2de6 + url: https://github.com/xavierdidelot/ClonalFrameML/archive/refs/tags/v{{ version }}.tar.gz + sha256: 6056109380c695020afa0c26f4ce49dcb9267f1a8f26dfb42629bfa63ac25e6e requirements: build: @@ -20,6 +25,8 @@ test: about: home: https://github.com/xavierdidelot/ClonalFrameML - license: GPLv3 + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE summary: Efficient inferencing of recombination in bacterial genomes - + doc_url: https://github.com/xavierdidelot/clonalframeml/wiki From 0ec5fdeac39602fc6463b005cf54ad3a4cfd41fb Mon Sep 17 00:00:00 2001 From: Daniel Standage Date: Thu, 1 Feb 2024 19:56:20 -0500 Subject: [PATCH 0249/1813] lusSTR: pin snakemake =1.0,<2.0 - xlrd >=1.0,<2.0 - openpyxl >=3.0.6 - - snakemake-minimal >=7.22.0 + - snakemake-minimal >=7.22.0,<8.0 - pyyaml >=6.0 - matplotlib-base >=3.5.3 From 07c82347f4a71879d59482e3242f2e6004625928 Mon Sep 17 00:00:00 2001 From: Manuel Tognon <51021763+ManuelTgn@users.noreply.github.com> Date: Fri, 2 Feb 2024 02:01:43 +0100 Subject: [PATCH 0250/1813] Update CRISPRme to v2.1.2 (#45544) * Update CRISPRme to v2.1.1 * update SHA256 * Update CRISPRme to v2.1.2 * add run_exports to recipe * Update sha256 --- recipes/crisprme/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/crisprme/meta.yaml b/recipes/crisprme/meta.yaml index 42d75db4871bf..8645e64e2d3dd 100644 --- a/recipes/crisprme/meta.yaml +++ b/recipes/crisprme/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.1.1" %} +{% set version = "2.1.2" %} package: name: crisprme @@ -6,9 +6,11 @@ package: source: url: https://github.com/pinellolab/CRISPRme/archive/refs/tags/v{{ version }}.tar.gz - sha256: d59a970c8210cbc5854d77101fe23b5f0ead899b53bcc4c9e6cfb3579c02db26 + sha256: 4f04cc791d2c562dffe6f88345a41795e5a0109490a9f33d91376677e41becc5 build: + run_exports: + - {{ pin_subpackage('crisprme', max_pin="x.x.x") }} number: 0 noarch: generic @@ -48,4 +50,4 @@ about: home: https://github.com/pinellolab/CRISPRme license: AGPL-3.0 license_file: LICENSE - summary: CRISPRme, tool package for CRISPR experiments assessment and analysis. \ No newline at end of file + summary: CRISPRme, tool package for CRISPR experiments assessment and analysis. From aa80fcad39a77296dc0f3212ad8de663549a7432 Mon Sep 17 00:00:00 2001 From: nickjcroucher Date: Fri, 2 Feb 2024 01:38:31 +0000 Subject: [PATCH 0251/1813] Update Gubbins (#45488) * Update version and dependencies * Whitespace versions * Correct URL * Change to codeload URL * Correct version number * Update version number * Update shasum256 * Update shasum256 again * Increment build number * Consistent numpy version --- recipes/gubbins/meta.yaml | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml index 34c62e3484b4a..41884170f7d23 100644 --- a/recipes/gubbins/meta.yaml +++ b/recipes/gubbins/meta.yaml @@ -7,13 +7,13 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [py < 38] run_exports: - {{ pin_subpackage('gubbins', max_pin="x") }} source: - url: https://github.com/nickjcroucher/{{ name|lower }}/archive/v{{ version }}.tar.gz + url: https://github.com/nickjcroucher/gubbins/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: @@ -28,28 +28,27 @@ requirements: host: - perl - zlib - - python - - scipy >=1.5.3 + - python >=3.8 + - scipy - setuptools - - dendropy >=4.0.2 - - biopython >=1.59 + - dendropy + - biopython - numpy <=1.23.0 - - numba >=0.53 + - numba run: - - python - - scipy >=1.5.3 - - reportlab >=3.0 - - dendropy >=4.0.2 - - biopython >=1.59 - - multiprocess >=0.70 + - python >=3.8 + - scipy + - dendropy + - biopython + - multiprocess - setuptools - raxml =8.2.12 - iqtree >=2.2 - rapidnj - raxml-ng =1.0.1 - fasttree =2.1.10 - - numpy >=1.2 - - numba >=0.56 + - numpy <=1.23.0 + - numba - ska2 >=0.3.0 - r-argparser - r-magrittr From 9bf0788129f7d693fd515f41781dfbc517c1e709 Mon Sep 17 00:00:00 2001 From: Yasuhiro Tanizawa <30499043+nigyta@users.noreply.github.com> Date: Fri, 2 Feb 2024 10:40:16 +0900 Subject: [PATCH 0252/1813] Updated submission-excel2xml recipe (#45528) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: 谷沢靖洋 --- recipes/submission-excel2xml/build.sh | 86 ++++++++++---------------- recipes/submission-excel2xml/meta.yaml | 26 ++++---- recipes/submission-excel2xml/patch | 60 ------------------ 3 files changed, 48 insertions(+), 124 deletions(-) delete mode 100644 recipes/submission-excel2xml/patch diff --git a/recipes/submission-excel2xml/build.sh b/recipes/submission-excel2xml/build.sh index e94caa89de577..a873d246167d1 100644 --- a/recipes/submission-excel2xml/build.sh +++ b/recipes/submission-excel2xml/build.sh @@ -1,58 +1,40 @@ #! /bin/bash -gem install date -v "3.0.0" -gem install open3 -v "0.1.2" -gem install mini_portile2 -v "2.4.0" -gem install nokogiri -v "1.15.3" -gem install rubyzip -v "2.3.2" -gem install roo -v "2.10.0" -gem install builder -v "3.2.4" -gem install rexml -v "3.2.5" +APPROOT=$PREFIX/opt/$PKG_NAME -APPROOT=$PREFIX/opt/submission-excel2xml +mkdir -p $APPROOT +bundle install && \ + bundle exec rake install && \ + bundle exec rake clobber + + +sed -i '1s|^.*$|#! /usr/bin/env ruby|' $PREFIX/share/rubygems/bin/excel2xml_dra +sed -i '1s|^.*$|#! /usr/bin/env ruby|' $PREFIX/share/rubygems/bin/excel2xml_jga +sed -i '1s|^.*$|#! /usr/bin/env ruby|' $PREFIX/share/rubygems/bin/submission-excel2xml +sed -i '1s|^.*$|#! /usr/bin/env ruby|' $PREFIX/share/rubygems/bin/validate_meta_dra +sed -i '1s|^.*$|#! /usr/bin/env ruby|' $PREFIX/share/rubygems/bin/validate_meta_jga + + + +# Downloading xsd files +# Files will be downloaded to $PREFIX/opt/submission-excel2xml/data +# "submission-excel2xml/data" is hard-coded in the source code. +export XDG_DATA_HOME=$PREFIX/opt +submission-excel2xml download_xsd + +# copy sample files +cp -r example/ $APPROOT/ + + +## Set variables on env activation +mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d +cat <> ${PREFIX}/etc/conda/activate.d/${PKG_NAME}.sh +export XDG_DATA_HOME=$PREFIX/opt +EOF + +cat <> ${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}.sh +unset XDG_DATA_HOME +EOF -mkdir -p $APPROOT -# sed -i.bak '1 s|^.*$|#!/usr/bin/env ruby|g' *.rb - -cp excel2xml_dra.rb $APPROOT/ -cp validate_meta_dra.rb $APPROOT/ -cp excel2xml_jga.rb $APPROOT/ -cp validate_meta_jga.rb $APPROOT/ - -chmod a+x $APPROOT/excel2xml_dra.rb -chmod a+x $APPROOT/validate_meta_dra.rb -chmod a+x $APPROOT/excel2xml_jga.rb -chmod a+x $APPROOT/validate_meta_jga.rb - - -mkdir -p $APPROOT/xsd - -cd $APPROOT/xsd - -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.analysis.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.annotation.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.common.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.experiment.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.package.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.run.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.sample.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.study.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.submission.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.analysis.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.common.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.dac.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.data.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.dataset.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.experiment.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.policy.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.sample.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.study.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.submission.xsd - -cd $PREFIX/bin -ln -s ../opt/submission-excel2xml/excel2xml_dra.rb ./ -ln -s ../opt/submission-excel2xml/validate_meta_dra.rb ./ -ln -s ../opt/submission-excel2xml/excel2xml_jga.rb ./ -ln -s ../opt/submission-excel2xml/validate_meta_jga.rb ./ diff --git a/recipes/submission-excel2xml/meta.yaml b/recipes/submission-excel2xml/meta.yaml index fe1bdec983d3e..aaa47188eaa55 100644 --- a/recipes/submission-excel2xml/meta.yaml +++ b/recipes/submission-excel2xml/meta.yaml @@ -1,6 +1,9 @@ +{% set version = "2.5" %} + package: name: submission-excel2xml - version: "2.0.0" + version: {{ version }} + build: number: 0 noarch: generic @@ -8,26 +11,25 @@ build: - {{ pin_subpackage('submission-excel2xml', max_pin="x") }} source: - url: https://github.com/ddbj/submission-excel2xml/archive/refs/heads/master.zip - md5: 746ef9a1e1bd13f20a0b348fd080eb45 - patches: - - patch + url: https://github.com/ddbj/submission-excel2xml/archive/refs/tags/v{{ version }}.tar.gz + md5: 14369dca823b18bc4c345913d689ae64 requirements: - build: - - make host: - - ruby 3.2.2 + - make + - ruby >=3.0 - compilers - - libxml2 run: - - ruby 3.2.2 - - compilers + - ruby >=3.0 - libxml2 test: commands: - - "excel2xml_jga.rb -h" + # - excel2xml_dra -h + # - excel2xml_jga -h + - excel2xml_dra -a example -i 0001 -p PRJDB7252 ${XDG_DATA_HOME}/submission-excel2xml/example/example-0001_dra_metadata.xlsx && validate_meta_dra -a example -i 0001 + - excel2xml_dra -a example -i 0002 -p PRJDB7252 -c "National Institute of Genetics" ${XDG_DATA_HOME}/submission-excel2xml/example/example-0002_dra_metadata.xlsx && validate_meta_dra -a example -i 0002 + - excel2xml_jga -j JSUB999999 ${XDG_DATA_HOME}/submission-excel2xml/example/JSUB999999_jga_metadata.xlsx && validate_meta_jga -j JSUB999999 about: home: https://github.com/ddbj/submission-excel2xml diff --git a/recipes/submission-excel2xml/patch b/recipes/submission-excel2xml/patch deleted file mode 100644 index 59faa15a8cfa7..0000000000000 --- a/recipes/submission-excel2xml/patch +++ /dev/null @@ -1,60 +0,0 @@ -diff --git a/excel2xml_dra.rb b/excel2xml_dra.rb -index ff30c77..2dbf2ba 100644 ---- a/excel2xml_dra.rb -+++ b/excel2xml_dra.rb -@@ -1,4 +1,4 @@ --#! /usr/bin/ruby -+#! /usr/bin/env ruby - # -*- coding: utf-8 -*- - - require 'rubygems' -diff --git a/excel2xml_jga.rb b/excel2xml_jga.rb -index 8bd6b32..0cdfebe 100644 ---- a/excel2xml_jga.rb -+++ b/excel2xml_jga.rb -@@ -1,4 +1,4 @@ --#! /usr/bin/ruby -+#! /usr/bin/env ruby - # -*- coding: utf-8 -*- - - require 'rubygems' -diff --git a/validate_meta_dra.rb b/validate_meta_dra.rb -index 47d417d..8256cfb 100644 ---- a/validate_meta_dra.rb -+++ b/validate_meta_dra.rb -@@ -1,4 +1,4 @@ --#! /usr/bin/ruby -+#! /usr/bin/env ruby - # -*- coding: utf-8 -*- - - require 'rubygems' -@@ -53,7 +53,7 @@ end - - ## Validate DRA XML against xsd - #xsd_path = "/opt/submission-excel2xml/" --xsd_path = "xsd/" -+xsd_path = __dir__ + "/xsd/" - - puts "\n== XML validation against SRA xsd ==" - if FileTest.exist?("#{submission_id}_dra_Submission.xml") -diff --git a/validate_meta_jga.rb b/validate_meta_jga.rb -index 055bc61..1d3d2f6 100644 ---- a/validate_meta_jga.rb -+++ b/validate_meta_jga.rb -@@ -1,4 +1,4 @@ --#! /usr/bin/ruby -+#! /usr/bin/env ruby - # -*- coding: utf-8 -*- - - require 'rexml/document' -@@ -41,8 +41,8 @@ meta_object = ['Submission', 'Study', 'Sample', 'Experiment', 'Data', 'Analysis' - ## - - ## Validate XMLs against JGA xsd --xsd_path = "/opt/submission-excel2xml/" --#xsd_path = "xsd/" -+#xsd_path = "/opt/submission-excel2xml/" -+xsd_path = __dir__ + "/xsd/" - - xml_a = [] - Dir.glob("#{submission_id}*xml").each{|xml| From 5631d47164a0a0c2cb1443e78d6aaafc28fe2c91 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 20:56:11 -0500 Subject: [PATCH 0253/1813] Update plassembler to 1.5.1 (#45572) --- recipes/plassembler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/plassembler/meta.yaml b/recipes/plassembler/meta.yaml index 85b1484bc031b..6eeca0a86bd9e 100644 --- a/recipes/plassembler/meta.yaml +++ b/recipes/plassembler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "plassembler" %} -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 35496f09241e9c5eb45e66146e0c24b1e77598c84a61db8bc9fbf0d11c3db5d5 + sha256: ab3a4f7b3b0cb391df9e8189bbf5af4ea6fbdd919da65467053f70ad0a7f9c12 build: number: 0 From f2d176a670f5eade3dad34b323765891a067b5db Mon Sep 17 00:00:00 2001 From: SantaMcCloud <100047964+SantaMcCloud@users.noreply.github.com> Date: Fri, 2 Feb 2024 02:58:17 +0100 Subject: [PATCH 0254/1813] Update bigscape to 1.1.8 (#45292) * update bigscape to the newest version * Update bigscape to 1.1.8 --- recipes/bigscape/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bigscape/meta.yaml b/recipes/bigscape/meta.yaml index 78c95f18aa48d..7915ed0a1a506 100644 --- a/recipes/bigscape/meta.yaml +++ b/recipes/bigscape/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.6" %} -{% set sha256 = "c38f633d4f1c5b9034c9ee2c96a14b7994884e2fc005fbead219068a618580a4" %} +{% set version = "1.1.8" %} +{% set sha256 = "9a9c256cb0464ca23408fe5a1738db21b8818b487216fb939d7aef037339a598" %} package: name: bigscape From 4af4f990fb1217f743fc4357e83864d00a74966f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 21:10:08 -0500 Subject: [PATCH 0255/1813] Update ucsc-cell-browser to 1.2.4 (#45445) * Update ucsc-cell-browser to 1.2.4 * add run_exports * try pinning python to <3.12 --------- Co-authored-by: mencian --- recipes/ucsc-cell-browser/meta.yaml | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/recipes/ucsc-cell-browser/meta.yaml b/recipes/ucsc-cell-browser/meta.yaml index b2e4b40352f61..a86e0702e4f9c 100644 --- a/recipes/ucsc-cell-browser/meta.yaml +++ b/recipes/ucsc-cell-browser/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.2.3' %} +{% set version = '1.2.4' %} {% set name = "cellbrowser" %} package: @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "081d55d1ecc3701c20b1f0275915e9b472b8b71eaa9cb1de7dcba1a0cd0501b1" + sha256: "9c7414dd377ce36c290b1eef0763d0e9d0b8fa9ddc697f6bcfd1e2efa49e67f9" build: number: 0 @@ -25,14 +25,16 @@ build: - cbGenes = cellbrowser.genes:cbGenesCli - cbHub = cellbrowser.hubmaker:cbHubCli noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('ucsc-cell-browser', max_pin="x") }} requirements: host: - - python >=3.6 + - python >=3.6,<3.12 - pip run: - - python >=3.6 + - python >=3.6,<3.12 - numpy - anndata @@ -53,7 +55,14 @@ test: - which cbGenes about: - home: http://cells.ucsc.edu - license: GPL + home: https://cells.ucsc.edu + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: A browser for single-cell data, main site at http://cells.ucsc.edu. UCSC Cellbrowser, an interactive browser for single cell data. Includes importers and basic pipelines for text files, Seurat, Scanpy and Cellranger. All Javascript - does not require a server backend. + doc_url: https://cellbrowser.readthedocs.io/en/master/ + dev_url: https://github.com/maximilianh/cellBrowser + +extra: + identifiers: + - doi:10.1093/bioinformatics/btab503 From 9d00909c3d712c49f9ac16072b2c8f16f13652c3 Mon Sep 17 00:00:00 2001 From: John Blischak Date: Thu, 1 Feb 2024 21:40:41 -0500 Subject: [PATCH 0256/1813] Package htslib LICENSE and update about section (#45048) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/htslib/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml index de0c0dc0023c1..db620cbb24b61 100644 --- a/recipes/htslib/meta.yaml +++ b/recipes/htslib/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('htslib', max_pin='x.x') }} @@ -40,7 +40,10 @@ test: about: home: https://github.com/samtools/htslib license: MIT + license_family: MIT + license_file: LICENSE summary: C library for high-throughput sequencing data formats. + doc_url: http://www.htslib.org/ extra: identifiers: From 22603a723221d1134c08acb434a529527d69d51d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 21:51:07 -0500 Subject: [PATCH 0257/1813] Update regenie to 3.4.1 (#45564) * Update regenie to 3.4.1 * Update regenie to 3.4.1 * add patch for v3.4.1 --------- Co-authored-by: Joelle Mbatchou Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/regenie/meta.yaml | 7 +- ...013-update-cmakelist-file-for-v3.4.1.patch | 343 ++++++++++++++++++ 2 files changed, 347 insertions(+), 3 deletions(-) create mode 100644 recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml index 3cdfe87d4c7b0..0ee50bfab1262 100644 --- a/recipes/regenie/meta.yaml +++ b/recipes/regenie/meta.yaml @@ -1,6 +1,6 @@ {% set name = "regenie" %} -{% set version = "3.4" %} -{% set sha256 = "c4c87f86ac42dc0ebc57f701e24cc88acd5fbf6cb9e6e3dac8c1b1c9ba4e6922" %} +{% set version = "3.4.1" %} +{% set sha256 = "e2683cd4078015ece44cfbea28957695155dbad3b6a5ef6017654b1d8254f214" %} package: name: {{ name|lower }} @@ -22,7 +22,8 @@ source: # - patches/0009-update-cmake-file-for-conda.patch # - patches/0010-update-cmakelist-file-for-v3.2.7.patch # - patches/0011-update-cmakelist-file-for-v3.2.9.patch - - patches/0012-update-cmakelist-file-for-v3.4.patch + # - patches/0012-update-cmakelist-file-for-v3.4.patch + - patches/0013-update-cmakelist-file-for-v3.4.1.patch build: number: 0 diff --git a/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch b/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch new file mode 100644 index 0000000000000..a3072766dad91 --- /dev/null +++ b/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch @@ -0,0 +1,343 @@ +From 40a095edbac9478fe818b43ae49c0d5e958d632f Mon Sep 17 00:00:00 2001 +From: Joelle Mbatchou +Date: Thu, 1 Feb 2024 17:14:05 -0500 +Subject: [PATCH] update cmakelist file for v3.4.1 + +--- + CMakeLists.txt | 228 +++++++++++++++++++++---------------------------- + 1 file changed, 95 insertions(+), 133 deletions(-) + mode change 100755 => 100644 CMakeLists.txt + +diff --git a/CMakeLists.txt b/CMakeLists.txt +old mode 100755 +new mode 100644 +index 4368ce0..2dc15fd +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -1,11 +1,3 @@ +-# For Intel MKL, set MKLROOT= when running cmake +-# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ +-# For OpenBLAS, set OPENBLAS_ROOT= when running cmake +-# note: it also requires lapacke library +-# For static compilation on Linux systems, set STATIC=1 when running cmake +-# -> this excludes GLIBC +- +- + cmake_minimum_required(VERSION 3.13) + + # detect OS architecture +@@ -33,57 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 + ###################################### + ######## check input variables + +-# check BGEN_PATH +-if("$ENV{BGEN_PATH}" STREQUAL "") +- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") +-else() +- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") +- if (NOT EXISTS ${BGEN_PATH}) +- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") +- endif() +-endif() +- + # check for static compilation +-if($ENV{STATIC}) ++if(BUILD_SHARED_LIBS) ++ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") ++ set(Boost_USE_STATIC_LIBS OFF) ++else() + set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") ++ set(Boost_USE_STATIC_LIBS ON) + message( STATUS "Static compilation mode") + endif() + +-# check Boost IOStreams +-if($ENV{HAS_BOOST_IOSTREAM}) +- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") +- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") +-else() +- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") +-endif() +- +-# check MKL +-if(NOT "$ENV{MKLROOT}" STREQUAL "") +- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") +- if (NOT EXISTS ${MKLROOT}) +- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") +- endif() +- message( STATUS "Will compile with Intel MKL library") +-endif() +- +-# check HTSlib +-if(NOT "$ENV{HTSLIB_PATH}" STREQUAL "") +- set(HTSLIB_PATH "$ENV{HTSLIB_PATH}" CACHE INTERNAL "Set HTSlib library path") +- if (NOT EXISTS ${HTSLIB_PATH}) +- message( FATAL_ERROR "Specified HTSlib library directory '${HTSLIB_PATH}' does not exist") +- endif() +- message( STATUS "Will compile with HTSlib") +-endif() +- +-# check OpenBLAS +-if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") +- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") +- if (NOT EXISTS ${OPENBLAS_ROOT}) +- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") +- endif() +- message( STATUS "Will compile with OpenBLAS library") +-endif() +- + ###################################### + ######## set flags and required libraries + +@@ -92,9 +43,10 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) + set(Boost_USE_DEBUG_LIBS OFF) + set(Boost_USE_MULTITHREADED ON) + set(Boost_USE_STATIC_RUNTIME OFF) ++set(MKLROOT "${CMAKE_PREFIX_PATH}") + +-# list each file specifically +-add_executable(regenie ++# list each file specifically ++add_executable(regenie + ${CMAKE_SOURCE_DIR}/src/Data.cpp + ${CMAKE_SOURCE_DIR}/src/Files.cpp + ${CMAKE_SOURCE_DIR}/src/Geno.cpp +@@ -112,32 +64,54 @@ add_executable(regenie + ${CMAKE_SOURCE_DIR}/src/MCC.cpp + ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp + ) +-target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) ++target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) + + set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") +-add_definitions(-DVERSION_NUMBER="${RG_VERSION}") + ++find_package(OpenMP REQUIRED) ++target_link_libraries(regenie OpenMP::OpenMP_CXX) + if("${UNAME_S}" STREQUAL "Linux") +- find_package(OpenMP REQUIRED) +- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) + if(${BUILD_STATIC}) +- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) ++ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) + endif() + elseif("${UNAME_S}" STREQUAL "Darwin") +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") + endif() + +-set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) ++set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") ++target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) ++ ++# for BGEN (choose static if present first) ++find_library(ZSTD_LIBRARY zstd REQUIRED) ++find_library(DB_LIBRARY ++ NAMES libdb.a db ++ REQUIRED ++ ) ++find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) ++find_package(Boost ++ REQUIRED COMPONENTS system filesystem thread ++ OPTIONAL_COMPONENTS iostreams ++ ) ++find_library(BGEN_LIBRARY ++ NAMES libbgen.a ++ REQUIRED ++ ) ++target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) ++target_include_directories(regenie ++ PUBLIC ++ $ ++ $ ++ $ ++ $ ++ ) ++add_definitions(${Boost_DEFINITIONS}) + +-# BGEN library and its dependencies +-find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) +-find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) +-find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) +-find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) +-find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) +-target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) +-target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) ++# Boost IO ++if(Boost_iostreams_FOUND) ++ add_definitions(-DHAS_BOOST_IOSTREAM) ++ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") ++ message( STATUS "Will compile with Boost Iostreams library") ++endif() + + # MVTNorm library + set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") +@@ -146,7 +120,7 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${MVTN_PATH} + ) +-target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) ++target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) + add_dependencies(regenie libMvtnorm) + + # QF library +@@ -156,7 +130,7 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${QF_PATH} + ) +-target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) ++target_link_libraries(regenie ${QF_PATH}/qf.a) + add_dependencies(regenie libqf) + + # Quadpack library +@@ -166,7 +140,7 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${QUAD_PATH} + ) +-target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) ++target_link_libraries(regenie ${QUAD_PATH}/libquad.a) + add_dependencies(regenie libquad) + + # PGEN library +@@ -176,12 +150,12 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${PGEN_PATH} + ) +-target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) +-target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) ++target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) ++target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) + add_dependencies(regenie pgenlib) + + # REMETA library +-if(EXISTS ${HTSLIB_PATH}) ++if(DEFINED HTSLIB_PATH) + set(REMETA_PATH "${EXTERN_LIBS_PATH}/remeta") + add_custom_target( + remeta +@@ -198,78 +172,66 @@ if(EXISTS ${HTSLIB_PATH}) + endif() + + # Intel MKL +-if(EXISTS ${MKLROOT}) ++if(DEFINED MKLROOT) + add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) +- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) +- if(${BUILD_STATIC}) # specify static libs +- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) +- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) ++ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) ++ find_library(MKL_LP64_LIB mkl_intel_lp64 ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ if("${UNAME_S}" STREQUAL "Linux") ++ find_library(MKL_THREAD_LIB mkl_gnu_thread ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ elseif("${UNAME_S}" STREQUAL "Darwin") ++ find_library(MKL_THREAD_LIB mkl_intel_thread ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ endif() ++ find_library(MKL_CORE_LIB mkl_core ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ if("${UNAME_S}" STREQUAL "Darwin") ++ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) ++ elseif(${BUILD_STATIC}) ++ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) + else() # use dynamic libs +- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) +- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) ++ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) + endif() +-elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS +- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) +- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) +- find_library(LAPACK_LIB lapack REQUIRED) +- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) +- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) ++ message( STATUS "Will compile with Intel MKL library") + endif() + + # cxxopts (header-only) +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) ++target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) + + # LBFGS (header-only) +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) ++target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) + + # Eigen (header-only) +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/) +- +-# Boost IO +-if(${HAS_BOOST_IOSTREAM}) +- if("${UNAME_S}" STREQUAL "Darwin") +- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) +- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) +- elseif(${BUILD_STATIC}) +- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) +- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) +- else() +- target_link_libraries(regenie PRIVATE -lboost_iostreams) +- endif() +- add_definitions(-DHAS_BOOST_IOSTREAM) +- message( STATUS "Will compile with Boost Iostreams library") +-endif() ++target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/) + + # Other libraries +-find_library(ZLIB_LIBRARY libz.a z REQUIRED) +-find_library(M_LIB m REQUIRED) +-find_library(DL_LIB dl REQUIRED) +-find_library(BZ2_LIB bz2) +-find_library(LZMA_LIB lzma) +-find_library(CURL_LIB curl) +-find_library(CRYPTO_LIB crypto) ++find_library(ZLIB_LIBRARY z REQUIRED) ++find_library(M_LIB m REQUIRED) ++find_library(DL_LIB dl REQUIRED) + if("${UNAME_S}" STREQUAL "Linux") + set(GFORTRAN_LIBRARY "-lgfortran") + elseif("${UNAME_S}" STREQUAL "Darwin") + find_library(GFORTRAN_LIBRARY gfortran REQUIRED) + endif() +-target_link_libraries( +- regenie PRIVATE +- ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} +- ${BZ2_LIB} ${LZMA_LIB} +- ${CURL_LIB} ${CRYPTO_LIB} ${GFORTRAN_LIBRARY} +-) ++target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) + +-install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) ++add_definitions(-DVERSION_NUMBER="${RG_VERSION}") ++install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) + message( STATUS "REGENIE v" ${RG_VERSION}) + +-add_custom_target(full-clean +- COMMAND cd "${MVTN_PATH}" && make clean +- COMMAND cd "${QF_PATH}" && make clean +- COMMAND cd "${QUAD_PATH}" && make clean +- COMMAND cd "${PGEN_PATH}" && make clean +- ) ++write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) ++install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) ++ ++set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) ++set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) ++set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) ++include(CPack) +-- +2.34.1 + From 44edda80cf206ccab2248c6f90cd4af1890ebf14 Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren <78838419+alejandrogzi@users.noreply.github.com> Date: Thu, 1 Feb 2024 22:01:12 -0500 Subject: [PATCH 0258/1813] Add gtfsort recipe (#45535) * new: gtfsort recipe * clean up recipe --------- Co-authored-by: mencian --- recipes/gtfsort/build.sh | 9 +++++++++ recipes/gtfsort/meta.yaml | 39 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 recipes/gtfsort/build.sh create mode 100644 recipes/gtfsort/meta.yaml diff --git a/recipes/gtfsort/build.sh b/recipes/gtfsort/build.sh new file mode 100644 index 0000000000000..8e10cdc3e3237 --- /dev/null +++ b/recipes/gtfsort/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/gtfsort/meta.yaml b/recipes/gtfsort/meta.yaml new file mode 100644 index 0000000000000..33e2dc96045a2 --- /dev/null +++ b/recipes/gtfsort/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "gtfsort" %} +{% set version = "0.2.1" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz + sha256: 0fdaa15e22bd34193e2b16b53697b413af0fcf485401f45d48ac48054f1d70f4 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('gtfsort', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.39 + - pkg-config + +test: + commands: + - gtfsort --help + - gtfsort --version + +about: + home: https://github.com/alejandrogzi/gtfsort + license: MIT + license_family: MIT + license_file: LICENSE + summary: "A chr/pos/feature GTF sorter that uses a lexicographically-based index ordering algorithm." + +extra: + recipe-maintainers: + - alejandrogzi + identifiers: + - doi:10.1101/2023.10.21.563454 From 409d834eadde293710b265a501eae9e4888ecb59 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 1 Feb 2024 23:02:15 -0600 Subject: [PATCH 0259/1813] Add recipe for cgelib v0.7.4 (#45576) --- recipes/cgelib/meta.yaml | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 recipes/cgelib/meta.yaml diff --git a/recipes/cgelib/meta.yaml b/recipes/cgelib/meta.yaml new file mode 100644 index 0000000000000..ddbcd260e9cc1 --- /dev/null +++ b/recipes/cgelib/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "cgelib" %} +{% set version = "0.7.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cgelib-{{ version }}.tar.gz + sha256: 213181bba24856ec367bdfd1e4615eeefff88243f8d29ad9446150927a434aed + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('cgelib', max_pin="x.x") }} + +requirements: + host: + - python >=3.6 + - pip + - wheel + run: + - python >=3.6 + - python-dateutil + - gitpython + +test: + imports: + - cgelib + +about: + home: https://genomicepidemiology.org/ + summary: "This package will in time replace the cgecore package. The package contains classes and functions intended to be utilized across the CGE tools." + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE.txt + dev_url: https://bitbucket.org/genomicepidemiology/cgelib From 72f89e5c6afdee2f504cc7f428db846a5ad391ca Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 1 Feb 2024 23:02:28 -0600 Subject: [PATCH 0260/1813] Update gmap to 2023.12.01 (#45574) --- recipes/gmap/build.sh | 5 ++--- recipes/gmap/meta.yaml | 9 ++++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/gmap/build.sh b/recipes/gmap/build.sh index ed5ed8319b2d8..f7a0c51aced84 100644 --- a/recipes/gmap/build.sh +++ b/recipes/gmap/build.sh @@ -16,8 +16,7 @@ export LANGUAGE=en_US.UTF-8 export LANG=en_US.UTF-8 export LC_ALL=en_US.UTF-8 -autoconf -autoheader +autoreconf -i ./configure CC="${CC}" CFLAGS="${CFLAGS}" \ CPPFLAGS="${CPPFLAGS}" \ LDFLAGS="${LDFLAGS}" \ @@ -48,5 +47,5 @@ sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/md_coords sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_genes sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_introns sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_splicesites +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/snpindex sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/vcf_iit - diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index 13f1ad8b29cb3..cceb395e938e3 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GMAP" %} -{% set version = "2023.10.10" %} -{% set sha256 = "f76cc3d0024c6c963ea1c13e46236b62a548d965ad8e295a181f138b82aca36e" %} +{% set version = "2023.12.01" %} +{% set sha256 = "878193a4ec16539d4aa2594424e55a9670e2bdae607e63e088962c904ec6ef69" %} package: name: {{ name|lower }} @@ -13,7 +13,8 @@ source: - single_quote_paths.patch build: - number: 1 + number: 0 + skip: True # [osx] run_exports: - {{ pin_subpackage('gmap', max_pin=None) }} @@ -22,6 +23,8 @@ requirements: - make - {{ compiler('c') }} - autoconf + - automake + - libtool - perl host: - zlib From 513954b61906f5dd0a1963d8a26cc5553c3c8960 Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren <78838419+alejandrogzi@users.noreply.github.com> Date: Fri, 2 Feb 2024 00:03:52 -0500 Subject: [PATCH 0261/1813] Add bed2gtf recipe (#45573) * new: gtfsort recipe * new: bed2gtf recipe * fix: clean recipe * feat: add build.sh * fix: delete gtfsort --- recipes/bed2gtf/build.sh | 9 +++++++++ recipes/bed2gtf/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/bed2gtf/build.sh create mode 100644 recipes/bed2gtf/meta.yaml diff --git a/recipes/bed2gtf/build.sh b/recipes/bed2gtf/build.sh new file mode 100644 index 0000000000000..8e10cdc3e3237 --- /dev/null +++ b/recipes/bed2gtf/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/bed2gtf/meta.yaml b/recipes/bed2gtf/meta.yaml new file mode 100644 index 0000000000000..9ce15cb1fe6a5 --- /dev/null +++ b/recipes/bed2gtf/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "bed2gtf" %} +{% set version = "1.9.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz + sha256: ae09861fa3474b3298a0469ad6d58bced91667792b5a20fdafe7b0dde6a05351 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('bed2gtf', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.39 + - pkg-config + +test: + commands: + - bed2gtf --help + - bed2gtf --version + +about: + home: https://github.com/alejandrogzi/bed2gtf + license: MIT + license_family: MIT + license_file: LICENSE + summary: "A high-performance BED-to-GTF converter written in Rust" + +extra: + recipe-maintainers: + - alejandrogzi From 88b9425f75edbcfaa817aa4b3a331ad4da33a3ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=B8ren=20Heidelbach?= <42008781+SorenHeidelbach@users.noreply.github.com> Date: Fri, 2 Feb 2024 06:36:06 +0100 Subject: [PATCH 0262/1813] nanomotif (#45287) * nanomotif * add run_exports * add home URL --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian --- recipes/nanomotif/meta.yaml | 52 +++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/nanomotif/meta.yaml diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml new file mode 100644 index 0000000000000..7e7f621cae175 --- /dev/null +++ b/recipes/nanomotif/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "nanomotif" %} +{% set version = "0.1.7" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz + sha256: 81ebdc88ad0147b48f20385079a10a6ba91f088e9d4325fd7f5206bdde800991 + +build: + entry_points: + - nanomotif = nanomotif.main:main + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('nanomotif', max_pin="x.x") }} + +requirements: + host: + - python + - pip + run: + - python + - wheel + - requests + - numpy ==1.24.4 + - pandas ==2.0.2 + - polars >=0.19 + - seaborn ==0.12.2 + - scipy ==1.10.1 + - networkx ==3.1 + - progressbar2 ==3.53.1 + +test: + imports: + - nanomotif + commands: + - nanomotif --help + +about: + home: https://pypi.org/project/nanomotif/ + summary: Identifying methlyation motifs in nanopore data + license: MIT + license_family: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - SorenHeidelbach From 46a8fdae9c68c0704230c8131733c6bdd6860f03 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 2 Feb 2024 00:29:27 -0600 Subject: [PATCH 0263/1813] Update resfinder to 4.4.2 (#45579) --- recipes/resfinder/LICENSE-2.0.txt | 202 ------------------ recipes/resfinder/build.sh | 6 +- recipes/resfinder/meta.yaml | 50 +++-- recipes/resfinder/python_path.patch | 6 +- .../resfinder/remove_version_git_tag.patch | 36 ---- 5 files changed, 31 insertions(+), 269 deletions(-) delete mode 100644 recipes/resfinder/LICENSE-2.0.txt delete mode 100644 recipes/resfinder/remove_version_git_tag.patch diff --git a/recipes/resfinder/LICENSE-2.0.txt b/recipes/resfinder/LICENSE-2.0.txt deleted file mode 100644 index d645695673349..0000000000000 --- a/recipes/resfinder/LICENSE-2.0.txt +++ /dev/null @@ -1,202 +0,0 @@ - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/recipes/resfinder/build.sh b/recipes/resfinder/build.sh index 9cecba2f5985c..3c65803ffd5ac 100644 --- a/recipes/resfinder/build.sh +++ b/recipes/resfinder/build.sh @@ -1,10 +1,6 @@ #!/bin/bash -mkdir -p ${PREFIX}/bin - -cp *.py ${PREFIX}/bin -chmod +x ${PREFIX}/bin/*.py -cp -r cge/ ${PREFIX}/bin/ +${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation # create folder for database download target=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION} diff --git a/recipes/resfinder/meta.yaml b/recipes/resfinder/meta.yaml index a4795a5d6cf2c..53c3e5a68befa 100644 --- a/recipes/resfinder/meta.yaml +++ b/recipes/resfinder/meta.yaml @@ -1,47 +1,51 @@ -{% set name = "ResFinder" %} -{% set version = "4.1.11" %} -{% set sha256 = "e312ff8dc23f329baf8b0a4dc3c41f0006778772e8f736086cf12d03bc76c9c8" %} +{% set name = "resfinder" %} +{% set version = "4.4.2" %} package: - name: '{{ name|lower }}' - version: '{{ version }}' + name: {{ name|lower }} + version: {{ version }} source: - url: https://bitbucket.org/genomicepidemiology/{{ name|lower }}/get/{{ version }}.tar.gz - sha256: '{{ sha256 }}' + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/resfinder-{{ version }}.tar.gz + sha256: 9660e58c3b3f63cf08335c0058f7ef3c56320be852009b714e773c71e8ea2659 patches: - python_path.patch - - remove_version_git_tag.patch build: number: 0 - noarch: generic + noarch: python + run_exports: + - {{ pin_subpackage('resfinder', max_pin="x") }} requirements: host: - - git - - kma + - python >=3.8 + - pip + - pdm-pep517 >=0.12.0 run: - - python >=3 + - python >=3.8 + # Needs cgelib in conda-forge/bioconda + - cgelib >=0.7.3 + - cgecore ==1.5.6 + - tabulate >=0.8.9 + - pandas >=1.4.2 + - biopython >=1.79 + - python-dateutil - kma - - biopython - blast >=2.8.1 - - cgecore 1.5.5 - - tabulate 0.7.7 - - gitpython - - python-dateutil - - git test: - commands: - - run_resfinder.py --help + imports: + - resfinder about: home: https://bitbucket.org/genomicepidemiology/resfinder - license: APACHE-2.0 + summary: "ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria." + license: Apache-2.0 license_family: APACHE - license_file: LICENSE-2.0.txt - summary: ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria. + license_file: LICENSE extra: notes: "ResFinder requires databases that can be downloaded with download-db.sh." + identifiers: + - doi:10.1093/jac/dkaa345 diff --git a/recipes/resfinder/python_path.patch b/recipes/resfinder/python_path.patch index a6b2bea47370b..59543ff0ea533 100644 --- a/recipes/resfinder/python_path.patch +++ b/recipes/resfinder/python_path.patch @@ -1,8 +1,8 @@ ---- run_resfinder.py.old 2022-03-24 02:00:31.990686268 -0500 -+++ run_resfinder.py 2022-03-24 02:01:00.924797159 -0500 +--- a/src/resfinder/run_resfinder.py ++++ b/src/resfinder/run_resfinder.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/opt/anaconda1anaconda2anaconda3/bin/python + import io import sys import os - import re diff --git a/recipes/resfinder/remove_version_git_tag.patch b/recipes/resfinder/remove_version_git_tag.patch deleted file mode 100644 index f1b80390791fe..0000000000000 --- a/recipes/resfinder/remove_version_git_tag.patch +++ /dev/null @@ -1,36 +0,0 @@ ---- run_resfinder.py.old 2022-03-24 02:18:37.191844209 -0500 -+++ run_resfinder.py 2022-03-24 02:19:40.497086660 -0500 -@@ -27,24 +27,6 @@ - # ######### FUNCTIONS ######### # - # ########################################################################### # - --def get_git_tag(): -- git_folders_path = os.path.dirname(os.path.realpath(__file__)) -- try: -- git_tag = str( -- subprocess.check_output( -- ['git', 'describe', '--tags', '--abbrev=0'], -- stderr=subprocess.STDOUT, cwd=git_folders_path, -- )).strip('\'b\\n') -- except subprocess.CalledProcessError as exc_info: -- match = re.search( -- 'fatal: no tag exactly matches \'(?P[a-z0-9]+)\'', str(exc_info.output)) -- if match: -- raise Exception( -- 'Bailing: there is no git tag for the current commit, {commit}'.format( -- commit=match.group('commit'))) -- raise Exception(str(exc_info.output)) -- return git_tag -- - def eprint(*args, **kwargs): - print(*args, file=sys.stderr, **kwargs) - -@@ -178,7 +160,7 @@ - ResFinder will be used.", - type=float, - default=None) --parser.add_argument("-v", "--version", action="version", version=get_git_tag(), -+parser.add_argument("-v", "--version", action="version", version="4.1.11", - help="Show program's version number and exit") - # Temporary option only available temporary - parser.add_argument("--pickle", From 91df519ea759be3e989787fbca66cc604aaa1f1e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 01:54:35 -0500 Subject: [PATCH 0264/1813] Update nanomotif to 0.1.13 (#45580) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index 7e7f621cae175..a9d41641151cb 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.7" %} +{% set version = "0.1.13" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: 81ebdc88ad0147b48f20385079a10a6ba91f088e9d4325fd7f5206bdde800991 + sha256: 97a236a5f8d56f7150292c043af057e44c8625ab92cef5e1046f3ba40a84b5d7 build: entry_points: From edef5231fe87025e014e1e1e9d7b9c09b75238a8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 04:08:23 -0500 Subject: [PATCH 0265/1813] Update trimnami to 0.1.2 (#45578) * Update trimnami to 0.1.2 * Update meta.yaml update dependencies --------- Co-authored-by: Michael Roach --- recipes/trimnami/meta.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/trimnami/meta.yaml b/recipes/trimnami/meta.yaml index 34ec5afd44ed6..74c441bf5757e 100644 --- a/recipes/trimnami/meta.yaml +++ b/recipes/trimnami/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trimnami" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 594d14c9535ed21270afb3c56f146cad786e9e619c25a89b30556d2284f8f461 + sha256: 5a045d74b3a3e388d32ef2b43429f3742adaa90566d44a52f7cd9bb70d428e69 build: noarch: python @@ -18,12 +18,13 @@ build: requirements: host: - - python >=3.8 + - python >=3.9 - pip run: - - python >=3.8 - - snaketool-utils >=0.0.3 - - snakemake >=7.14.0 + - python >=3.9 + - snaketool-utils >=0.0.4 + - snakemake >=7.14.0,<8 + - pulp <2.8 - pyyaml >=6.0 - Click >=8.1.3 - metasnek >=0.0.8 From a959187fd695d8ffb25d476a1c830baac74a0ab2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 05:00:38 -0500 Subject: [PATCH 0266/1813] Update pypolca to 0.3.1 (#45581) --- recipes/pypolca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pypolca/meta.yaml b/recipes/pypolca/meta.yaml index 84b6e54e58dca..05b761f65d25c 100644 --- a/recipes/pypolca/meta.yaml +++ b/recipes/pypolca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypolca" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8f65a6f010a65ced2f0e470d6f1ae9703236fece666674afe76cfb4475bfa440 + sha256: bb48e81a8a3a11979a3edc8091dbfac4b14ec3a57f0952075ae44c8638bac620 build: number: 0 From 666f148b1007a5c873017998d7d5eea62d76d5e4 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 2 Feb 2024 11:02:19 +0100 Subject: [PATCH 0267/1813] Update centrifuge to 1.0.4.1 (#45577) * Update centrifuge * Apply suggestions from code review * Correct hash * Update meta.yaml * Update build-fail-blacklist * Sync with centrifuge-core --- build-fail-blacklist | 1 - recipes/centrifuge/meta.yaml | 10 +++++++--- recipes/centrifuge/patch | 13 +++++++++++++ 3 files changed, 20 insertions(+), 4 deletions(-) create mode 100644 recipes/centrifuge/patch diff --git a/build-fail-blacklist b/build-fail-blacklist index 31d92e56cbae9..743eb04f0d076 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -175,7 +175,6 @@ recipes/bwa/0.6.2 # fails compilation in bulk on Linux recipes/paragraph recipes/selectsequencesfrommsa -recipes/centrifuge recipes/nasp recipes/mmvc recipes/gemma diff --git a/recipes/centrifuge/meta.yaml b/recipes/centrifuge/meta.yaml index 2156e793478fb..9aa11c129bd5c 100644 --- a/recipes/centrifuge/meta.yaml +++ b/recipes/centrifuge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "centrifuge" %} -{% set version = "1.0.4" %} +{% set version = "1.0.4.1" %} package: name: {{ name|lower }} @@ -7,10 +7,13 @@ package: build: number: 0 + skip: true # [osx] + run_exports: + - {{ pin_subpackage("centrifuge", max_pin="x.x") }} source: url: https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v{{ version }}.tar.gz - sha256: 929daed0f84739f7636cc1ea2757527e83373f107107ffeb5937a403ba5201bc + sha256: 638cc6701688bfdf81173d65fa95332139e11b215b2d25c030f8ae873c34e5cc requirements: build: @@ -23,7 +26,7 @@ requirements: - perl - wget - tar - - python <3 + - python >=3.6 test: commands: @@ -32,6 +35,7 @@ test: about: home: https://github.com/DaehwanKimLab/centrifuge license: GPL3 + license_file: LICENSE summary: 'Classifier for metagenomic sequences.' extra: diff --git a/recipes/centrifuge/patch b/recipes/centrifuge/patch new file mode 100644 index 0000000000000..5a968e69311d7 --- /dev/null +++ b/recipes/centrifuge/patch @@ -0,0 +1,13 @@ +diff --git a/processor_support.h b/processor_support.h +index f68ee65..135a768 100644 +--- a/processor_support.h ++++ b/processor_support.h +@@ -49,7 +49,7 @@ public: + #elif defined(USING_GCC_COMPILER) + __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX); + #else +- std::cerr << “ERROR: please define __cpuid() for this build.\n”; ++ std::cerr << "ERROR: please define __cpuid() for this build.\n"; + assert(0); + #endif + if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; \ No newline at end of file From e358e93efc064249e3ad04ece70e93cab1bbdd1e Mon Sep 17 00:00:00 2001 From: VinzentRisch <100149044+VinzentRisch@users.noreply.github.com> Date: Fri, 2 Feb 2024 16:44:48 +0100 Subject: [PATCH 0268/1813] Add RNAnorm recipe (#45512) * added recipe for rnanorm * Revert "added recipe for rnanorm" This reverts commit 6c3b14b96a68c2be4c92a1928831313d5e272673. * added recipe for rnanorm * added home url and run_exports * removed LICENSE.txt and changed run_export statement --- recipes/rnanorm/meta.yaml | 52 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/rnanorm/meta.yaml diff --git a/recipes/rnanorm/meta.yaml b/recipes/rnanorm/meta.yaml new file mode 100644 index 0000000000000..ee38e16598b55 --- /dev/null +++ b/recipes/rnanorm/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "rnanorm" %} +{% set version = "2.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/rnanorm-{{ version }}.tar.gz + sha256: 651bce77059548b907a4719615646898b6b51fe6915ba713686d2e6aa42d687f + +build: + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + entry_points: + - rnanorm = rnanorm.cli:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python >=3.8,<3.13 + - setuptools >=64.0.0 + - setuptools-scm >=6.4.0 + - pip + run: + - python >=3.8,<3.13 + - click + - numpy >=1.0.0 + - pandas >=1.0.0 + - scikit-learn >=1.0.0 + - pandera + +test: + imports: + - rnanorm + commands: + - pip check + - rnanorm --help + requires: + - pip + +about: + summary: Common RNA-seq normalization methods + license: Apache-2.0 + license_file: LICENSE + home: https://github.com/genialis/RNAnorm + +extra: + recipe-maintainers: + - VinzentRisch From c919d0ae97752949f7bf0e3be03d8d38264f3ba4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 10:54:45 -0500 Subject: [PATCH 0269/1813] Update hiphase to 1.3.0 (#45585) --- recipes/hiphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index 5f949dfe8a40b..59ee793e0ae92 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "1.2.1" %} -{% set hiphase_sha256 = "a5bd4926bb57f934fae5d72859d530991ce804ca7127fc134ca7e4c8245fe9f0" %} +{% set version = "1.3.0" %} +{% set hiphase_sha256 = "dd2708f5dd057009be555bf548aecfe30b189c4da086d026bdbb226bd4fb576e" %} package: name: {{ name }} From 475b1242fd7f70ce4cae93ad3f21e312e74ebebc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 15:17:58 -0500 Subject: [PATCH 0270/1813] Update cptac to 1.5.11 (#45589) --- recipes/cptac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cptac/meta.yaml b/recipes/cptac/meta.yaml index 8a64077d86dde..bab54c17e1958 100644 --- a/recipes/cptac/meta.yaml +++ b/recipes/cptac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cptac" %} -{% set version = "1.5.10" %} +{% set version = "1.5.11" %} package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 85176554062e73dd0226027baa876357056acd4c81e233082403817252e4fa1e + sha256: f890f69e78193a61f0017f1f2585d1d4bca0a4af5221baeb624b08177f9d0b5b build: number: 0 From 27313e55019030c2750d091798c1114a9ed8ba8d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 15:18:19 -0500 Subject: [PATCH 0271/1813] Update snakemake-interface-common to 1.15.3 (#45587) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 4cfc57b3f3c14..525b28533b34c 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.15.2" %} +{% set version = "1.15.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: f2a4908a5ec5d6e657723f90221da3c136e70a1c5897b4e1d65a703bc08e8d7a + sha256: 7587c5e553c6ddaf0e2542bad1ffda55c3adf5b8ca651f4bc359a17d3f747ceb build: noarch: python From 0220ca4529f83a35f274c14a511341f1b68f1a15 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 15:18:39 -0500 Subject: [PATCH 0272/1813] Update snakemake to 8.4.3 (#45582) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 614c8729ad5bc..d3b7e490033f6 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.2" %} +{% set version = "8.4.3" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: ea9273d7a27706b635fafae87bb21100dad02275570e138fdcff125cb3cba4f4 + sha256: 2c1aad84792beeed8f05933978849b787409d8b96b44890fb96baee737844fbc build: number: 0 From 2142db2e447e8e7e4bee423cdfa766f7bd6b91b2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 15:19:01 -0500 Subject: [PATCH 0273/1813] Update matchms to 0.24.2 (#45584) --- recipes/matchms/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 9cb15af6297b8..051eb033c05c7 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.24.1" %} +{% set version = "0.24.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8cb7098f0e5149c3ab5ad7b39789472b35e12f7668a79c12a3c58e51b50c255c + sha256: 1fe2b241b7d07e066ee92ddf549b22d135c16634b2755aadb774855a46ff55c3 build: number: 0 From 75db9679a8191853f249a13a7a7162162a8258b2 Mon Sep 17 00:00:00 2001 From: Marco Matthies <71844+marcom@users.noreply.github.com> Date: Sat, 3 Feb 2024 10:59:59 +0100 Subject: [PATCH 0274/1813] Update rnastructure to 6.4 (#45594) * Update rnastructure to 6.4 Changelog: https://rna.urmc.rochester.edu/Overview/Updates.html * Add missing jinja template definition --- recipes/rnastructure/meta.yaml | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/recipes/rnastructure/meta.yaml b/recipes/rnastructure/meta.yaml index d994092a66833..10976d6e6a4e0 100644 --- a/recipes/rnastructure/meta.yaml +++ b/recipes/rnastructure/meta.yaml @@ -1,13 +1,19 @@ +{% set name = "RNAstructure" %} +{% set version = "6.4" %} +{% set sha256 = "e2a372a739153293185eeffee3d3265f9f50dc6976053a1d013ccf086b06d975" %} + package: - name: rnastructure - version: '6.3' + name: {{ name | lower }} + version: {{ version }} source: - sha256: e922591ceaa99e0db8ab4572a8716ff625fc0109906650415e92d099d927b310 - url: http://rna.urmc.rochester.edu/Releases/6.3/RNAstructureSource.tgz + sha256: {{ sha256 }} + url: http://rna.urmc.rochester.edu/Releases/{{ version }}/RNAstructureSource.tgz build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage(name | lower, max_pin="x.x") }} requirements: build: From 4210fefe79678d7501e949adeb6d28aef01d18b4 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Sat, 3 Feb 2024 02:02:15 -0800 Subject: [PATCH 0275/1813] Update unikseq to 1.3.5 (#45591) * Update unikseq to 1.3.5 Needed to add run_exports section * Update summary --- recipes/unikseq/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/unikseq/meta.yaml b/recipes/unikseq/meta.yaml index 7acad68484a8d..6eee8a084f202 100644 --- a/recipes/unikseq/meta.yaml +++ b/recipes/unikseq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.4" %} +{% set version = "1.3.5" %} package: name: unikseq @@ -6,7 +6,7 @@ package: source: url: https://github.com/bcgsc/unikseq/releases/download/v{{ version }}/unikseq-{{ version }}.tar.gz - sha256: e5abe93ccd3bd4b66a67516cde0d877fe82d0ac275833d7d3cc9d95c19f68cf4 + sha256: 9b497384ce023a06fd79353c2488455f1517f10e575c86f1f5df1e21463d09e8 patches: - unikseq-bloom.patch - unikseq-write-bloom.patch @@ -14,6 +14,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('unikseq', max_pin="x") }} requirements: run: @@ -27,7 +29,7 @@ test: - writeBloom.pl |grep "Usage" about: - summary: Unique DNA sequence region identification, using a k-mer approach + summary: Unique DNA sequence region identification using a k-mer approach home: https://github.com/bcgsc/unikseq license: GPL-3.0 license_file: LICENSE From 0758ad9ca5ccc53a940d456e631e5ce5eabd072a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 3 Feb 2024 22:52:38 -0500 Subject: [PATCH 0276/1813] Update koverage to 0.1.10 (#45597) * Update koverage to 0.1.10 * Update meta.yaml update dependencies --------- Co-authored-by: Michael Roach --- recipes/koverage/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/koverage/meta.yaml b/recipes/koverage/meta.yaml index a05f96e6afbb5..d7047f608650d 100644 --- a/recipes/koverage/meta.yaml +++ b/recipes/koverage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "koverage" %} -{% set version = "0.1.9" %} +{% set version = "0.1.10" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 45e3e3ae21669f0c7a45f023ee130d4494ebc2637c0aa4529e95a3867c4b488a + sha256: 46d7d444350932a88f6d0158c946671f2f0a6b4769f3c9c68e4b13fa76ecefc2 build: noarch: python @@ -18,18 +18,18 @@ build: requirements: host: - - python >=3.8 + - python >=3.10 - pip run: - - python >=3.8 + - python >=3.10 - snaketool-utils >=0.0.4 - metasnek >=0.0.8 - - snakemake >=7.14.0 + - snakemake >=7.14.0,<8 + - pulp <2.8 - pyyaml >=6.0 - Click >=8.1.3 - zstandard >=0.21.0 - numpy >=1.24.3 - - py-spy >=0.3.14 - datapane >=0.16.7 - plotly >=5.15.0 From 690c5f2921c274575874e98515125c50629bc5af Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 12:08:51 -0500 Subject: [PATCH 0277/1813] Update olivar to 1.1.4 (#45604) --- recipes/olivar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/olivar/meta.yaml b/recipes/olivar/meta.yaml index 312f353f707f4..cacb4b80f87e8 100644 --- a/recipes/olivar/meta.yaml +++ b/recipes/olivar/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: olivar @@ -6,7 +6,7 @@ package: source: url: 'https://github.com/treangenlab/Olivar/archive/refs/tags/v{{version}}.tar.gz' - sha256: f7a04661321a33c8c4142fcb65397e13fdbcc3be2e6f429d2a5056e3f16fb567 + sha256: d671e9cc3befd34ccaefc46dbf01d20de7de3bc7a23b66c30c47409509fb18de build: number: 0 From 0bc9b6f704e7d0a50cef78f6de9c194df5d7f9d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 19:23:02 -0500 Subject: [PATCH 0278/1813] Update breseq to 0.38.3 (#45606) --- recipes/breseq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/breseq/meta.yaml b/recipes/breseq/meta.yaml index 2b9c00862c815..8696fa41b547e 100644 --- a/recipes/breseq/meta.yaml +++ b/recipes/breseq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.38.2" %} +{% set version = "0.38.3" %} package: name: breseq @@ -6,7 +6,7 @@ package: source: url: https://github.com/barricklab/breseq/releases/download/v{{ version }}/breseq-{{ version }}-Source.tar.gz - sha256: "d451670b9e7e3c87b76d3107efe7f1a9a94904011a32e5d407f4cce7ee3b2892" + sha256: "4d0c772fb87947e028094839f090ee130c87d0d5951adf5b845b79ac87449900" build: number: 0 From c6de247462c4892497650f59295e2227cd7091c2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 19:23:11 -0500 Subject: [PATCH 0279/1813] Update hecatomb to 1.3.1 (#45603) --- recipes/hecatomb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hecatomb/meta.yaml b/recipes/hecatomb/meta.yaml index b5783bce3c181..6793fb605bf02 100644 --- a/recipes/hecatomb/meta.yaml +++ b/recipes/hecatomb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "Hecatomb" %} -{% set version = "1.3.0" %} +{% set version = "1.3.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/shandley/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: ad53c9ab16b9db9a8d6bff2874c96727cffd030d3f5f8d7213496248a8f3659e + sha256: ce078b0d8327e07ba2a814d054b3f7b8c09ec76ad8dd421549676c792ff35ab1 build: number: 0 From e049d660a98d4badcba798db011789af6712dde5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 19:23:19 -0500 Subject: [PATCH 0280/1813] Update sage-proteomics to 0.14.6 (#45599) --- recipes/sage-proteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sage-proteomics/meta.yaml b/recipes/sage-proteomics/meta.yaml index 75e03453a0b0e..c6e19501ae077 100644 --- a/recipes/sage-proteomics/meta.yaml +++ b/recipes/sage-proteomics/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sage-proteomics" %} -{% set version = "0.14.5" %} -{% set sha256 = "a85b91c6651dfd028d5807163bdb62aa4a8eb222cac03348bd607323af1238c9" %} +{% set version = "0.14.6" %} +{% set sha256 = "5df02517d7c3e4f99785177d595c3106db8df6e443618837bab840c664886f54" %} package: name: {{ name }} From 8a3e1bddb5ecfe28cf4afc6aecaf2f2e8e5713c4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 19:23:30 -0500 Subject: [PATCH 0281/1813] Update pxblat to 1.1.18 (#45595) --- recipes/pxblat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index 2a0c29693aa1f..62cb7b33e4200 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "1.1.10" %} -{% set sha256 = "d20b48ac4c761ad26c680cd1a10e7fb22f581212d5221cbfc2bc7f522a6b81d2" %} +{% set version = "1.1.18" %} +{% set sha256 = "b5d0c4f3ca6e92e01aac24503212760501bd812bff7886b2a28e1219c1511f4d" %} package: name: {{ name|lower }} From 5e070352f0d7b4aeb5c2e93735b3ea86b5b05e04 Mon Sep 17 00:00:00 2001 From: Paimon Goulart Date: Sun, 4 Feb 2024 16:44:42 -0800 Subject: [PATCH 0282/1813] Update vcfsim (#45601) * Removed skip true from meta.yaml * Small change * Small change * Small changes * Small changes * Small changes * Small changes * Small changes * Small changes * Small changes * Small changes * Small changes --- recipes/vcfsim/meta.yaml | 45 ++++++++++++++-------------------------- 1 file changed, 15 insertions(+), 30 deletions(-) diff --git a/recipes/vcfsim/meta.yaml b/recipes/vcfsim/meta.yaml index 4123c6047645d..96d58274dcb6d 100644 --- a/recipes/vcfsim/meta.yaml +++ b/recipes/vcfsim/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcfsim" %} -{% set version = "1.0.5.alpha" %} +{% set version = "1.0.8.alpha" %} package: name: {{ name|lower }} @@ -7,62 +7,47 @@ package: source: url: https://github.com/Pie115/VCFSimulator-SamukLab/archive/{{ version }}.tar.gz - sha256: 3930958c2e52f62e5dd9e685307ff03e5387ae80158339806152da7f7aaa57ac + sha256: 67a2be52bb06b44dfb3cb96cff766cae866181b0b1e136d1d8737a229438068c build: + noarch: python entry_points: - vcfsim=vcfsim.__main__:main script: {{ PYTHON }} -m pip install . -vv number: 0 - skip: True run_exports: - {{ pin_subpackage('vcfsim', max_pin="x") }} - -requirements: - build: - - {{ compiler('c') }} - - cross-python_{{ target_platform }} - - python - - pybind11 - - numpy +requirements: host: - - python >=3.8 - - cython + - python >=3.6 - pip - setuptools - numpy - - setuptools_scm - - gsl - + - pandas + - msprime + - ipython # Include this only if IPython features are used outside notebooks + run: - - python >=3.8 - - pandas >=1.5.2 + - python >=3.6 - numpy - - msprime >=1.0.1 - - tskit >=0.4 - - demes >=0.2 - - gsl - - scikit-allel >=1.3.5 - - scikit-learn >=1.2.0 - - scipy >=1.9.3 + - pandas + - msprime + - ipython # Include this only if IPython features are used outside notebooks test: imports: - vcfsim commands: - - pip check - vcfsim --help - requires: - - pip about: home: https://github.com/Pie115/VCFSimulator-SamukLab license: MIT license_file: LICENSE.txt - summary: "Script for generating simulated VCF's" + summary: "Script for generating simulated VCF's leveraging a coalescent simulating backend." description: | - "vcfsim is a new command-line tool for generating simulated VCF's(variant call format files for encoding genetic data). Leveraging a coalescent simulating backend and providing an interface from Msprime coalescent simulating package to pandas. VCF's can now be easily simulated with just a few command line arguments!" + "VCFSim is a new command-line tool for generating simulated VCF's(variant call format files for encoding genetic data). Leveraging a coalescent simulating backend and providing an interface from Msprime coalescent simulating package to pandas. VCF's can now be easily simulated with just a few command line arguments!" extra: recipe-maintainers: From ada87efcd7222fa48ab00042a5ecfb693ebba660 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 20:21:35 -0500 Subject: [PATCH 0283/1813] Update novoplasty to 4.3.5 (#45605) * Update novoplasty to 4.3.5 * add run_exports --------- Co-authored-by: mencian --- recipes/novoplasty/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/novoplasty/meta.yaml b/recipes/novoplasty/meta.yaml index dac1892e5cb5e..ded9b844226cf 100644 --- a/recipes/novoplasty/meta.yaml +++ b/recipes/novoplasty/meta.yaml @@ -1,5 +1,5 @@ {% set name = "NOVOPlasty" %} -{% set version = "4.3.3" %} +{% set version = "4.3.5" %} package: name: {{ name|lower }} @@ -7,17 +7,18 @@ package: source: url: https://github.com/ndierckx/NOVOPlasty/archive/NOVOPlasty{{ version }}.tar.gz - sha256: 305759167b63d08f8f8191c1f735aa29c90b0a9de9e8c67cdca9ab43c8c13490 + sha256: b2555f2c10548a882d397a3c18d59d41905c0693ecf417d63aee24d5ac738d36 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('novoplasty', max_pin="x") }} requirements: host: - perl - perl-module-build - run: - perl @@ -30,10 +31,11 @@ test: about: home: https://github.com/ndierckx/NOVOPlasty summary: "The organelle assembler and heteroplasmy caller" - license: other + license: Other license_file: LICENSE description: | NOVOPlasty is a de novo assembler for short circular genomes. + extra: identifiers: - doi:10.1093/nar/gkw955 From 18f0a52f861e7a8e29bb526d0b86d237f9c0b54b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 20:21:51 -0500 Subject: [PATCH 0284/1813] Update somaticseq to 3.7.4 (#45602) * Update somaticseq to 3.7.4 * add run_exports --------- Co-authored-by: mencian --- recipes/somaticseq/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/somaticseq/meta.yaml b/recipes/somaticseq/meta.yaml index 7dd1f0e852f15..cd81c589f93e9 100644 --- a/recipes/somaticseq/meta.yaml +++ b/recipes/somaticseq/meta.yaml @@ -1,6 +1,6 @@ {% set name = "somaticseq" %} -{% set version = "3.7.3" %} -{% set sha256 = "3721c03646496980a17141fe63a90e09ee10328edc1b692aae57bc07c2477e3c" %} +{% set version = "3.7.4" %} +{% set sha256 = "d072300bc403f12265fcadba74c4e6ba82175e749f22f66b46a1e32bf851e24d" %} package: name: {{ name|lower }} @@ -13,7 +13,9 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('somaticseq', max_pin="x") }} requirements: host: @@ -25,7 +27,7 @@ requirements: - pysam - scipy - pandas - - xgboost + - xgboost >=1.4 - r-base - r-ada - bedtools @@ -45,7 +47,7 @@ test: - makeSomaticScripts.py --help about: - home: http://bioinform.github.io/somaticseq/ + home: https://bioinform.github.io/somaticseq/ license: BSD-2-Clause license_file: LICENSE.txt license_family: BSD From c9057304684e344e78de7f63ed59108fcdde19c1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 20:22:17 -0500 Subject: [PATCH 0285/1813] Update ipyrad to 0.9.94 (#45592) * Update ipyrad to 0.9.94 * add run_exports --------- Co-authored-by: mencian --- recipes/ipyrad/meta.yaml | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/recipes/ipyrad/meta.yaml b/recipes/ipyrad/meta.yaml index 4375514b5f3e1..f1cf832e4036c 100644 --- a/recipes/ipyrad/meta.yaml +++ b/recipes/ipyrad/meta.yaml @@ -1,21 +1,23 @@ {% set name = "ipyrad" %} -{% set version = "0.9.93" %} -{% set sha256 = "7f42396c0baa284dde0e9896270006f3c7e2211fa93bb149decccd39b4ab557e" %} +{% set version = "0.9.94" %} +{% set sha256 = "7a9ed2982cdec30afe480d38ae3208458c513f6302ca2a6c947935e5c03736cf" %} package: - name: {{name}} - version: {{version}} + name: {{ name }} + version: {{ version }} source: - url: https://github.com/dereneaton/{{name}}/archive/{{version}}.tar.gz - sha256: {{sha256}} + url: https://github.com/dereneaton/{{ name }}/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} build: number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " - noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vv" + noarch: python entry_points: - ipyrad = ipyrad.__main__:main + run_exports: + - {{ pin_subpackage('ipyrad', max_pin="x.x") }} requirements: host: @@ -36,7 +38,7 @@ requirements: - mpi4py >=3.0 # [ py >= 37 ] - notebook - bedtools - - muscle <5 # Pin muscle < v5 see issue #477 + - muscle <5 # Pin muscle < v5 see issue #477 - vsearch >=2.13 - bwa - samtools @@ -52,5 +54,6 @@ test: about: home: http://github.com/dereneaton/ipyrad license: GPL-3.0-only + license_family: GPL3 license_file: LICENSE.txt summary: Interactive assembly and analysis of RAD-seq data sets. From cb7459a1b3b2c4c36d47b9e7d7fa2bf6dd24392f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 20:41:23 -0500 Subject: [PATCH 0286/1813] Update cogent3 to 2024.2.5a1 (#45607) --- recipes/cogent3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cogent3/meta.yaml b/recipes/cogent3/meta.yaml index 8b5b4792d7e2f..a113597567360 100644 --- a/recipes/cogent3/meta.yaml +++ b/recipes/cogent3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cogent3" %} -{% set version = "2023.12.15a1" %} +{% set version = "2024.2.5a1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8cccfdb39aff746c9225b1e063a6506502c840276c843bcb93fea10bb2f31bfb + sha256: 4b0d59ba1c31b8257a56258d992fb201b53f265aa6f041da24ed9dc412a7782f build: noarch: python From 3456f7b2ab542d6e946f503f88d7d30636a2aa31 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sun, 4 Feb 2024 20:13:32 -0600 Subject: [PATCH 0287/1813] Add recipe for Monopogen v1.1.0 (#45608) --- recipes/monopogen/LICENSE | 674 ++++++++++++++++++++++++++++++++++++ recipes/monopogen/meta.yaml | 56 +++ 2 files changed, 730 insertions(+) create mode 100644 recipes/monopogen/LICENSE create mode 100644 recipes/monopogen/meta.yaml diff --git a/recipes/monopogen/LICENSE b/recipes/monopogen/LICENSE new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/monopogen/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + + Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/monopogen/meta.yaml b/recipes/monopogen/meta.yaml new file mode 100644 index 0000000000000..974c5c784f73d --- /dev/null +++ b/recipes/monopogen/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "Monopogen" %} +{% set version = "1.1.0" %} +{% set sha256 = "d6d049792ae277327e2c08ba675af3c9ae2bfccfbee14bed4ab2e20da2be4805" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/KChen-lab/Monopogen/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('monopogen', max_pin="x") }} + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + - pandas >=1.2.3 + - pysam >=0.16.0.1 + - numpy >=1.19.5 + - scipy >=1.6.3 + - pillow >=8.2.0 + - openjdk + - samtools + - bcftools + - beagle + - tabix + - r-base + - r-data.table + - r-e1071 + - r-ggplot2 + +test: + imports: + - Monopogen + +about: + home: https://github.com/KChen-lab/Monopogen + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: "Monopogen is an analysis package for SNV calling from single-cell sequencing datasets generated from single cell RNA 10x 5', 10x 3', single ATAC-seq technoloiges, scDNA-seq, etc." + +extra: + recipe-maintainers: + - mencian + identifiers: + - doi:10.1038/s41587-023-01873-x From 64f691d5871aaa5387770942d2a4f95c1e923777 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 21:33:48 -0500 Subject: [PATCH 0288/1813] Update ashlar to 1.18.0 (#45588) * Update ashlar to 1.18.0 * add run_exports * pin python to <3.12 --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ashlar/meta.yaml | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/recipes/ashlar/meta.yaml b/recipes/ashlar/meta.yaml index 56f3226e440d9..0f70c9431a7f1 100644 --- a/recipes/ashlar/meta.yaml +++ b/recipes/ashlar/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ashlar" %} -{% set version = "1.17.0" %} +{% set version = "1.18.0" %} package: name: "{{ name|lower }}" @@ -7,31 +7,34 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3c4fb3a2d1ffee986f86c633d12f753544904ddccbd8499851badbdeec3142be + sha256: 2c0e8997a49daf64fc56b3afabc2e58a0eb2f6f9985d0c3c22be957bf8b03760 build: number: 0 entry_points: - ashlar=ashlar.scripts.ashlar:main - script: "{{ PYTHON }} -m pip install . -vv" + - preview_slide=ashlar.scripts.preview_slide:main + - make_alignment_movie=ashlar.scripts.make_alignment_movie:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('ashlar', max_pin="x") }} requirements: host: - pip - - python + - python <3.12 run: - blessed >=1.17 - matplotlib-base >=3.1.2 - networkx >=2.4 - numpy >=1.18.1 - - pip - pyjnius >=1.2.1 - - python + - python <3.12 - scikit-image ==0.19 - scikit-learn >=0.21.1 - scipy >=1.4.1 - - tifffile>=2022.4.8 + - tifffile >=2022.4.8 - zarr test: @@ -44,6 +47,8 @@ test: about: home: "https://github.com/sorgerlab/ashlar" license: MIT + license_family: MIT + license_file: LICENSE summary: "Alignment by Simultaneous Harmonization of Layer/Adjacency Registration" doc_url: https://labsyspharm.github.io/ashlar/ From 33d7761b6a224cc66980d428b2fb73b6d598111c Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren <78838419+alejandrogzi@users.noreply.github.com> Date: Sun, 4 Feb 2024 21:40:45 -0500 Subject: [PATCH 0289/1813] Add bed2gff recipe (#45575) * new: gtfsort recipe * new: bed2gtf recipe * new: bed2gff recipe * fix: clean recipe * feat: add build.sh * fix: clean recipe; add build.sh * fix: delete other recipes already in PRs * fix spacing * Update meta.yaml --------- Co-authored-by: mencian --- recipes/bed2gff/build.sh | 9 +++++++++ recipes/bed2gff/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/bed2gff/build.sh create mode 100644 recipes/bed2gff/meta.yaml diff --git a/recipes/bed2gff/build.sh b/recipes/bed2gff/build.sh new file mode 100644 index 0000000000000..8e10cdc3e3237 --- /dev/null +++ b/recipes/bed2gff/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/bed2gff/meta.yaml b/recipes/bed2gff/meta.yaml new file mode 100644 index 0000000000000..8dd9a3b9338c3 --- /dev/null +++ b/recipes/bed2gff/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "bed2gff" %} +{% set version = "0.1.3" %} + +package: + name: bed2gff + version: {{ version }} + +source: + url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz + sha256: c278185aba8c352ec2b14cc7db6eb08afb5b81e000b0acb9330bfccdad10506c + +build: + number: 0 + run_exports: + - {{ pin_subpackage('bed2gff', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.39 + - pkg-config + +test: + commands: + - bed2gff --help + - bed2gff --version + +about: + home: https://github.com/alejandrogzi/bed2gff + license: MIT + license_family: MIT + license_file: LICENSE + summary: "BED-to-GFF3 converter that runs in parallel" + +extra: + recipe-maintainers: + - alejandrogzi From ea3f307dd8247132f7831a2b41d7ae982796cbc3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 5 Feb 2024 11:56:36 +0100 Subject: [PATCH 0290/1813] Restrict version of python in centrifuge due to python 2 evaluation scripts (#45611) --- recipes/centrifuge/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/centrifuge/meta.yaml b/recipes/centrifuge/meta.yaml index 9aa11c129bd5c..e3d21ca909841 100644 --- a/recipes/centrifuge/meta.yaml +++ b/recipes/centrifuge/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage("centrifuge", max_pin="x.x") }} @@ -26,7 +26,7 @@ requirements: - perl - wget - tar - - python >=3.6 + - python <3 test: commands: @@ -36,7 +36,7 @@ about: home: https://github.com/DaehwanKimLab/centrifuge license: GPL3 license_file: LICENSE - summary: 'Classifier for metagenomic sequences.' + summary: 'Classifier for metagenomic sequences. Supports classifier scripts' extra: identifiers: From cbd93594aa666a373f76e38393aa4044356f255d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 12:44:23 -0500 Subject: [PATCH 0291/1813] Update r-easydifferentialgenecoexpression to 1.4 (#45613) * Update r-easydifferentialgenecoexpression to 1.4 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-easydifferentialgenecoexpression/meta.yaml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/recipes/r-easydifferentialgenecoexpression/meta.yaml b/recipes/r-easydifferentialgenecoexpression/meta.yaml index 3ca98180e3570..da710a321155f 100644 --- a/recipes/r-easydifferentialgenecoexpression/meta.yaml +++ b/recipes/r-easydifferentialgenecoexpression/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.0' %} +{% set version = '1.4' %} package: name: r-easydifferentialgenecoexpression @@ -8,41 +8,39 @@ source: url: - {{ cran_mirror }}/src/contrib/easyDifferentialGeneCoexpression_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/easyDifferentialGeneCoexpression/easyDifferentialGeneCoexpression_{{ version }}.tar.gz - sha256: 19156037a2fa498dc28d8db8d53797d74007135c43e53bc5f20d61a66100f5b7 + sha256: d0e1653a311d5e5834ef4b9c333ae3fe5aee8333c1201517ee5f6cb556b054c7 build: - number: 2 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-easydifferentialgenecoexpression', max_pin='x') }} requirements: host: - r-base - bioconductor-biobase - bioconductor-geoquery - - r-r.utils - bioconductor-annotate - bioconductor-diffcoexp - r-geneexpressionfromgeo - r-jetset - bioconductor-limma - r-magrittr - - r-stringi - r-xml2 run: - r-base - bioconductor-biobase - bioconductor-geoquery - - r-r.utils - bioconductor-annotate - bioconductor-diffcoexp - r-geneexpressionfromgeo - r-jetset - bioconductor-limma - r-magrittr - - r-stringi - r-xml2 test: From a08297d5ae98628412a9d4aab6ecb1f7b70e972e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 14:22:49 -0500 Subject: [PATCH 0292/1813] Update seq2science to 1.2.2 (#45614) --- recipes/seq2science/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seq2science/meta.yaml b/recipes/seq2science/meta.yaml index dd78a09be0e26..87aeaebd5f332 100644 --- a/recipes/seq2science/meta.yaml +++ b/recipes/seq2science/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: seq2science @@ -6,7 +6,7 @@ package: source: url: https://github.com/vanheeringen-lab/seq2science/archive/v{{ version }}.tar.gz - sha256: f4543413118f9bdf69e1143f14708f4debf2f1089952569d55a1ca539d676bff + sha256: 5adbaf1689e8f302ec2d5c98f85a206b51f17d0e70e3fc0f16d872ae2099fdc5 build: noarch: python From d650e94e8d0dd2c604b304add9b92b891e7bf4fe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 14:59:45 -0500 Subject: [PATCH 0293/1813] Update dxpy to 0.369.0 (#45625) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 2f93229ada451..5dd102f8d5615 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.368.1" %} +{% set version = "0.369.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: e8fd366edfbe7c9ffd86be14e89d1a0086843442807bea3c404146ca7e96de62 + sha256: dc2f58723d70c6d02155c08d4ac65f41f63aeb05000e4782940d2196b05a962b build: number: 0 From 51f00337242de20c7dfc247ef3cb4e7e0acce259 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 15:00:05 -0500 Subject: [PATCH 0294/1813] Update degenotate to 1.3 (#45624) --- recipes/degenotate/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/degenotate/meta.yaml b/recipes/degenotate/meta.yaml index f66a7025ab294..df8b230b1460e 100644 --- a/recipes/degenotate/meta.yaml +++ b/recipes/degenotate/meta.yaml @@ -1,6 +1,6 @@ {% set name = "degenotate" %} -{% set version = "1.2.4" %} -{% set sha256 = "46359a6d33e660b21c0a0384c641e1aac15f7546f1fbb7463f01d94ad27abf60" %} +{% set version = "1.3" %} +{% set sha256 = "1c12673fd743c24845fec1dd503bf01114faa6b7f4545429e62747e65d323a66" %} package: name: {{ name|lower }} From c9764b599f111f549d49a7de500be65e31f6b591 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 15:00:34 -0500 Subject: [PATCH 0295/1813] Update ncbi-amrfinderplus to 3.12.8 (#45621) --- recipes/ncbi-amrfinderplus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-amrfinderplus/meta.yaml b/recipes/ncbi-amrfinderplus/meta.yaml index a1c878034c0f5..1e8066c9c665a 100644 --- a/recipes/ncbi-amrfinderplus/meta.yaml +++ b/recipes/ncbi-amrfinderplus/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.11.26" %} -{% set sha256 = "49d98d0f66e121d3ed5a3d9a817089ee69399b0bd06af52f79d796bfe8b2d8b2" %} +{% set version = "3.12.8" %} +{% set sha256 = "a199bc332877bad9033a7620bc5e8e849db1f19a9ba8b7357ec5451a6a283aa0" %} package: name: ncbi-amrfinderplus From 8107d878fd88259425ebd6c84908f514379842ed Mon Sep 17 00:00:00 2001 From: Chenkai Li Date: Mon, 5 Feb 2024 12:04:37 -0800 Subject: [PATCH 0296/1813] Update amplify to 2.0.0 (#45596) * Update amplify to 2.0.0 * Specify package version * Add run_exports * Specify version information for all packages * Add more detailed version information * Change everything back * Add run_exports * Update version * update tensorflow version * change order * try host * change back * try channels * change back * try * change back * try * try * change back * try * change back * try * change back * try * try * try * switch source * try * try * try * try * try * try * try * try * try * try * try * try * update version * remove pip --------- Co-authored-by: mark0428 --- recipes/amplify/build.sh | 4 ++-- recipes/amplify/meta.yaml | 10 +++++++--- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/recipes/amplify/build.sh b/recipes/amplify/build.sh index 94a9322f414cc..3795944d08f32 100644 --- a/recipes/amplify/build.sh +++ b/recipes/amplify/build.sh @@ -4,8 +4,8 @@ mkdir -p ${PREFIX}/bin/ mkdir -p ${PREFIX}/share/amplify/ mkdir -p ${PREFIX}/share/amplify/src/ mkdir -p ${PREFIX}/share/amplify/models/ -cp -r src/. ${PREFIX}/share/amplify/src -cp -r models/. ${PREFIX}/share/amplify/models +cp -r src/. ${PREFIX}/share/amplify/src/ +cp -r models/. ${PREFIX}/share/amplify/models/ echo "#!/bin/bash" > ${PREFIX}/bin/AMPlify echo "${PREFIX}/share/amplify/src/AMPlify.py \$@" >> ${PREFIX}/bin/AMPlify diff --git a/recipes/amplify/meta.yaml b/recipes/amplify/meta.yaml index 28e7d52ba1728..ec02b944b75d4 100644 --- a/recipes/amplify/meta.yaml +++ b/recipes/amplify/meta.yaml @@ -1,5 +1,5 @@ {% set name = "amplify" %} -{% set version = "1.1.0" %} +{% set version = "2.0.0" %} package: name: '{{ name|lower }}' @@ -7,17 +7,21 @@ package: source: url: https://github.com/bcgsc/AMPlify/archive/v{{ version }}.tar.gz - sha256: 8ce9cc10fbb73048b8d8906a387130d9a1ac24928c4762cd190861d44ebb4466 + sha256: 94418a9e2f09b1cfc63eff047fab6d15cce5a7afae5283e50ab809dac2de8752 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: + host: + - python =3.6 run: - python =3.6 - keras =2.2.4 - - tensorflow =1.12 + - tensorflow >=1.10, <1.13 - numpy <1.17 - biopython - pandas From 781071738ac26efeb4f48b0b412243028c77048b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 15:06:05 -0500 Subject: [PATCH 0297/1813] Update cadd-scripts to 1.7 (#45615) --- recipes/cadd-scripts/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cadd-scripts/meta.yaml b/recipes/cadd-scripts/meta.yaml index 97cc5f5adcd16..57183b15af886 100644 --- a/recipes/cadd-scripts/meta.yaml +++ b/recipes/cadd-scripts/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.6.post1" %} -{% set sha256 = "0f83361c2e3b0f4bbd096d2e07a8cda4593a0d8b82f68ebff3153b161cad78a4" %} +{% set version = "1.7" %} +{% set sha256 = "46f06c31adc7bdde612c60120f892f2a622494b02812fc047e0d3cee6bd25a0f" %} package: name: cadd-scripts From 1eef478a1630988f31d6cc1a0a58f3661a3f91f4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 15:06:51 -0500 Subject: [PATCH 0298/1813] Update pyteomics to 4.7 (#45618) --- recipes/pyteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyteomics/meta.yaml b/recipes/pyteomics/meta.yaml index 1f42dfe14a83d..3a7d5dfd42122 100644 --- a/recipes/pyteomics/meta.yaml +++ b/recipes/pyteomics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.6.3" %} +{% set version = "4.7" %} package: name: pyteomics @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz - sha256: e3bb11e57da3e52ca768d94fed12c9f66d7300fd58bccbc6736dfc0707fd9546 + sha256: 9f3f83da617c9e7576a927f1dd668f0725789384545e3bc1fd53401d829534c2 build: noarch: python From cd5027d272e093218559cd9558b31699405cced7 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Mon, 5 Feb 2024 15:10:21 -0800 Subject: [PATCH 0299/1813] Update ntjoin (#45626) --- recipes/ntjoin/meta.yaml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/recipes/ntjoin/meta.yaml b/recipes/ntjoin/meta.yaml index 6d7500b02bc9f..d49a1ecaaa371 100644 --- a/recipes/ntjoin/meta.yaml +++ b/recipes/ntjoin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: ntjoin @@ -6,16 +6,15 @@ package: source: url: https://github.com/bcgsc/ntJoin/releases/download/v{{ version }}/ntJoin-{{ version }}.tar.gz - sha256: 5c54522841730f454dbdf2ea2ffee01ba647276022d01ecbe74273a1a705265b + sha256: ec24330e11ea63948d1b124273dae79e80088d672f7e536e7d97787f0c2bb644 build: number: 0 - skip: True # [py<38] - run_exports: {{ pin_subpackage("ntjoin", max_pin="x") }} + noarch: generic + run_exports: + - {{ pin_subpackage("ntjoin", max_pin="x") }} requirements: - build: - - {{ compiler('cxx') }} host: - make - python From 2d9e384909e161825c51d5506d24646bfb96b33b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 18:48:48 -0500 Subject: [PATCH 0300/1813] Update pxblat to 1.1.19 (#45632) --- recipes/pxblat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index 62cb7b33e4200..5cb72a84836ff 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "1.1.18" %} -{% set sha256 = "b5d0c4f3ca6e92e01aac24503212760501bd812bff7886b2a28e1219c1511f4d" %} +{% set version = "1.1.19" %} +{% set sha256 = "06a0b96ee259357dfb9838866fd528e21ce893173c26f89ded700907e6e010de" %} package: name: {{ name|lower }} From f20cd2ddd2f5a5fa60d23bf2129e5d3d0dd55b62 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 18:48:58 -0500 Subject: [PATCH 0301/1813] Update ncbi-datasets-pylib to 16.4.5 (#45630) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index ed48d3f17a024..1659ccf273071 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.4" %} -{% set sha256 = "34db22fd526188b0c819c1b9487a183c98c33f65ca940876b52e1debb8a8e450" %} +{% set version = "16.4.5" %} +{% set sha256 = "c7b0aaeda5327e1fccd41774c43bfa936bb176e7790b63bd9ef7d8e14bbd0e27" %} package: name: {{ name|lower }} From 03843c586e24fc71ac76bdadd8190ed8dfbb4ae5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 18:49:07 -0500 Subject: [PATCH 0302/1813] Update fasten to 0.8.0 (#45628) --- recipes/fasten/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fasten/meta.yaml b/recipes/fasten/meta.yaml index dc2a8ac7831b5..f9f67c4e70b88 100644 --- a/recipes/fasten/meta.yaml +++ b/recipes/fasten/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.2" %} -{% set sha256 = "95e6c224c9afe30b857f002c425929f10ef022180915c0e26199cf01ca18dcab" %} +{% set version = "0.8.0" %} +{% set sha256 = "9f699b659b96d32c22f0c42e6a435b31e7ac3c4b45c8ccf8f57f7739f241e6fb" %} package: name: fasten From 905568bf873d5d445597830031df5a19b64cf7cb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 18:49:39 -0500 Subject: [PATCH 0303/1813] Update geofetch to 0.12.6 (#45619) --- recipes/geofetch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/geofetch/meta.yaml b/recipes/geofetch/meta.yaml index b98bdafa490ec..bddae8d83699a 100644 --- a/recipes/geofetch/meta.yaml +++ b/recipes/geofetch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "geofetch" %} -{% set version = "0.12.5" %} +{% set version = "0.12.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 350cad0e7117ae76087b229f1ea0191bebb3bff53d90484aa8cea117c16f812f + sha256: 7ce07c05bad3f18b6f44b79579342604c2b56890e1dec293373b462bf06690b6 build: number: 0 From 3a54c51a356c8376f9756f8dd4ff4b7e371093c7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 18:49:48 -0500 Subject: [PATCH 0304/1813] Update pybiolib to 1.1.1745 (#45612) * Update pybiolib to 1.1.1711 * Update pybiolib to 1.1.1718 * Update pybiolib to 1.1.1734 * Update pybiolib to 1.1.1741 * Update pybiolib to 1.1.1745 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 9676b29d9dd02..102a78061d184 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1703" %} +{% set version = "1.1.1745" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: fce4db168dccecd6500d5967d307a3fbd26bd4c4d586668a189f72103b75edbf + sha256: 3215bc496f4ddaf85d3cb327ccc19bf6a6b5f4c0edc339e0967804239dfb44e5 build: noarch: python From 4b0265d358dd3e143f12f2e087f9ceb0259e2769 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 19:19:14 -0500 Subject: [PATCH 0305/1813] Update snakemake to 8.4.4 (#45617) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index d3b7e490033f6..925989c5dbf9c 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.3" %} +{% set version = "8.4.4" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 2c1aad84792beeed8f05933978849b787409d8b96b44890fb96baee737844fbc + sha256: 03cc7383d7ab0fb5b8a18d5b842a27cb686b87c4eef1bc9922b914f405d90370 build: number: 0 From 5dba445993e89785062542faeb9a48abc585e1d5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 19:19:28 -0500 Subject: [PATCH 0306/1813] Update wfmash to 0.12.6 (#45629) --- recipes/wfmash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wfmash/meta.yaml b/recipes/wfmash/meta.yaml index 8ba197d1380e3..ac6ba6133b387 100644 --- a/recipes/wfmash/meta.yaml +++ b/recipes/wfmash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "wfmash" %} -{% set version = "0.12.5" %} +{% set version = "0.12.6" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/waveygang/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 797e2f968c85c631f60835ec63268fed2aba39858e7e3b30f29613b8defc40c1 + sha256: 1be1a103bf2a346b8b31aaf2a945e2477a43bb03ff4484090deedb5bb0b4e78d build: skip: True # [osx] From 73840649d408111f91d61ba80729c44eeef2542c Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Mon, 5 Feb 2024 16:39:40 -0800 Subject: [PATCH 0307/1813] Update meta.yaml (#45631) --- recipes/ampliconsuite/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index 24da7d68a4da9..84d1fa2b1de45 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,7 +1,7 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.2.1" %} -{% set AA_version="1.3.r7" %} -{% set AC_version="1.1.1" %} +{% set AS_version="1.2.2" %} +{% set AA_version="1.3.r8" %} +{% set AC_version="1.1.2" %} package: name: {{ name }} @@ -11,12 +11,12 @@ source: # the sha256 sum is generated by doing # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: 79515b2c1a57a8ea22905737f3c02047a4319d7ab91554dff1a058ead653c720 + sha256: 40d3b4560fb2c9fd0cbc5166b9d136751ff16217a6228fb38b74e12207ef5b63 - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz - sha256: be65a0293da9ced3f6f744657db475c16dd4dcaf9f037e17ee1a19f4ceaa7430 + sha256: 44466fb4a275f5dd1a142269bb72dc53a651b9d9193e5ba799eee14f0f693f89 folder: ampliconarchitectlib - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz - sha256: 040400d2eb0b4c847245666a481de927eb0c9a368088c1e97f117e7a228c8c5d + sha256: 0f57d0775d7b68a76fab6cc375e45410fe76dd9245697855f257378bd1f21650 build: noarch: python From 80485ae7a76a60e8ebe7c207ee7920eacc7d018b Mon Sep 17 00:00:00 2001 From: Kristina Gagalova Date: Tue, 6 Feb 2024 08:45:13 +0800 Subject: [PATCH 0308/1813] Add occultercut to recipe (#45510) * occultercut recepy added * updated occultercut * update for run_exports * adding gcc libs * updated meta * test with excluded prefix * lint test * clean up recipe * edit build.sh --------- Co-authored-by: mencian --- recipes/occultercut/build.sh | 17 ++++++++++++++ recipes/occultercut/meta.yaml | 44 +++++++++++++++++++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 recipes/occultercut/build.sh create mode 100644 recipes/occultercut/meta.yaml diff --git a/recipes/occultercut/build.sh b/recipes/occultercut/build.sh new file mode 100644 index 0000000000000..9e2e9cc3758cf --- /dev/null +++ b/recipes/occultercut/build.sh @@ -0,0 +1,17 @@ +#!/bin/bash +set -eu -o pipefail +# +# CONDA build script variables +# +# $PREFIX The install prefix +# + +mkdir -p "${PREFIX}/bin" + +export CPLUS_INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +make CC="${GXX} ${LDFLAGS}" CFLAGS="${CFLAGS}" + +cp OcculterCut "${PREFIX}/bin" diff --git a/recipes/occultercut/meta.yaml b/recipes/occultercut/meta.yaml new file mode 100644 index 0000000000000..9cee221adf90c --- /dev/null +++ b/recipes/occultercut/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "occultercut" %} +{% set version = "1.1" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: "https://downloads.sourceforge.net/project/{{ name }}/OcculterCut_v{{ version }}.tar.gz" + sha256: 34aa8c3ef4c216435b4f722ea25f9dc431ef6937e47cfeb5afa323d451cc06ae + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('occultercut', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - libgomp # [linux] + - llvm-openmp # [osx] + run: + - gnuplot + +test: + commands: + - OcculterCut | grep "OcculterCut" + +about: + license: GPL-3.0-or-later + license_family: GPL3 + license_file: COPYING + summary: 'A package for measuring the local GC-content bias in genomes and fungal species' + home: https://sourceforge.net/projects/occultercut + +extra: + identifiers: + - doi:10.1093/gbe/evw121 + recipe-maintainers: + - KristinaGagalova From 2dcd65120c6f85dbfe06ef93e5b8a6ca69332bca Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 20:02:16 -0500 Subject: [PATCH 0309/1813] Update viralmsa to 1.1.43 (#45635) --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 51aad2edd4c70..8c476c2293244 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.42" %} +{% set version = "1.1.43" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: dd4ba1779681479f86c3fa38c486ee36ee8f2ca5d66301e583125dc9767d1171 + sha256: 15adaed42f65e2b6a0ba7e6db498fd67f3227b4658f555313194d5b73234ed89 requirements: run: From 0b7f7f00a6a30763db6ef0383006ef10c3c341c6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 20:52:32 -0500 Subject: [PATCH 0310/1813] Update last to 1541 (#45638) --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 0bb421e9f8b58..9298623f84248 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1540" %} +{% set version = "1541" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 047d5ec2f3745f14e29de72c606fa9e74393723ebac9286584435650201de0cf + sha256: 80165ad97bd651b038ca187cc990c930ec96a0a9f5715a2179b5b75304ed64f9 build: number: 0 From da36dfa42c9ec55809127008b77d80a5997d27a5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 20:55:58 -0500 Subject: [PATCH 0311/1813] Update dnaapler to 0.7.0 (#45637) --- recipes/dnaapler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index 3417697c03deb..afdd8db8dc58a 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.6.0" %} +{% set version = "0.7.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b68c138bf11285f5f09add09ae44e5342c8809ce349a1bce6446d8e64f06510d + sha256: 1ae921824055e8c4e9f7651ddd4d4011612f863f17cb95b496849de03560304f build: number: 0 From c0d1a880eac3ee2dbbbbfe0509d89cba39e723f9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 22:05:13 -0500 Subject: [PATCH 0312/1813] Update ontime to 0.3.0 (#45647) --- recipes/ontime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ontime/meta.yaml b/recipes/ontime/meta.yaml index 84e0131fe612f..1528ba3889c8a 100644 --- a/recipes/ontime/meta.yaml +++ b/recipes/ontime/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.3" %} +{% set version = "0.3.0" %} {% set name = "ontime" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: 6ac4f5e76cb01c16e306661d865a11918604873b5d057afa1a8a37dc4829e682 + sha256: 808833ade04fa7fb318e37b2f0aad2f19a46ba678decdd34e208bf3042050ee1 build: number: 0 From 02a2c6ec09843d2298bf81380638e3e609d5d34b Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Tue, 6 Feb 2024 13:39:02 +0100 Subject: [PATCH 0313/1813] Fix deeptoolsintervals license (#45655) Co-authored-by: Devon Ryan --- recipes/deeptoolsintervals/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/deeptoolsintervals/meta.yaml b/recipes/deeptoolsintervals/meta.yaml index 592130b2c9fbe..c5b740e31279a 100644 --- a/recipes/deeptoolsintervals/meta.yaml +++ b/recipes/deeptoolsintervals/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6 build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage("deeptoolsintervals", max_pin="x.x") }} From f1956c415384f8e879f92a4dd6cab0fb21bc7053 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 10:38:00 -0500 Subject: [PATCH 0314/1813] Update orthanq to 1.2.0 (#45656) --- recipes/orthanq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/orthanq/meta.yaml b/recipes/orthanq/meta.yaml index 946b26b7f0fd4..fcd3ab4b27ca6 100644 --- a/recipes/orthanq/meta.yaml +++ b/recipes/orthanq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} package: name: orthanq @@ -11,7 +11,7 @@ build: source: url: https://github.com/orthanq/orthanq/archive/v{{ version }}.tar.gz - sha256: 5ce1d2826404c04f1de8e5c543c0e23cc23b693f5d190c2602e654d510375bbd + sha256: dbb7e68ef2c16d23aad479978b5403ae652e05a0b37635f55b59c61e08197477 requirements: build: From 59cd4ae30912ad61724e97260de00e793f0cbdc2 Mon Sep 17 00:00:00 2001 From: Tim15-tech <116898385+Tim15-tech@users.noreply.github.com> Date: Tue, 6 Feb 2024 17:08:49 +0100 Subject: [PATCH 0315/1813] Add neat (#45517) Authored-by: Tim15-tech --- recipes/neat/meta.yaml | 49 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/neat/meta.yaml diff --git a/recipes/neat/meta.yaml b/recipes/neat/meta.yaml new file mode 100644 index 0000000000000..e302227fc03b2 --- /dev/null +++ b/recipes/neat/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "NEAT" %} +{% set version = "4.0" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://github.com/ncsa/{{ name }}/archive/{{ version }}.tar.gz + sha256: 89abf23f202e4e93fc333a2b6f2a7c7b63ef3db691f8372b659d8627df3616c3 + + +build: + run_exports: + - {{ pin_subpackage('neat', max_pin="x") }} + script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed --no-cache-dir -vvv ." + number: 0 + noarch: python + +requirements: + host: + - python >=3.10 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.10 + - biopython =1.79 + - pkginfo + - matplotlib-base + - numpy + - seaborn + - pyyaml + - scipy + - bedtools + - pybedtools >=0.9.0 + - htslib + - pysam + - frozendict + +test: + commands: + - neat -h | grep read-simulator + +about: + home: https://github.com/ncsa/NEAT/ + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE.md + summary: Toolset for generating synthethic FASTQ, VCF and BAM files. From bff7893c4c459342d4ed4af2aef28f2f9a19732f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 11:21:26 -0500 Subject: [PATCH 0316/1813] Update recentrifuge to 1.14.0 (#45650) --- recipes/recentrifuge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/recentrifuge/meta.yaml b/recipes/recentrifuge/meta.yaml index 8f89c36bb4498..792c16374b7da 100644 --- a/recipes/recentrifuge/meta.yaml +++ b/recipes/recentrifuge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recentrifuge" %} -{% set version = "1.13.2" %} +{% set version = "1.14.0" %} package: name: {{ name }} @@ -14,7 +14,7 @@ build: source: url: https://github.com/khyox/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 548cfe12d075e3d9e9c01e380891acc5278eae20e075818d7863136e7cf20b81 + sha256: 8151fe3f7d6581f487eb10fab61ef211b132b0774128ed7d060b5fe389d69674 requirements: host: From 83c133a2bc8e53f9e31ddabb8379768342e82f89 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 11:58:28 -0500 Subject: [PATCH 0317/1813] Update phylophlan to 3.1 (#45652) * Update phylophlan to 3.1 --------- Co-authored-by: Francesco Asnicar --- recipes/phylophlan/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/phylophlan/meta.yaml b/recipes/phylophlan/meta.yaml index e5e40d9312b5b..30b9723246e4e 100644 --- a/recipes/phylophlan/meta.yaml +++ b/recipes/phylophlan/meta.yaml @@ -1,6 +1,6 @@ {% set name = "phylophlan" %} -{% set version = "3.0.3" %} -{% set sha256 = "d8d0082c95d58d7b11a60c1e2214b35c1a23a65675005f1393e7647d76c6a054" %} +{% set version = "3.1" %} +{% set sha256 = "9428a8fceb2626325fb6b93cc47143b100183c314f50eb96b32467e42a5bc4ad" %} package: name: "{{ name|lower }}" @@ -15,6 +15,8 @@ build: noarch: python number: 0 script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + run_exports: + - {{ pin_subpackage('phylophlan', max_pin='x.x') }} requirements: host: @@ -39,13 +41,14 @@ requirements: - raxml >=8.2.10 - iqtree >=1.6.6 - mash + - requests test: commands: - phylophlan --version - phylophlan_draw_metagenomic --version - phylophlan_get_reference --version - - phylophlan_metagenomic --version + - phylophlan_assign_sgbs --version - phylophlan_setup_database --version - phylophlan_strain_finder --version - phylophlan_write_config_file --version From 21b9391d4851e48a3f8e9299a2e34707fac222ad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 12:40:41 -0500 Subject: [PATCH 0318/1813] Update thapbi-pict to 1.0.8 (#45660) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 176bda0e09969..9ea4719fe92bd 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.7" %} +{% set version = "1.0.8" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: 30381e97d0af98fd4d0924130f4efaa722e8e5a3cc7a4719c7bc597d87d9e5fa + sha256: 3e0eac668b35351ea5588b0e1890ccf2e10e7aa847efd7777fd5eca497f4eef0 build: noarch: python From f47d059a40b2fb6ccfc39ce706aba680fe6f796c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 13:53:10 -0500 Subject: [PATCH 0319/1813] Update lusstr to 0.9 (#45659) --- recipes/lusstr/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/lusstr/meta.yaml b/recipes/lusstr/meta.yaml index 53b7162c304b2..58fb667975528 100644 --- a/recipes/lusstr/meta.yaml +++ b/recipes/lusstr/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8" %} -{% set sha256 = "3da4c843744c84ac4bc3057b84783cbd95062df05565a66a868541e1170506ca" %} +{% set version = "0.9" %} +{% set sha256 = "abb32bac6d4fd86fbbcd630ef2b254ff66a5658bb3ef6efeb014c7304118561e" %} package: name: lusstr @@ -14,7 +14,7 @@ build: entry_points: - lusstr = lusSTR.cli:main script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv - number: 1 + number: 0 run_exports: - {{ pin_subpackage('lusstr', max_pin="x.x") }} From 9051c1bb4e568c5e22331f9e3877d243d3e66a74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Loraine=20Brillet-Gu=C3=A9guen?= Date: Tue, 6 Feb 2024 20:52:31 +0100 Subject: [PATCH 0320/1813] Update kmer-jellyfish to 2.3.1 (#45651) * update to 2.3.1 * Remove from blasklist. Bump version. Add run_exports * fix run_exports location * fix paxkage name in run_exports * following jellyfish installation doc from tar ball --- build-fail-blacklist | 1 - recipes/kmer-jellyfish/build.sh | 3 +-- recipes/kmer-jellyfish/meta.yaml | 14 +++++--------- 3 files changed, 6 insertions(+), 12 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 743eb04f0d076..e6c6649ef9f6f 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1044,7 +1044,6 @@ recipes/sweepfinder2 # syntax error in configure script recipes/kat -recipes/kmer-jellyfish # unicode error when packaging license file recipes/mapseq diff --git a/recipes/kmer-jellyfish/build.sh b/recipes/kmer-jellyfish/build.sh index c10cb1869a9c5..071a68120b44c 100644 --- a/recipes/kmer-jellyfish/build.sh +++ b/recipes/kmer-jellyfish/build.sh @@ -1,6 +1,5 @@ #!/bin/bash -autoreconf -fi ./configure --prefix=$PREFIX -make +make -j 4 make install diff --git a/recipes/kmer-jellyfish/meta.yaml b/recipes/kmer-jellyfish/meta.yaml index 14cf2981e3866..9d58c7c727f83 100644 --- a/recipes/kmer-jellyfish/meta.yaml +++ b/recipes/kmer-jellyfish/meta.yaml @@ -1,26 +1,22 @@ -{% set version = "2.3.0" %} +{% set version = "2.3.1" %} package: name: kmer-jellyfish version: {{ version }} build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage("kmer-jellyfish", max_pin="2.3.1") }} source: url: https://github.com/gmarcais/Jellyfish/releases/download/v{{ version }}/jellyfish-{{ version }}.tar.gz - sha256: e195b7cf7ba42a90e5e112c0ed27894cd7ac864476dc5fb45ab169f5b930ea5a + sha256: ee032b57257948ca0f0610883099267572c91a635eecbd88ae5d8974c2430fcd requirements: build: - make - {{ compiler('cxx') }} - - autoconf <2.7 # configure script has a problem with later autoconf - - automake - - gettext - - libtool - - pkg-config - - yaggo >=1.5.8 test: commands: From 2c2756d2f5e916ed2681357b3ffe1f83e69d48d5 Mon Sep 17 00:00:00 2001 From: Jaebeom Kim <68528165+jaebeom-kim@users.noreply.github.com> Date: Wed, 7 Feb 2024 05:14:58 +0900 Subject: [PATCH 0321/1813] metabuli1.0.3 (#45648) --- recipes/metabuli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metabuli/meta.yaml b/recipes/metabuli/meta.yaml index 3c74fd689a9fd..f096860d05815 100644 --- a/recipes/metabuli/meta.yaml +++ b/recipes/metabuli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.0.2" %} -{% set sha256 = "cf5c74a7aa585457c0014614e59cf850aaacfab03f326e6113466fa2b436d2c2" %} +{% set version = "1.0.3" %} +{% set sha256 = "facfc3c411b4732e80ac4dfaccf1057cf8b86da4a8d4f05667b1f07dbb18077d" %} package: name: metabuli From f0b6eab6d297730995d3b9bb2184d7250977cbc2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:37:19 -0500 Subject: [PATCH 0322/1813] Update earlgrey to 4.0.7 (#45654) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index 19c3246edd5ab..c9c4b8f190d19 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.6" %} -{% set sha256 = "bc4ba13a2f7cf10ef6eedec17529bf8e191ecdd81d85d9db8a788467e282d655" %} +{% set version = "4.0.7" %} +{% set sha256 = "d986ede4ffd3f06c5ea6ac3578c656942214031786b7e7e462b4b0ed4dbec6bd" %} package: name: {{ name|lower }} From f15d5564b19604f3a957a665788b0cd9d3c8ea01 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:37:34 -0500 Subject: [PATCH 0323/1813] Update fasten to 0.8.1 (#45658) --- recipes/fasten/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fasten/meta.yaml b/recipes/fasten/meta.yaml index f9f67c4e70b88..79537796084c4 100644 --- a/recipes/fasten/meta.yaml +++ b/recipes/fasten/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.0" %} -{% set sha256 = "9f699b659b96d32c22f0c42e6a435b31e7ac3c4b45c8ccf8f57f7739f241e6fb" %} +{% set version = "0.8.1" %} +{% set sha256 = "35314fa8b6c8d2139338ed070f1c171b06bb7760efecf3e06064bc521399e2cd" %} package: name: fasten From 3a79d44486944b1d5971a5bff278cc36d6e728ac Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:38:09 -0500 Subject: [PATCH 0324/1813] Update clipkit to 2.1.2 (#45661) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index 561c6ffd1651e..5f005ed5c3b4f 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.1.1" %} +{% set version = "2.1.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 21120216b1211db5dfbd97e575af882072e90065872aefdf1b34d55544ea881c + sha256: 37d1c5a877174048dc78e6a658dc2879e3385d054dbbc6fba0f336e457146a16 build: number: 0 From d8f470dfd012a46db8a77b8f0b9d94d61f760e17 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:41:14 -0500 Subject: [PATCH 0325/1813] Update snakemake to 8.4.6 (#45662) * Update snakemake to 8.4.5 * Update snakemake to 8.4.6 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 925989c5dbf9c..4a8831860540c 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.4" %} +{% set version = "8.4.6" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 03cc7383d7ab0fb5b8a18d5b842a27cb686b87c4eef1bc9922b914f405d90370 + sha256: 173df5ef2674191fe61c67f9a9e13fc7cbcca318d470a1d8e652f556ce706545 build: number: 0 From 39552766d0a7b7e3b7508870b2650a148ab73042 Mon Sep 17 00:00:00 2001 From: Leonid Kostrykin Date: Wed, 7 Feb 2024 00:04:58 +0100 Subject: [PATCH 0326/1813] Update superdsm to 0.2.0 (#45664) * Update superdsm to 0.2.0 * Fix `missing_run_exports` --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> --- recipes/superdsm/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/superdsm/meta.yaml b/recipes/superdsm/meta.yaml index 12aa1e1c73a4d..2cd31150b245f 100644 --- a/recipes/superdsm/meta.yaml +++ b/recipes/superdsm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SuperDSM" %} -{% set version = "0.1.3" %} +{% set version = "0.2.0" %} {% set repo_url = "https://github.com/BMCV/SuperDSM" %} {% set docs_url = "https://superdsm.readthedocs.io" %} @@ -9,12 +9,14 @@ package: source: url: "{{ repo_url }}/archive/refs/tags/v{{ version }}.zip" - sha256: f55abbd6818a66886ddfe3f7fd9c5dd93c63ed2b6e3179552106e560a000ad5f + sha256: 9e9365f8df6e925851dd2bf2adeb71cdb52a6d20c775b1da4c7d8e641a02f8d7 build: - number: 1 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv " + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} requirements: host: From 30586d369228b0fe53516842dbbb7bc0ddd45b2e Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 10:33:31 +1100 Subject: [PATCH 0327/1813] Add hmftools-bam-tools 1.2 (#45642) --- recipes/hmftools-bam-tools/bamtools.sh | 69 ++++++++++++++++++++++++++ recipes/hmftools-bam-tools/build.sh | 12 +++++ recipes/hmftools-bam-tools/meta.yaml | 30 +++++++++++ 3 files changed, 111 insertions(+) create mode 100755 recipes/hmftools-bam-tools/bamtools.sh create mode 100644 recipes/hmftools-bam-tools/build.sh create mode 100644 recipes/hmftools-bam-tools/meta.yaml diff --git a/recipes/hmftools-bam-tools/bamtools.sh b/recipes/hmftools-bam-tools/bamtools.sh new file mode 100755 index 0000000000000..bee5781030da9 --- /dev/null +++ b/recipes/hmftools-bam-tools/bamtools.sh @@ -0,0 +1,69 @@ +#!/bin/bash +# hmftools BamTools executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/bam-tools +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' + then + pass_args="$arg" + else + pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg + fi + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/bamtools.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/bamtools.jar" $pass_args +fi +exit diff --git a/recipes/hmftools-bam-tools/build.sh b/recipes/hmftools-bam-tools/build.sh new file mode 100644 index 0000000000000..4f02d98736648 --- /dev/null +++ b/recipes/hmftools-bam-tools/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p "$TGT" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +mv bam-tools*.jar $TGT/bamtools.jar + +cp $RECIPE_DIR/bamtools.sh $TGT/bamtools +ln -s $TGT/bamtools $PREFIX/bin +chmod 0755 "${PREFIX}/bin/bamtools" diff --git a/recipes/hmftools-bam-tools/meta.yaml b/recipes/hmftools-bam-tools/meta.yaml new file mode 100644 index 0000000000000..138a0147d66af --- /dev/null +++ b/recipes/hmftools-bam-tools/meta.yaml @@ -0,0 +1,30 @@ +{% set version = "1.2" %} +{% set sha256 = "552f157861c22a0af22ce19400e6771a8034bdbfedbc760f287a30ac794d36c8" %} + +package: + name: hmftools-bam-tools + version: '{{ version }}' + +source: + url: https://github.com/hartwigmedical/hmftools/releases/download/bam-tools-v{{ version }}/bam-tools_v{{ version }}.jar + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("hmftools-bam-tools", max_pin="x.x") }} + +requirements: + run: + - openjdk >=8 + +test: + commands: + - 'bamtools -version | grep BamTools' + +about: + home: https://github.com/hartwigmedical/hmftools/blob/master/bam-tools/README.md + license: GPL-3.0-only + license_family: GPL3 + summary: Rapidly process BAMs for various tasks. From 4f6f76b6825ed6eae8eca20c5be1f5b4fb6e663c Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 10:36:26 +1100 Subject: [PATCH 0328/1813] Add hmftools-virus-interpreter 1.3 (#45644) --- recipes/hmftools-virus-interpreter/build.sh | 12 ++++ recipes/hmftools-virus-interpreter/meta.yaml | 30 ++++++++ .../virusinterpreter.sh | 69 +++++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 recipes/hmftools-virus-interpreter/build.sh create mode 100644 recipes/hmftools-virus-interpreter/meta.yaml create mode 100755 recipes/hmftools-virus-interpreter/virusinterpreter.sh diff --git a/recipes/hmftools-virus-interpreter/build.sh b/recipes/hmftools-virus-interpreter/build.sh new file mode 100644 index 0000000000000..9016c03d49166 --- /dev/null +++ b/recipes/hmftools-virus-interpreter/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p "$TGT" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +mv virus-interpreter*.jar $TGT/virusinterpreter.jar + +cp $RECIPE_DIR/virusinterpreter.sh $TGT/virusinterpreter +ln -s $TGT/virusinterpreter $PREFIX/bin +chmod 0755 "${PREFIX}/bin/virusinterpreter" diff --git a/recipes/hmftools-virus-interpreter/meta.yaml b/recipes/hmftools-virus-interpreter/meta.yaml new file mode 100644 index 0000000000000..d667dc1e799d2 --- /dev/null +++ b/recipes/hmftools-virus-interpreter/meta.yaml @@ -0,0 +1,30 @@ +{% set version = "1.3" %} +{% set sha256 = "b2abfcd2526e0de335455fa687fae0bfeda2f9358c53c7aa0a07bb765ea50545" %} + +package: + name: hmftools-virus-interpreter + version: '{{ version }}' + +source: + url: https://github.com/hartwigmedical/hmftools/releases/download/virus-interpreter-v{{ version }}/virus-interpreter_v{{ version }}.jar + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("hmftools-virus-interpreter", max_pin="x.x") }} + +requirements: + run: + - openjdk >=8 + +test: + commands: + - 'virusinterpreter | grep "Virus Interpreter"' + +about: + home: https://github.com/hartwigmedical/hmftools/blob/master/virus-interpreter/README.md + license: GPL-3.0-only + license_family: GPL3 + summary: Post-process VIRUSBreakend summary results. diff --git a/recipes/hmftools-virus-interpreter/virusinterpreter.sh b/recipes/hmftools-virus-interpreter/virusinterpreter.sh new file mode 100755 index 0000000000000..7ee6eced678ff --- /dev/null +++ b/recipes/hmftools-virus-interpreter/virusinterpreter.sh @@ -0,0 +1,69 @@ +#!/bin/bash +# hmftools Virus Interpreter executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/virus-interpreter +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' + then + pass_args="$arg" + else + pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg + fi + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/virusinterpreter.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/virusinterpreter.jar" $pass_args +fi +exit From cce790c8b88bd2913452a2e903685c26996a36b5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 18:41:33 -0500 Subject: [PATCH 0329/1813] Update pxblat to 1.1.20 (#45666) --- recipes/pxblat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index 5cb72a84836ff..d3b6b59fc8765 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "1.1.19" %} -{% set sha256 = "06a0b96ee259357dfb9838866fd528e21ce893173c26f89ded700907e6e010de" %} +{% set version = "1.1.20" %} +{% set sha256 = "38820df0fc8ae988446b0d69ab75ff93250e02c603c5a529d23e7b1debc34749" %} package: name: {{ name|lower }} From 2527a1fba2757ffc0d6a396fec279d1cc993edae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 18:42:25 -0500 Subject: [PATCH 0330/1813] Update mass2chem to 0.5.0 (#45668) --- recipes/mass2chem/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mass2chem/meta.yaml b/recipes/mass2chem/meta.yaml index 7f7f765b95914..c5a5ce11d8bf2 100644 --- a/recipes/mass2chem/meta.yaml +++ b/recipes/mass2chem/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mass2chem" %} -{% set version = "0.4.9" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mass2chem-{{ version }}.tar.gz - sha256: 5f570440aa217f2f2847f8b2d7cba06c2b46a4088921079db1ed0941b30c1e4b + sha256: 0ef8a49e9ae7e39502edf881249bbdeb445225ae91e6b96da3828a3793f0f8f5 build: noarch: python From decf1eadb865e7460332cd0bd0dd1e2e0e939deb Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 11:36:52 +1100 Subject: [PATCH 0331/1813] Add r-mutsigextractor 1.14 (#45646) --- recipes/r-mutsigextractor/build.sh | 2 ++ recipes/r-mutsigextractor/meta.yaml | 40 +++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 recipes/r-mutsigextractor/build.sh create mode 100644 recipes/r-mutsigextractor/meta.yaml diff --git a/recipes/r-mutsigextractor/build.sh b/recipes/r-mutsigextractor/build.sh new file mode 100644 index 0000000000000..af6547bf3c22e --- /dev/null +++ b/recipes/r-mutsigextractor/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +$R CMD INSTALL --build . diff --git a/recipes/r-mutsigextractor/meta.yaml b/recipes/r-mutsigextractor/meta.yaml new file mode 100644 index 0000000000000..69edb0f20c627 --- /dev/null +++ b/recipes/r-mutsigextractor/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.14" %} +{% set sha256 = "96b5b7071209e8cf973b3147866f41d4e51c941c6a469be87f953deacfc3b1a6" %} + +package: + name: r-mutsigextractor + version: '{{ version }}' + +source: + url: https://github.com/UMCUGenetics/mutSigExtractor/archive/refs/tags/{{ version }}.tar.gz + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("r-mutsigextractor", max_pin="x.x") }} + +requirements: + host: + - r-base + - bioconductor-genomeinfodb + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 + run: + - r-base + - bioconductor-genomeinfodb + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 + +test: + commands: + - $R -e "library('mutSigExtractor')" + +about: + home: https://github.com/UMCUGenetics/mutSigExtractor + license: GPL-3.0-only + license_family: GPL3 + summary: Extract mutational signatures from VCF files From 813e7d69148dd129dc61a33685b4b6c6e063e021 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:04:42 -0500 Subject: [PATCH 0332/1813] Update r-mutsigextractor to 1.28 (#45670) --- recipes/r-mutsigextractor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-mutsigextractor/meta.yaml b/recipes/r-mutsigextractor/meta.yaml index 69edb0f20c627..43ca06abbf2c8 100644 --- a/recipes/r-mutsigextractor/meta.yaml +++ b/recipes/r-mutsigextractor/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.14" %} -{% set sha256 = "96b5b7071209e8cf973b3147866f41d4e51c941c6a469be87f953deacfc3b1a6" %} +{% set version = "1.28" %} +{% set sha256 = "395d89050444f87babf22e3341d4898e3b0d283462ffb1f161da3b8bdc975aee" %} package: name: r-mutsigextractor From 50f47d16abda9d897f90041e1000ac5ece87bd0b Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 13:05:37 +1100 Subject: [PATCH 0333/1813] Add r-chord 2.02 (#45645) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/r-chord/build.sh | 2 ++ recipes/r-chord/meta.yaml | 42 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 recipes/r-chord/build.sh create mode 100644 recipes/r-chord/meta.yaml diff --git a/recipes/r-chord/build.sh b/recipes/r-chord/build.sh new file mode 100644 index 0000000000000..af6547bf3c22e --- /dev/null +++ b/recipes/r-chord/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +$R CMD INSTALL --build . diff --git a/recipes/r-chord/meta.yaml b/recipes/r-chord/meta.yaml new file mode 100644 index 0000000000000..1053fe03cb7e8 --- /dev/null +++ b/recipes/r-chord/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "2.02" %} +{% set sha256 = "9db52b2d01ddea7d8b97c530683296988e98003a5ee859ae03503666a9013f9f" %} + +package: + name: r-chord + version: '{{ version }}' + +source: + url: https://github.com/UMCUGenetics/CHORD/archive/refs/tags/{{ version }}.tar.gz + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("r-chord", max_pin="x.x") }} + +requirements: + host: + - r-base + - r-mutsigextractor ==1.14 + - r-randomforest + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 + run: + - r-base + - r-mutsigextractor ==1.14 + - r-randomforest + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 + +test: + commands: + - $R -e "library('CHORD')" + +about: + home: https://github.com/UMCUGenetics/CHORD + license: GPL-3.0-only + license_family: GPL3 + summary: Predict HRD using somatic mutations contexts From 8cb7dc800063a98ce8338ca2ed18a7a68d99652e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:06:54 -0500 Subject: [PATCH 0334/1813] Update hmftools-gripss to 2.4 (#45610) * Update hmftools-gripss to 2.4 * Update descriptions * Update test command --------- Co-authored-by: Stephen Watts --- recipes/hmftools-gripss/gripss.sh | 2 +- recipes/hmftools-gripss/meta.yaml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/hmftools-gripss/gripss.sh b/recipes/hmftools-gripss/gripss.sh index fe4779d219887..4798d83fbba05 100755 --- a/recipes/hmftools-gripss/gripss.sh +++ b/recipes/hmftools-gripss/gripss.sh @@ -1,5 +1,5 @@ #!/bin/bash -# hmftools gripss executable shell script +# hmftools GRIPSS executable shell script # https://github.com/hartwigmedical/hmftools/tree/master/gripss set -eu -o pipefail diff --git a/recipes/hmftools-gripss/meta.yaml b/recipes/hmftools-gripss/meta.yaml index a0aab8147d630..60be672c9e61f 100644 --- a/recipes/hmftools-gripss/meta.yaml +++ b/recipes/hmftools-gripss/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.3.5" %} -{% set sha256 = "7df02379f416c6131de5f81ad062ab253277b68d7eb71eae0dc9e9bfe34f3bc6" %} +{% set version = "2.4" %} +{% set sha256 = "7e8fb3631c8bb410650e9d84d43d40c85322e0f73e537feae4d186d54d412411" %} package: name: hmftools-gripss @@ -21,10 +21,10 @@ requirements: test: commands: - - 'gripss 2>&1 | grep -q "loading reference data"' + - 'gripss -version | grep Gripss' about: home: https://github.com/hartwigmedical/hmftools/tree/master/gripss license: GPL-3.0-only license_family: GPL - summary: 'GRIPSS applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output to produce a high confidence set of somatic SV for a tumor sample.' + summary: GRIPSS applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output to produce a high confidence set of somatic SV for a tumor sample. From 8f38e99f8418595ebbe825158191df27fb5715ee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:07:44 -0500 Subject: [PATCH 0335/1813] Update hmftools-sage to 3.4 (#43438) * Update hmftools-sage to 3.3 * Update hmftools-sage to 3.3.1 * add run_exports * Update hmftools-sage to 3.4 * Use lowercasing for BASH script for consistency * Update source URL * Update descriptions * Update test command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Stephen Watts --- recipes/hmftools-sage/build.sh | 6 +++--- recipes/hmftools-sage/meta.yaml | 12 +++++++----- recipes/hmftools-sage/{SAGE.sh => sage.sh} | 2 +- 3 files changed, 11 insertions(+), 9 deletions(-) rename recipes/hmftools-sage/{SAGE.sh => sage.sh} (97%) diff --git a/recipes/hmftools-sage/build.sh b/recipes/hmftools-sage/build.sh index 2763b3328ad10..d7f5400c6ef21 100644 --- a/recipes/hmftools-sage/build.sh +++ b/recipes/hmftools-sage/build.sh @@ -7,6 +7,6 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" cd "${SRC_DIR}" mv sage*.jar $TGT/sage.jar -cp $RECIPE_DIR/SAGE.sh $TGT/SAGE -ln -s $TGT/SAGE $PREFIX/bin -chmod 0755 "${PREFIX}/bin/SAGE" +cp $RECIPE_DIR/sage.sh $TGT/sage +ln -s $TGT/sage $PREFIX/bin +chmod 0755 "${PREFIX}/bin/sage" diff --git a/recipes/hmftools-sage/meta.yaml b/recipes/hmftools-sage/meta.yaml index 04abf8dab70df..8f31690dab7d3 100644 --- a/recipes/hmftools-sage/meta.yaml +++ b/recipes/hmftools-sage/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "3.2.3" %} -{% set sha256 = "a49438afee0f7595ff13f7d44e5ae08edc785dc8f04ef605482d9af59ae940f9" %} +{% set version = "3.4" %} +{% set sha256 = "f4fa9788cd3492a612fafaeb8ea1748c549a644fa4e45b98e6cb19f316793467" %} package: name: hmftools-sage version: '{{ version }}' source: - url: 'https://github.com/hartwigmedical/hmftools/releases/download/sage-v{{ version }}/sage_v{{ version }}.jar' + url: https://github.com/hartwigmedical/hmftools/releases/download/sage-v{{ version }}/sage_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-sage', max_pin="x") }} requirements: run: @@ -27,10 +29,10 @@ requirements: test: commands: - - 'SAGE 2>&1 | grep -q "Sage version"' + - 'sage -version | grep Sage' about: home: https://github.com/hartwigmedical/hmftools/tree/master/sage license: GPL-3.0-only license_family: GPL - summary: SAGE is a somatic SNV, MNV and small INDEL caller optimised to call narrow regions of the genome with high prior chance of a variant with very high sensitivity. + summary: SAGE is a somatic SNV, MNV and small INDEL caller optimised 100x tumor / 40x normal coverage, but has a flexible set of filters that can be adapted to lower or higher depth coverage. diff --git a/recipes/hmftools-sage/SAGE.sh b/recipes/hmftools-sage/sage.sh similarity index 97% rename from recipes/hmftools-sage/SAGE.sh rename to recipes/hmftools-sage/sage.sh index 5e9159203c37f..d5a456e118ba2 100755 --- a/recipes/hmftools-sage/SAGE.sh +++ b/recipes/hmftools-sage/sage.sh @@ -1,6 +1,6 @@ #!/bin/bash # hmftools SAGE executable shell script -# https://github.com/hartwigmedical/hmftools/tree/master/SAGE +# https://github.com/hartwigmedical/hmftools/tree/master/sage set -eu -o pipefail export LC_ALL=en_US.UTF-8 From 38b5edaf4df91fb9a679d806ee48169feb6eed09 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:08:21 -0500 Subject: [PATCH 0336/1813] Update hmftools-purple to 4.0 (#43445) * Update hmftools-purple to 3.8.4 * Update hmftools-purple to 3.9 * Update hmftools-purple to 3.9.1 * Update hmftools-purple to 3.9.2 * add run_exports * edit tests * Update hmftools-purple to 4.0 * Use lowercasing for BASH script for consistency * Update about section * Update test command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Stephen Watts --- recipes/hmftools-purple/build.sh | 6 +++--- recipes/hmftools-purple/meta.yaml | 16 +++++++++------- recipes/hmftools-purple/{PURPLE.sh => purple.sh} | 6 +++--- 3 files changed, 15 insertions(+), 13 deletions(-) rename recipes/hmftools-purple/{PURPLE.sh => purple.sh} (94%) diff --git a/recipes/hmftools-purple/build.sh b/recipes/hmftools-purple/build.sh index 963fc41560196..05ac0857d05be 100644 --- a/recipes/hmftools-purple/build.sh +++ b/recipes/hmftools-purple/build.sh @@ -7,6 +7,6 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" cd "${SRC_DIR}" mv purple*.jar $TGT/purple.jar -cp $RECIPE_DIR/PURPLE.sh $TGT/PURPLE -ln -s $TGT/PURPLE $PREFIX/bin -chmod 0755 "${PREFIX}/bin/PURPLE" +cp $RECIPE_DIR/purple.sh $TGT/purple +ln -s $TGT/purple $PREFIX/bin +chmod 0755 "${PREFIX}/bin/purple" diff --git a/recipes/hmftools-purple/meta.yaml b/recipes/hmftools-purple/meta.yaml index 929b228c38a8b..a5aa250c79fa7 100644 --- a/recipes/hmftools-purple/meta.yaml +++ b/recipes/hmftools-purple/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.7.1" %} -{% set sha256 = "23c5fc9832bfd5e3686c8d2ae2285aff4d6c2ac4683021ff17ec59c48d75694c" %} +{% set version = "4.0" %} +{% set sha256 = "58b2457143f77e7752a907a59f1fdd9550fae7483def373ad39ea4ac8fdbc383" %} package: name: hmftools-purple @@ -12,6 +12,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-purple', max_pin="x") }} requirements: run: @@ -28,10 +30,10 @@ requirements: test: commands: - - 'PURPLE -version' + - 'purple -version | grep Purple' about: - home: https://github.com/hartwigmedical/hmftools/tree/master/purity-ploidy-estimator - license: MIT - license_family: MIT - summary: Purity/ploidy estimator. Leverages the read depth and tumor BAF to estimate the purity of a sample and generate a copy number profile + home: https://github.com/hartwigmedical/hmftools/tree/master/purple + license: GPL-3.0-only + license_family: GPL3 + summary: PURPLE is a purity ploidy estimator for tumor samples. diff --git a/recipes/hmftools-purple/PURPLE.sh b/recipes/hmftools-purple/purple.sh similarity index 94% rename from recipes/hmftools-purple/PURPLE.sh rename to recipes/hmftools-purple/purple.sh index 72618b94ab858..68dfb735ed9b0 100755 --- a/recipes/hmftools-purple/PURPLE.sh +++ b/recipes/hmftools-purple/purple.sh @@ -1,6 +1,6 @@ #!/bin/bash # hmftools PURPLE executable shell script -# https://github.com/hartwigmedical/hmftools/tree/master/purity-ploidy-estimator +# https://github.com/hartwigmedical/hmftools/tree/master/purple set -eu -o pipefail export LC_ALL=en_US.UTF-8 @@ -46,8 +46,8 @@ for arg in "$@"; do ;; *) if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' - then - pass_args="$arg" + then + pass_args="$arg" else pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg fi From b687f5cdf68ff9d7ec5b85025d836af27d65461b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:08:38 -0500 Subject: [PATCH 0337/1813] Update hmftools-pave to 1.6 (#43447) * Update hmftools-pave to 1.4.5 * Update hmftools-pave to 1.5 * add run_exports * edit tests * edit tests against * try lowercase pave * Update hmftools-pave to 1.5.1 * Update hmftools-pave to 1.5.1 * Update hmftools-pave to 1.6 * Update descriptions and licence family * Update source URL * Update test command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Stephen Watts --- recipes/hmftools-pave/meta.yaml | 12 +++++++----- recipes/hmftools-pave/pave.sh | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/hmftools-pave/meta.yaml b/recipes/hmftools-pave/meta.yaml index 8bb0808513d02..84156f65d0e6f 100644 --- a/recipes/hmftools-pave/meta.yaml +++ b/recipes/hmftools-pave/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "1.4.1" %} -{% set sha256 = "eb6dbf7ff5d2729807e5a33709b256fa1537235eb263c1f0b34fba45e60fc4b3" %} +{% set version = "1.6" %} +{% set sha256 = "c553b5224dae4f61958030d2b544ad990aca6fde145ee03f43214856f3dbf634" %} package: name: hmftools-pave version: '{{ version }}' source: - url: 'https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}.jar' + url: https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-pave', max_pin="x.x") }} requirements: run: @@ -20,10 +22,10 @@ requirements: test: commands: - - 'pave 2>&1 | grep -q "Pave version"' + - 'pave -version | grep Pave' about: home: https://github.com/hartwigmedical/hmftools/tree/master/pave license: GPL-3.0-only license_family: GPL - summary: Pave annotates a somatic variant VCF with gene and transcript coding and protein effects. + summary: PAVE annotates SNV/MNV/INDEL calls with consequence on corresponding genes, transcripts, and proteins. diff --git a/recipes/hmftools-pave/pave.sh b/recipes/hmftools-pave/pave.sh index 73ae4b947b422..d3108a6244903 100755 --- a/recipes/hmftools-pave/pave.sh +++ b/recipes/hmftools-pave/pave.sh @@ -1,5 +1,5 @@ #!/bin/bash -# hmftools pave executable shell script +# hmftools PAVE executable shell script # https://github.com/hartwigmedical/hmftools/tree/master/pave set -eu -o pipefail From bb1d8a7c728fd06b49342f2929eaedfbc31119f6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:09:29 -0500 Subject: [PATCH 0338/1813] Update hmftools-linx to 1.25 (#43443) * Update hmftools-linx to 1.24 * Update hmftools-linx to 1.24.1 * add run_exports * Update hmftools-linx to 1.25 * Update descriptions * Update test command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Stephen Watts --- recipes/hmftools-linx/linx.sh | 2 +- recipes/hmftools-linx/meta.yaml | 10 ++++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/hmftools-linx/linx.sh b/recipes/hmftools-linx/linx.sh index 7fe7ef75a7882..7bc92d4b403cb 100755 --- a/recipes/hmftools-linx/linx.sh +++ b/recipes/hmftools-linx/linx.sh @@ -1,5 +1,5 @@ #!/bin/bash -# hmftools linx executable shell script +# hmftools LINX executable shell script # https://github.com/hartwigmedical/hmftools/tree/master/linx set -eu -o pipefail diff --git a/recipes/hmftools-linx/meta.yaml b/recipes/hmftools-linx/meta.yaml index bf53e28de0d52..b7d512fde85ad 100644 --- a/recipes/hmftools-linx/meta.yaml +++ b/recipes/hmftools-linx/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.23.6" %} -{% set sha256 = "6dfeb9c15369d33953193e65db8454e678772c79218643bd122293e59288d297" %} +{% set version = "1.25" %} +{% set sha256 = "2fa9a91801239ded3e82fcd0ee9987e6181d0e400855420ef7f5000f3b4a96da" %} package: name: hmftools-linx @@ -12,6 +12,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-linx', max_pin="x") }} requirements: run: @@ -27,10 +29,10 @@ requirements: test: commands: - - 'linx 2>&1 | grep -q "LINX version"' + - 'linx -version | grep Linx' about: home: https://github.com/hartwigmedical/hmftools/tree/master/linx license: GPL-3.0-only license_family: GPL - summary: Linx is an annotation, interpretation and visualisation tool for structural variants + summary: LINX is an annotation, interpretation and visualisation tool for structural variants. From f3bdce8398674ebf2104f937fce398d3ae51c0ca Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:09:42 -0500 Subject: [PATCH 0339/1813] Update hmftools-lilac to 1.6 (#43421) * Update hmftools-lilac to 1.5 * Update hmftools-lilac to 1.5.1 * Update hmftools-lilac to 1.5.2 * add run_exports * Update hmftools-lilac to 1.5.2 * Update hmftools-lilac to 1.6 * Use lowercasing for BASH script for consistency * Update source URL * Update test command * Use consistent license details, update home URL * Correct malformed build command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Stephen Watts --- recipes/hmftools-lilac/build.sh | 6 +++--- recipes/hmftools-lilac/{LILAC.sh => lilac.sh} | 0 recipes/hmftools-lilac/meta.yaml | 12 +++++++----- 3 files changed, 10 insertions(+), 8 deletions(-) rename recipes/hmftools-lilac/{LILAC.sh => lilac.sh} (100%) diff --git a/recipes/hmftools-lilac/build.sh b/recipes/hmftools-lilac/build.sh index a90fcee0b3303..a65c6f98505e2 100644 --- a/recipes/hmftools-lilac/build.sh +++ b/recipes/hmftools-lilac/build.sh @@ -7,6 +7,6 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" cd "${SRC_DIR}" mv lilac*.jar $TGT/lilac.jar -cp $RECIPE_DIR/LILAC.sh $TGT/LILAC -ln -s $TGT/LILAC $PREFIX/bin -chmod 0755 "${PREFIX}/bin/LILAC" +cp $RECIPE_DIR/lilac.sh $TGT/lilac +ln -s $TGT/lilac $PREFIX/bin +chmod 0755 "${PREFIX}/bin/lilac" diff --git a/recipes/hmftools-lilac/LILAC.sh b/recipes/hmftools-lilac/lilac.sh similarity index 100% rename from recipes/hmftools-lilac/LILAC.sh rename to recipes/hmftools-lilac/lilac.sh diff --git a/recipes/hmftools-lilac/meta.yaml b/recipes/hmftools-lilac/meta.yaml index 0ca7fb2315494..c444f5345d0a3 100644 --- a/recipes/hmftools-lilac/meta.yaml +++ b/recipes/hmftools-lilac/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "1.4.2" %} -{% set sha256 = "1df4a34f3ea777db8da21cd9eaeca19a30795e5eb0bb44c5b38cd705df5c82fe" %} +{% set version = "1.6" %} +{% set sha256 = "d5f5fc5c2fb047fdbc6292a36dc3a164f5bbf820f87ceebafecf1412c41632f6" %} package: name: hmftools-lilac version: '{{ version }}' source: - url: 'https://github.com/hartwigmedical/hmftools/releases/download/lilac-v{{ version }}/lilac_v{{ version }}.jar' + url: https://github.com/hartwigmedical/hmftools/releases/download/lilac-v{{ version }}/lilac_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-lilac', max_pin="x") }} requirements: run: @@ -20,10 +22,10 @@ requirements: test: commands: - - 'LILAC 2>&1 | grep -q "LilacApplication"' + - 'lilac -version | grep Lilac' about: home: https://github.com/hartwigmedical/hmftools/blob/master/lilac/README.md - license: "GNU General Public v3 (GPLv3)" + license: GPL-3.0-only license_family: GPL3 summary: LILAC is a WGS tool to determine HLA Class I types. From a1c2940abf438136cb16e49751e8c339a1f4f2b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:10:41 -0500 Subject: [PATCH 0340/1813] Update hmftools-isofox to 1.7.1 (#43433) * Update hmftools-isofox to 1.7 * add run_exports * Update hmftools-isofox to 1.7.1 * Update descriptions * Update test command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Thanh Lee Co-authored-by: Stephen Watts --- recipes/hmftools-isofox/isofox.sh | 2 +- recipes/hmftools-isofox/meta.yaml | 10 ++++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/hmftools-isofox/isofox.sh b/recipes/hmftools-isofox/isofox.sh index 91bb67218a3dc..1c57bf313dfd7 100755 --- a/recipes/hmftools-isofox/isofox.sh +++ b/recipes/hmftools-isofox/isofox.sh @@ -1,5 +1,5 @@ #!/bin/bash -# hmftools isofox executable shell script +# hmftools Isofox executable shell script # https://github.com/hartwigmedical/hmftools/tree/master/isofox set -eu -o pipefail diff --git a/recipes/hmftools-isofox/meta.yaml b/recipes/hmftools-isofox/meta.yaml index 9cc47f9fe3d22..e3cd0ebf68cfd 100644 --- a/recipes/hmftools-isofox/meta.yaml +++ b/recipes/hmftools-isofox/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.6.2" %} -{% set sha256 = "b681b48f0a0fc31de30a0721c0094f294b1e8fe1fb567447b7bf153120981cd2" %} +{% set version = "1.7.1" %} +{% set sha256 = "978db2ea04f4b8ba07910ad01c145bb23f57c279608b9bd7f27447403a5e25ae" %} package: name: hmftools-isofox @@ -12,6 +12,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-isofox', max_pin="x.x") }} requirements: run: @@ -19,10 +21,10 @@ requirements: test: commands: - - 'isofox 2>&1 | grep -q "Isofox version"' + - 'isofox -version | grep Isofox' about: home: https://github.com/hartwigmedical/hmftools/tree/master/isofox license: GPL-3.0-only license_family: GPL - summary: 'Isofox is a tool for counting fragment support for identifying and counting gene and transcript features using genome aligned RNASeq data in tumor samples.' + summary: Isofox is a tool for counting fragment support for identifying and counting gene and transcript features using genome aligned RNASeq data in tumor samples. From 39ac37c87b8521499c0c50abd76d6b18357abe8c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:14:07 -0500 Subject: [PATCH 0341/1813] Update clipkit to 2.1.3 (#45669) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index 5f005ed5c3b4f..f2d9cc734178e 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.1.2" %} +{% set version = "2.1.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 37d1c5a877174048dc78e6a658dc2879e3385d054dbbc6fba0f336e457146a16 + sha256: e56e6c2c3a0c938f5026151ea191ff8fc2df7822d4aaf6487a65e9357c292487 build: number: 0 From 93b9a26549fc1a447ff8fcff1e8b40beb29445d8 Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren <78838419+alejandrogzi@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:16:05 -0500 Subject: [PATCH 0342/1813] Add gxf2bed (#45665) * new: gtfsort recipe * new: bed2gtf recipe * new: bed2gff recipe * fix: clean recipe * feat: add build.sh * fix: clean recipe; add build.sh * fix: delete other recipes already in PRs * gxt2bed! * fix: typo * gxf2bed recipe! * fix: sha256 * fix: delete other recipes already in PRs --- recipes/gxf2bed/build.sh | 9 +++++++++ recipes/gxf2bed/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/gxf2bed/build.sh create mode 100644 recipes/gxf2bed/meta.yaml diff --git a/recipes/gxf2bed/build.sh b/recipes/gxf2bed/build.sh new file mode 100644 index 0000000000000..8e10cdc3e3237 --- /dev/null +++ b/recipes/gxf2bed/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/gxf2bed/meta.yaml b/recipes/gxf2bed/meta.yaml new file mode 100644 index 0000000000000..0104d86e074a6 --- /dev/null +++ b/recipes/gxf2bed/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "gxf2bed" %} +{% set version = "0.1.0" %} + +package: + name: gxf2bed + version: {{ version }} + +source: + url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 75aa006736b7e03a16bf7cb1dd1e2a7fef87a5cc9d114b2ea603df79042cd2a9 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('gxf2bed', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.39 + - pkg-config + +test: + commands: + - gxf2bed --help + - gxf2bed --version + +about: + home: https://github.com/alejandrogzi/gxf2bed + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Fastest GTF/GFF-to-BED converter chilling around" + +extra: + recipe-maintainers: + - alejandrogzi From d57f07116862a7116e2fa3bb3385f9f0d1be2cfb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:25:43 -0500 Subject: [PATCH 0343/1813] Update nextstrain-cli to 8.2.0 (#45671) --- recipes/nextstrain-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml index e0bbbca25862b..1cef58d2d3db1 100644 --- a/recipes/nextstrain-cli/meta.yaml +++ b/recipes/nextstrain-cli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.0.1" %} +{% set version = "8.2.0" %} package: name: nextstrain-cli @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain-cli-{{ version }}.tar.gz - sha256: b552463d4c4195c9b2e57cf20bfc72e9e6927231715d88ebaec13481328fb080 + sha256: 9b48dd8f32416d43b5f7db8a4a5ca045913a41a4967a5ae189240cbd67c285a2 build: number: 0 From 175142f6ebf760a2a0c4e1316f14e13583f16836 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 13:26:30 +1100 Subject: [PATCH 0344/1813] Apply patches to GRIDSS 2.13.2 (#45641) * Add patches * Bump build number * Add run exports --- recipes/gridss/0001-fix-samtools-version-check.patch | 11 +++++++++++ ...-set-gridssargs-for-virusbreakend-annotation.patch | 10 ++++++++++ recipes/gridss/meta.yaml | 7 ++++++- 3 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 recipes/gridss/0001-fix-samtools-version-check.patch create mode 100644 recipes/gridss/0002-set-gridssargs-for-virusbreakend-annotation.patch diff --git a/recipes/gridss/0001-fix-samtools-version-check.patch b/recipes/gridss/0001-fix-samtools-version-check.patch new file mode 100644 index 0000000000000..7111cf0e23670 --- /dev/null +++ b/recipes/gridss/0001-fix-samtools-version-check.patch @@ -0,0 +1,11 @@ +--- a/gridss_extract_overlapping_fragments ++++ b/gridss_extract_overlapping_fragments +@@ -206,7 +206,7 @@ for tool in gridsstools samtools ; do + fi + write_status "Found $(which $tool)" + done +-samtools_version=$(samtools --version | grep samtools | cut -b 10-) ++samtools_version=$(samtools --version | head -n1 | grep samtools | cut -b 10-) + write_status "samtools version: $samtools_version" + samtools_major_version=$(echo $samtools_version | cut -f 1 -d ".") + samtools_minor_version=$(echo $samtools_version | cut -f 2 -d ".") diff --git a/recipes/gridss/0002-set-gridssargs-for-virusbreakend-annotation.patch b/recipes/gridss/0002-set-gridssargs-for-virusbreakend-annotation.patch new file mode 100644 index 0000000000000..0cab94a467907 --- /dev/null +++ b/recipes/gridss/0002-set-gridssargs-for-virusbreakend-annotation.patch @@ -0,0 +1,10 @@ +--- a/virusbreakend ++++ b/virusbreakend +@@ -777,6 +777,7 @@ if [[ ! -f $file_host_annotated_vcf ]] ; then + -t $threads \ + -r $reference \ + -j $gridss_jar \ ++ $gridssargs \ + -s setupreference \ + 1>&2 2>> $logfile + $timecmd java -Xmx4g $jvm_args \ diff --git a/recipes/gridss/meta.yaml b/recipes/gridss/meta.yaml index 68671af6301ce..478a47b6b0629 100644 --- a/recipes/gridss/meta.yaml +++ b/recipes/gridss/meta.yaml @@ -8,9 +8,14 @@ package: source: url: https://github.com/PapenfussLab/gridss/releases/download/v{{ version }}/gridss-{{ version }}.tar.gz sha256: '{{ sha256 }}' + patches: + - 0001-fix-samtools-version-check.patch + - 0002-set-gridssargs-for-virusbreakend-annotation.patch build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage('gridss', max_pin="x.x.x") }} skip: True # [osx] requirements: From d008acb330d03de84f3ce15ff6474e9cc57fe1b1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:28:38 -0500 Subject: [PATCH 0345/1813] Update phykit to 1.13.0 (#45672) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index 65ffccc3794fc..fdbe8d3ddefe3 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.12.5" %} +{% set version = "1.13.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1a1b33a683663a6fb8be56e00a41803b7e7d09183fc46d7c3a0e193a79e7584b + sha256: 22d074a5862dc6ee8402eaae9202d49d7c38e1ca15f4b55188ad14a99c292aaa build: noarch: python From 6203e5bd3c394de7153078307a5e46ed995ce20b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:35:17 -0500 Subject: [PATCH 0346/1813] Update hmftools-sigs to 1.2.1 (#45609) * Update hmftools-sigs to 1.2 * Update meta.yaml * Adjust for consistency with other hmftools recipes * Update hmftools-sigs to 1.2.1 --------- Co-authored-by: Christian Brueffer Co-authored-by: Stephen Watts --- recipes/hmftools-sigs/meta.yaml | 12 +++++++----- recipes/hmftools-sigs/sigs.sh | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/hmftools-sigs/meta.yaml b/recipes/hmftools-sigs/meta.yaml index 2a510330aeb72..386cadd737c51 100644 --- a/recipes/hmftools-sigs/meta.yaml +++ b/recipes/hmftools-sigs/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "1.1" %} -{% set sha256 = "ef38b1d36e6c326ff06e71f0d690b7503fe38efc91b1e4c4b170277f83093276" %} +{% set version = "1.2.1" %} +{% set sha256 = "b2af1ce3ac401adb145d77b031deb0edcc1d1a5257686cb67a1fc3355a7820e5" %} package: name: hmftools-sigs version: '{{ version }}' source: - url: 'https://github.com/hartwigmedical/hmftools/releases/download/sigs-v{{ version }}/sigs_v{{ version }}.jar' + url: https://github.com/hartwigmedical/hmftools/releases/download/sigs-v{{ version }}/sigs_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-sigs', max_pin='x') }} requirements: run: @@ -20,10 +22,10 @@ requirements: test: commands: - - 'sigs 2>&1 | grep -q "running sample signature fit"' + - 'sigs -version | grep -o Sigs' about: home: https://github.com/hartwigmedical/hmftools/blob/master/sigs/README.md - license: "GNU General Public v3 (GPLv3)" + license: GPL-3.0-only license_family: GPL3 summary: Fits sample SNV counts to trinucleotide signature definitions. diff --git a/recipes/hmftools-sigs/sigs.sh b/recipes/hmftools-sigs/sigs.sh index 85cccef267a09..14bd78f53b009 100755 --- a/recipes/hmftools-sigs/sigs.sh +++ b/recipes/hmftools-sigs/sigs.sh @@ -1,5 +1,5 @@ #!/bin/bash -# hmftools sigs executable shell script +# hmftools Sigs executable shell script # https://github.com/hartwigmedical/hmftools/tree/master/sigs set -eu -o pipefail From 0ac68f8837435211a11727b31796f1f7b6676f7a Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 13:39:14 +1100 Subject: [PATCH 0347/1813] Update hmftools-amber to 4.0 (#45639) * Use lowercasing for BASH script for consistency * Update hmftools-amber to 4.0 * Update source URL * Update test command * Update about section --- recipes/hmftools-amber/{AMBER.sh => amber.sh} | 0 recipes/hmftools-amber/build.sh | 6 +++--- recipes/hmftools-amber/meta.yaml | 14 +++++++------- 3 files changed, 10 insertions(+), 10 deletions(-) rename recipes/hmftools-amber/{AMBER.sh => amber.sh} (100%) diff --git a/recipes/hmftools-amber/AMBER.sh b/recipes/hmftools-amber/amber.sh similarity index 100% rename from recipes/hmftools-amber/AMBER.sh rename to recipes/hmftools-amber/amber.sh diff --git a/recipes/hmftools-amber/build.sh b/recipes/hmftools-amber/build.sh index 60125bce3446e..b6c245c28bb8e 100644 --- a/recipes/hmftools-amber/build.sh +++ b/recipes/hmftools-amber/build.sh @@ -7,6 +7,6 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" cd "${SRC_DIR}" mv amber*.jar $TGT/amber.jar -cp $RECIPE_DIR/AMBER.sh $TGT/AMBER -ln -s $TGT/AMBER $PREFIX/bin -chmod 0755 "${PREFIX}/bin/AMBER" +cp $RECIPE_DIR/amber.sh $TGT/amber +ln -s $TGT/amber $PREFIX/bin +chmod 0755 "${PREFIX}/bin/amber" diff --git a/recipes/hmftools-amber/meta.yaml b/recipes/hmftools-amber/meta.yaml index 0b7a3cc9085f9..d9db37e2a08f3 100644 --- a/recipes/hmftools-amber/meta.yaml +++ b/recipes/hmftools-amber/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "3.9.1" %} -{% set sha256 = "47d2dba76b56252bd0f3a21f535096a97e2d51bc66c087f4f975272c4aaf92ef" %} +{% set version = "4.0" %} +{% set sha256 = "9fad1e78b4f177a8d2a9b6e29a34e86b82ec1239959b1f68c8f9c279fe21dc13" %} package: name: hmftools-amber version: '{{ version }}' source: - url: https://github.com/hartwigmedical/hmftools/releases/download/amber-v{{ version }}/amber-{{ version }}.jar + url: https://github.com/hartwigmedical/hmftools/releases/download/amber-v{{ version }}/amber_v{{ version }}.jar sha256: '{{ sha256 }}' build: @@ -24,10 +24,10 @@ requirements: test: commands: - - 'AMBER 2>&1 | grep -q "tumor_bam"' + - 'amber -version | grep Amber' about: home: https://github.com/hartwigmedical/hmftools/blob/master/amber/README.md - license: MIT - license_family: MIT - summary: Generates a tumor BAF file for use in PURPLE + license: GPL-3.0-only + license_family: GPL3 + summary: Generates a tumor BAF file for use in PURPLE. From a70058b719042a5622b3ec7976111efd9e2e0ae1 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 13:39:38 +1100 Subject: [PATCH 0348/1813] Update hmftools-cobalt to 1.16 (#45640) * Use lowercasing for BASH script for consistency * Update hmftools-cobalt to 1.16 * Update source URL * Update test command * Update about section * Add run exports --- recipes/hmftools-cobalt/build.sh | 8 ++++---- .../hmftools-cobalt/{COBALT.sh => cobalt.sh} | 0 recipes/hmftools-cobalt/meta.yaml | 18 ++++++++++-------- 3 files changed, 14 insertions(+), 12 deletions(-) rename recipes/hmftools-cobalt/{COBALT.sh => cobalt.sh} (100%) diff --git a/recipes/hmftools-cobalt/build.sh b/recipes/hmftools-cobalt/build.sh index 990ea8634c707..092a2525d3136 100644 --- a/recipes/hmftools-cobalt/build.sh +++ b/recipes/hmftools-cobalt/build.sh @@ -5,8 +5,8 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" [ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" cd "${SRC_DIR}" -mv *.jar $TGT/cobalt.jar +mv cobalt*.jar $TGT/cobalt.jar -cp $RECIPE_DIR/COBALT.sh $TGT/COBALT -ln -s $TGT/COBALT $PREFIX/bin -chmod 0755 "${PREFIX}/bin/COBALT" +cp $RECIPE_DIR/cobalt.sh $TGT/cobalt +ln -s $TGT/cobalt $PREFIX/bin +chmod 0755 "${PREFIX}/bin/cobalt" diff --git a/recipes/hmftools-cobalt/COBALT.sh b/recipes/hmftools-cobalt/cobalt.sh similarity index 100% rename from recipes/hmftools-cobalt/COBALT.sh rename to recipes/hmftools-cobalt/cobalt.sh diff --git a/recipes/hmftools-cobalt/meta.yaml b/recipes/hmftools-cobalt/meta.yaml index 9a4418e1c2878..1819596469f37 100644 --- a/recipes/hmftools-cobalt/meta.yaml +++ b/recipes/hmftools-cobalt/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "1.13" %} -{% set sha256 = "d70a6bc73da518d159525caa5186551a771c88441efe1103a3425befd2445215" %} +{% set version = "1.16" %} +{% set sha256 = "9fe1d0f3a1f4270d354b6d3e4a6fa7a556dfbcb2e06775cd6328e1f5dba7a77c" %} package: name: hmftools-cobalt version: '{{ version }}' source: - url: https://github.com/hartwigmedical/hmftools/releases/download/cobalt-v{{ version }}/cobalt-{{ version }}.jar + url: https://github.com/hartwigmedical/hmftools/releases/download/cobalt-v{{ version }}/cobalt_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage("hmftools-cobalt", max_pin="x.x") }} requirements: run: @@ -21,10 +23,10 @@ requirements: test: commands: - - 'COBALT 2>&1 | grep -q "tumor_bam"' + - 'cobalt -version | grep Cobalt' about: home: https://github.com/hartwigmedical/hmftools/blob/master/cobalt/README.md - license: MIT - license_family: MIT - summary: Counts read starts within each 1000 base window to use in PURPLE + license: GPL-3.0-only + license_family: GPL3 + summary: Calculate read-depth counts and GC ratios to use in PURPLE. From 84011f70617327184d333081028f9adceb2b2909 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:40:00 -0500 Subject: [PATCH 0349/1813] Update chromap to 0.2.6 (#45657) * Update chromap to 0.2.6 * add run_exports --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/chromap/meta.yaml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/chromap/meta.yaml b/recipes/chromap/meta.yaml index 1805040802a97..05010a6f787c2 100644 --- a/recipes/chromap/meta.yaml +++ b/recipes/chromap/meta.yaml @@ -1,15 +1,17 @@ -{% set version = "0.2.5" %} +{% set version = "0.2.6" %} package: name: chromap version: {{ version }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('chromap', max_pin="x.x") }} source: url: https://github.com/haowenz/chromap/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9cc77d7412304d41a0a419ba1da11e6794c1dab73cee2e2d71957376b1ddbc7a + sha256: bea2fc76bd7d8931f69db0b63aef19e50070b24c0ab1415569b59d490fff42e8 requirements: build: @@ -28,6 +30,8 @@ test: about: home: https://github.com/haowenz/chromap - license: GPL-3.0 + license: MIT + license_family: MIT license_file: LICENSE summary: Fast alignment and preprocessing of chromatin profiles + doc_url: https://zhanghaowen.com/chromap/ From ce1189e39aee5ce464c2cbb02185c369dd689c15 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 23:37:21 -0500 Subject: [PATCH 0350/1813] Update planemo to 0.75.20 (#45491) * Update planemo to 0.75.20 * bump galaxy-tool version --------- Co-authored-by: mencian --- recipes/planemo/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 344b78da1932e..2fa68f4e4e03e 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.19" %} -{% set sha256 = "4e935cc359071c0aea4a65c965eb96cb5330a33e3dcf66e1a7ad937d72a36083" %} +{% set version = "0.75.20" %} +{% set sha256 = "de61edcb2496c9301b751ac12d0c83441dfcb36cff3a279db3e7942e3fc4b873" %} package: name: {{ name|lower }} @@ -15,7 +15,7 @@ build: noarch: python run_exports: - {{ pin_subpackage('planemo', max_pin='x.x') }} - script: {{ PYTHON }} -m pip install . --no-deps -vvv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - planemo = planemo.cli:planemo @@ -33,8 +33,8 @@ requirements: - docutils - ephemeris >=0.10.3 - galaxy-containers - - galaxy-tool-util >=23.0,<23.1 - - galaxy-util >=23.0,<23.1 + - galaxy-tool-util >=23.1,<24.0 + - galaxy-util >=23.1,<24.0 - glob2 - gxformat2 >=0.14.0 - h5py From 97a3d74fa5347aeadda2a4613d317fe898852133 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 23:37:37 -0500 Subject: [PATCH 0351/1813] Update r-chord to 2.03 (#45673) --- recipes/r-chord/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-chord/meta.yaml b/recipes/r-chord/meta.yaml index 1053fe03cb7e8..112ef12290bf6 100644 --- a/recipes/r-chord/meta.yaml +++ b/recipes/r-chord/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.02" %} -{% set sha256 = "9db52b2d01ddea7d8b97c530683296988e98003a5ee859ae03503666a9013f9f" %} +{% set version = "2.03" %} +{% set sha256 = "def578e8e3764231d0711d0fb2542862c064fe9e355fbc6c5b61da153f50e7bc" %} package: name: r-chord From 87568b0bbf79233075c2a5b7f6fed9482730a236 Mon Sep 17 00:00:00 2001 From: Travis Wrightsman Date: Tue, 6 Feb 2024 23:39:08 -0500 Subject: [PATCH 0352/1813] Update sonlib (#45415) * Fix segfault in sonLib phylogeny tests * Update sonLib to ~2.0 * Remove commit from version string --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/quicktree/meta.yaml | 4 +- ...001-Add-rule-to-build-shared-library.patch | 4 +- ...x-segfault-in-sonLib-phylogeny-tests.patch | 34 +++ recipes/sonlib/build.sh | 11 + recipes/sonlib/meta.yaml | 55 +++- ...-Add-devendored-shared-library-build.patch | 247 ++++++++++++++++++ ...-Remove-need-for-CuTest-during-build.patch | 24 ++ recipes/sonlib/run_test.sh | 7 + 8 files changed, 372 insertions(+), 14 deletions(-) create mode 100644 recipes/quicktree/patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch create mode 100644 recipes/sonlib/patches/0001-Add-devendored-shared-library-build.patch create mode 100644 recipes/sonlib/patches/0002-Remove-need-for-CuTest-during-build.patch create mode 100644 recipes/sonlib/run_test.sh diff --git a/recipes/quicktree/meta.yaml b/recipes/quicktree/meta.yaml index 5c6cb7814f9f8..8e9fe92a91c7a 100644 --- a/recipes/quicktree/meta.yaml +++ b/recipes/quicktree/meta.yaml @@ -10,13 +10,13 @@ source: sha256: 731aa845ce3f1f0645bd0df2b54df75f78fce065d6a3ddc47fedf4bdcb11c248 patches: - patches/0001-Add-rule-to-build-shared-library.patch + - patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage(name, max_pin="x") }} - requirements: build: - make diff --git a/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch b/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch index 509748c0811eb..37c17acd29c9b 100644 --- a/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch +++ b/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch @@ -1,6 +1,6 @@ -From 390c2db84a0fd0ff3a05d77407d18da3b9c26d63 Mon Sep 17 00:00:00 2001 +From 6c92fb5efd973d1fa6a7ae05515ba54302be95c5 Mon Sep 17 00:00:00 2001 From: Travis Wrightsman -Date: Sat, 20 Jan 2024 17:46:20 -0500 +Date: Tue, 23 Jan 2024 23:01:04 -0500 Subject: [PATCH] Add rule to build shared library --- diff --git a/recipes/quicktree/patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch b/recipes/quicktree/patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch new file mode 100644 index 0000000000000..0e3f87c7aac7e --- /dev/null +++ b/recipes/quicktree/patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch @@ -0,0 +1,34 @@ +From c4470daeed25f720de4376a5f43820ba32c2cf61 Mon Sep 17 00:00:00 2001 +From: Travis Wrightsman +Date: Tue, 23 Jan 2024 23:02:51 -0500 +Subject: [PATCH] Fix segfault in sonLib phylogeny tests + +--- + src/tree.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/tree.c b/src/tree.c +index 5b5187f..3bd8626 100644 +--- a/src/tree.c ++++ b/src/tree.c +@@ -60,7 +60,7 @@ struct Tnode *clone_Tnode( struct Tnode *source) { + struct Tnode *dest = NULL; + + if (source != NULL) { +- dest = (struct Tnode *) malloc_util( sizeof( struct Tnode ) ); ++ dest = (struct Tnode *) calloc_util(1, sizeof( struct Tnode ) ); + + dest->distance = source->distance; + dest->nodenumber = source->nodenumber; +@@ -334,7 +334,7 @@ struct Tree *get_root_Tnode( struct Tree *source ) { + struct Tnode *new_interior_Tnode( unsigned int label ) { + struct Tnode *newNode; + +- newNode = (struct Tnode *) malloc_util(sizeof(struct Tnode)); ++ newNode = (struct Tnode *) calloc_util(1, sizeof(struct Tnode)); + newNode->left = NULL; + newNode->right = NULL; + newNode->parent = NULL; +-- +2.39.2 + diff --git a/recipes/sonlib/build.sh b/recipes/sonlib/build.sh index 3786386a73c83..79758c33af1fb 100644 --- a/recipes/sonlib/build.sh +++ b/recipes/sonlib/build.sh @@ -1,3 +1,14 @@ #!/bin/bash +set -eux + +# prevent header contamination +rm -rf externalTools/ + +make -j $CPU_COUNT shlib +mkdir -p "$PREFIX"/{bin,lib,include/sonLib} +install sonLib_daemonize.py "${PREFIX}/bin/" +# some header files are named generic enough to warrant namespacing +cp lib/*.h "${PREFIX}/include/sonLib/" +cp lib/*.so "${PREFIX}/lib/" $PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/sonlib/meta.yaml b/recipes/sonlib/meta.yaml index 73ab7fdf6ae2d..21f47d0c439bb 100644 --- a/recipes/sonlib/meta.yaml +++ b/recipes/sonlib/meta.yaml @@ -1,27 +1,62 @@ +{% set name = "sonlib" %} +# No version is tagged upstream yet, but commit e25181b changes the setup.py version to 2.0 +# For now, set the .dev version to number of commits on master since then: +# git tag v2.0 e25181b && git describe --tags +{% set version = "2.0.dev88" %} +{% set commit = "9734083dffb180e3d76c323609c082b401336c0a" %} + package: - name: sonlib - version: "1.1.0" + name: {{ name }} + version: {{ version }} source: - url: https://pypi.python.org/packages/c5/63/5c597eb4895ad59e6b57050de0dbc579b400e9e2bfc7a698d6b19d91caaf/sonLib-1.1.0.tar.gz - md5: b6051a1c664ad51f8620d80a3652aa05 + url: https://github.com/ComparativeGenomicsToolkit/sonLib/archive/{{ commit }}.tar.gz + sha256: 6669056081bc96205de14b3c59c70c379dd57ab031d630480e8110e3d448628b + patches: + - patches/0001-Add-devendored-shared-library-build.patch + - patches/0002-Remove-need-for-CuTest-during-build.patch build: - noarch: python - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: + build: + - {{ compiler('c') }} + - make + - pkg-config host: - - python <3 - - pip + - python + - zlib + - quicktree run: - - python <3 + - python + - networkx test: imports: - sonLib + - sonLib.bioio + - sonLib.misc + - sonLib.nxnewick + - sonLib.nxtree + - sonLib.tree + requires: + - {{ compiler('c') }} + - make + - zlib + - cutest + source_files: + - Makefile + - include.mk + - allTests.py + - bioioTest.py + - cigarsTest.py + - C/Makefile + - C/tests/* about: - home: https://github.com/benedictpaten/sonLib + home: https://github.com/ComparativeGenomicsToolkit/sonLib license: MIT summary: 'Small general purpose library for C and Python with focus on bioinformatics.' diff --git a/recipes/sonlib/patches/0001-Add-devendored-shared-library-build.patch b/recipes/sonlib/patches/0001-Add-devendored-shared-library-build.patch new file mode 100644 index 0000000000000..3de5a2a9f3c45 --- /dev/null +++ b/recipes/sonlib/patches/0001-Add-devendored-shared-library-build.patch @@ -0,0 +1,247 @@ +From 1e06372425d4492bc943b34ade7a9ef443cb1bec Mon Sep 17 00:00:00 2001 +From: Travis Wrightsman +Date: Tue, 23 Jan 2024 21:04:37 -0500 +Subject: [PATCH] Add devendored shared library build + +--- + C/Makefile | 14 ++++++++++++++ + C/impl/stPhylogeny.c | 6 +++--- + C/tests/cigarsTest.c | 10 +++++----- + C/tests/fastaCTest.c | 6 +++--- + C/tests/kvDatabaseTestCommon.c | 2 +- + C/tests/sonLibCommonTest.c | 2 +- + C/tests/sonLibExceptTest.c | 6 +++--- + C/tests/sonLibGlobalsTest.h | 2 +- + C/tests/stPhylogenyTest.c | 4 ++-- + C/tests/stThreadPoolTest.c | 2 +- + C/tests/stUnionFindTest.c | 2 +- + Makefile | 6 ++++++ + setup.py | 2 +- + 13 files changed, 42 insertions(+), 22 deletions(-) + +diff --git a/C/Makefile b/C/Makefile +index fcb627a..92856ac 100644 +--- a/C/Makefile ++++ b/C/Makefile +@@ -1,4 +1,6 @@ + rootPath = .. ++BINDIR = ../bin ++LIBDIR = ../lib + + include ../include.mk + +@@ -23,6 +25,13 @@ LDLIBS = ${LIBDIR}/sonLib.a ${dblibs} ${LIBS} + + all : ${LIBDIR}/sonLib.a ${testProgs} ${libHeadersDep} + ++shlib : ${LIBDIR}/libsonLib.so ++ ++tests-shlib: ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -o ${rootPath}/sonLibTests tests/allTests.c ${libTests} -lsonLib -lcutest -lz -lm -lpthread ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -o ${rootPath}/sonLib_cigarTest tests/cigarsTest.c -l sonLib -lz -lpthread ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -o ${rootPath}/sonLib_fastaCTest tests/fastaCTest.c -l sonLib -lz -lpthread ++ + # note: old Makefile put .o files in this directory, clean if for now (FIXME: remove soon) + clean : + rm -rf ${BINDIR} ${LIBDIR} ${libObjs} *.o +@@ -62,5 +71,10 @@ ${LIBDIR}/sonLib.a : ${libObjs} + ${RANLIB} sonLib.a + mv sonLib.a ${LIBDIR}/ + ++${LIBDIR}/libsonLib.so : ${libObjs} ++ @mkdir -p $(dir $@) ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -shared -fPIC ${libObjs} -lquicktree -lz -o libsonLib.so ++ mv libsonLib.so ${LIBDIR}/ ++ + test: + ${PYTHON} allTests.py --testLength=SHORT --logLevel CRITICAL +diff --git a/C/impl/stPhylogeny.c b/C/impl/stPhylogeny.c +index fd0fcf4..33b594d 100644 +--- a/C/impl/stPhylogeny.c ++++ b/C/impl/stPhylogeny.c +@@ -2,9 +2,9 @@ + #include "sonLib.h" + #include "stPhylogeny.h" + // QuickTree includes +-#include "cluster.h" +-#include "tree.h" +-#include "buildtree.h" ++#include "quicktree/cluster.h" ++#include "quicktree/tree.h" ++#include "quicktree/buildtree.h" + // Spimap C/C++ translation layer include + #include "stSpimapLayer.h" + +diff --git a/C/tests/cigarsTest.c b/C/tests/cigarsTest.c +index 5189f69..a4547ba 100644 +--- a/C/tests/cigarsTest.c ++++ b/C/tests/cigarsTest.c +@@ -9,11 +9,11 @@ + #include + #include + +-#include "fastCMaths.h" +-#include "avl.h" +-#include "commonC.h" +-#include "bioioC.h" +-#include "pairwiseAlignment.h" ++#include "sonLib/fastCMaths.h" ++#include "sonLib/avl.h" ++#include "sonLib/commonC.h" ++#include "sonLib/bioioC.h" ++#include "sonLib/pairwiseAlignment.h" + + int main(int argc, char *argv[]) { + int64_t i; +diff --git a/C/tests/fastaCTest.c b/C/tests/fastaCTest.c +index 9cc81db..4d41ca4 100644 +--- a/C/tests/fastaCTest.c ++++ b/C/tests/fastaCTest.c +@@ -9,9 +9,9 @@ + #include + #include + +-#include "fastCMaths.h" +-#include "commonC.h" +-#include "bioioC.h" ++#include "sonLib/fastCMaths.h" ++#include "sonLib/commonC.h" ++#include "sonLib/bioioC.h" + + int main(int argc, char *argv[]) { + FILE *fileHandle; +diff --git a/C/tests/kvDatabaseTestCommon.c b/C/tests/kvDatabaseTestCommon.c +index eccf3c3..b5a9b21 100644 +--- a/C/tests/kvDatabaseTestCommon.c ++++ b/C/tests/kvDatabaseTestCommon.c +@@ -9,7 +9,7 @@ + */ + #include "sonLibGlobalsTest.h" + #include "kvDatabaseTestCommon.h" +-#include "stSafeC.h" ++#include "sonLib/stSafeC.h" + #include + + /* usage message and exit */ +diff --git a/C/tests/sonLibCommonTest.c b/C/tests/sonLibCommonTest.c +index 1c208fc..6924ffa 100644 +--- a/C/tests/sonLibCommonTest.c ++++ b/C/tests/sonLibCommonTest.c +@@ -11,7 +11,7 @@ + * Author: benedictpaten + */ + #include "sonLibGlobalsTest.h" +-#include "bioioC.h" ++#include "sonLib/bioioC.h" + + static void test_st_logging(CuTest *testCase) { + /* +diff --git a/C/tests/sonLibExceptTest.c b/C/tests/sonLibExceptTest.c +index db00120..4d3f1cf 100644 +--- a/C/tests/sonLibExceptTest.c ++++ b/C/tests/sonLibExceptTest.c +@@ -7,12 +7,12 @@ + /* + * basic tests of stExcept. + */ +-#include "sonLibExcept.h" ++#include "sonLib/sonLibExcept.h" + #include "sonLibGlobalsTest.h" +-#include "sonLibCommon.h" ++#include "sonLib/sonLibCommon.h" + #include + #include +-#include "stSafeC.h" ++#include "sonLib/stSafeC.h" + + /* test throwing through two levels */ + static const char *const ERR1 = "err1"; +diff --git a/C/tests/sonLibGlobalsTest.h b/C/tests/sonLibGlobalsTest.h +index ddb1293..a704b99 100644 +--- a/C/tests/sonLibGlobalsTest.h ++++ b/C/tests/sonLibGlobalsTest.h +@@ -28,6 +28,6 @@ + #include + + #include "CuTest.h" +-#include "sonLib.h" ++#include "sonLib/sonLib.h" + + #endif // SONLIB_GLOBALS_TEST_H_ +diff --git a/C/tests/stPhylogenyTest.c b/C/tests/stPhylogenyTest.c +index ea4c84b..93c3f1d 100644 +--- a/C/tests/stPhylogenyTest.c ++++ b/C/tests/stPhylogenyTest.c +@@ -1,8 +1,8 @@ + #include + #include + #include "CuTest.h" +-#include "sonLib.h" +-#include "stPhylogeny.h" ++#include "sonLib/sonLib.h" ++#include "sonLib/stPhylogeny.h" + + static stIndexedTreeInfo *getIndex(stTree *node) { + assert(node != NULL); +diff --git a/C/tests/stThreadPoolTest.c b/C/tests/stThreadPoolTest.c +index 8a456a6..a3f3128 100644 +--- a/C/tests/stThreadPoolTest.c ++++ b/C/tests/stThreadPoolTest.c +@@ -1,5 +1,5 @@ + #include "CuTest.h" +-#include "sonLib.h" ++#include "sonLib/sonLib.h" + + // Test sorting a few sublists into a larger list to try to catch out + // any race conditions. +diff --git a/C/tests/stUnionFindTest.c b/C/tests/stUnionFindTest.c +index c39826d..b7caf53 100644 +--- a/C/tests/stUnionFindTest.c ++++ b/C/tests/stUnionFindTest.c +@@ -1,5 +1,5 @@ + #include "CuTest.h" +-#include "sonLib.h" ++#include "sonLib/sonLib.h" + + // Simple static test. + static void stUnionFind_staticTest(CuTest *testCase) { +diff --git a/Makefile b/Makefile +index b244b55..e04e298 100644 +--- a/Makefile ++++ b/Makefile +@@ -5,6 +5,9 @@ BINDIR = ./bin + + all : cP ${BINDIR}/sonLib_daemonize.py + ++shlib: ++ cd C && ${MAKE} shlib ++ + clean : cP.clean externalToolsP.clean + rm -f ${BINDIR}/sonLib_daemonize.py + +@@ -23,6 +26,9 @@ externalToolsP.clean : + test : all + PYTHONPATH=src:. PATH=$$(pwd)/bin:$$PATH ${PYTHON} allTests.py --testLength=SHORT --logLevel=WARN + ++tests-shlib: ++ cd C && ${MAKE} tests-shlib ++ + ${BINDIR}/sonLib_daemonize.py : sonLib_daemonize.py cP + cp sonLib_daemonize.py ${BINDIR}/sonLib_daemonize.py + chmod +x ${BINDIR}/sonLib_daemonize.py +diff --git a/setup.py b/setup.py +index 9d96fd0..7db446e 100755 +--- a/setup.py ++++ b/setup.py +@@ -12,7 +12,7 @@ class BuildWithMake(distutils.command.build_py.build_py): + """ + def run(self): + # Call make. +- subprocess.check_call(["make"]) ++ #subprocess.check_call(["make"]) + + # Keep building the Python stuff + distutils.command.build_py.build_py.run(self) +-- +2.39.2 + diff --git a/recipes/sonlib/patches/0002-Remove-need-for-CuTest-during-build.patch b/recipes/sonlib/patches/0002-Remove-need-for-CuTest-during-build.patch new file mode 100644 index 0000000000000..bdb17a155cc5d --- /dev/null +++ b/recipes/sonlib/patches/0002-Remove-need-for-CuTest-during-build.patch @@ -0,0 +1,24 @@ +From 9852a11e4c38f92725f72eefc041cfe5fadc2ea6 Mon Sep 17 00:00:00 2001 +From: Travis Wrightsman +Date: Tue, 23 Jan 2024 22:18:44 -0500 +Subject: [PATCH] Remove need for CuTest during build + +--- + C/impl/sonLibGlobalsInternal.h | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/C/impl/sonLibGlobalsInternal.h b/C/impl/sonLibGlobalsInternal.h +index f8542a0..9a2e51d 100644 +--- a/C/impl/sonLibGlobalsInternal.h ++++ b/C/impl/sonLibGlobalsInternal.h +@@ -29,7 +29,6 @@ + #include + #include + +-#include "CuTest.h" + #include "sonLib.h" + #include "sonLibListPrivate.h" + +-- +2.39.2 + diff --git a/recipes/sonlib/run_test.sh b/recipes/sonlib/run_test.sh new file mode 100644 index 0000000000000..21a8a0e080ad4 --- /dev/null +++ b/recipes/sonlib/run_test.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +set -eux + +make tests-shlib + +PATH="$PWD:$PATH" python allTests.py From d04bec7e9ee29d6490c3376126d2a3a2218775a5 Mon Sep 17 00:00:00 2001 From: msantorsola Date: Wed, 7 Feb 2024 11:07:47 +0100 Subject: [PATCH 0353/1813] Add gametes new recipe (#43783) * building gametes recipe * fixing linting errors * fixed run_exports * fixing gametes yaml * fixed gametes jar path * fixing path error * fixing path * fixing path * fixing meta.yaml * fixing path * fixing path * fixing path * fixing path * fixing path * fixing path * fixing path * fixing path * fixing path error * fixing gametes build file * fixing gametes test * check paths * fixing exit grep error * set java home * fixing tests --------- Co-authored-by: Mariangela Santorsola --- recipes/gametes/LICENSE | 362 +++++++++++++++++++++++++++++++++++++ recipes/gametes/build.sh | 24 +++ recipes/gametes/gametes.py | 88 +++++++++ recipes/gametes/meta.yaml | 38 ++++ 4 files changed, 512 insertions(+) create mode 100644 recipes/gametes/LICENSE create mode 100644 recipes/gametes/build.sh create mode 100644 recipes/gametes/gametes.py create mode 100644 recipes/gametes/meta.yaml diff --git a/recipes/gametes/LICENSE b/recipes/gametes/LICENSE new file mode 100644 index 0000000000000..8a8f06b2d908f --- /dev/null +++ b/recipes/gametes/LICENSE @@ -0,0 +1,362 @@ +# GNU GENERAL PUBLIC LICENSE + +Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +## Preamble + +The licenses for most software are designed to take away your freedom +to share and change it. 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In such case, this License incorporates +the limitation as if written in the body of this License. + +**9.** The Free Software Foundation may publish revised and/or new +versions of the General Public License from time to time. Such new +versions will be similar in spirit to the present version, but may +differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies a version number of this License which applies to it and +"any later version", you have the option of following the terms and +conditions either of that version or of any later version published by +the Free Software Foundation. If the Program does not specify a +version number of this License, you may choose any version ever +published by the Free Software Foundation. + +**10.** If you wish to incorporate parts of the Program into other +free programs whose distribution conditions are different, write to +the author to ask for permission. For software which is copyrighted by +the Free Software Foundation, write to the Free Software Foundation; +we sometimes make exceptions for this. Our decision will be guided by +the two goals of preserving the free status of all derivatives of our +free software and of promoting the sharing and reuse of software +generally. + +**NO WARRANTY** + +**11.** BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO +WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. +EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR +OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY +KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE +PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME +THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +**12.** IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN +WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY +AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU +FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR +CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE +PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING +RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A +FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF +SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH +DAMAGES. + +END OF TERMS AND CONDITIONS + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these +terms. + +To do so, attach the following notices to the program. It is safest to +attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + one line to give the program's name and an idea of what it does. + Copyright (C) yyyy name of author + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License + as published by the Free Software Foundation; either version 2 + of the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +Also add information on how to contact you by electronic and paper +mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details + type `show w'. This is free software, and you are welcome + to redistribute it under certain conditions; type `show c' + for details. + +The hypothetical commands \`show w' and \`show c' should show the +appropriate parts of the General Public License. Of course, the +commands you use may be called something other than \`show w' and +\`show c'; they could even be mouse-clicks or menu items--whatever +suits your program. + +You should also get your employer (if you work as a programmer) or +your school, if any, to sign a "copyright disclaimer" for the program, +if necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright + interest in the program `Gnomovision' + (which makes passes at compilers) written + by James Hacker. + + signature of Ty Coon, 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, +you may consider it more useful to permit linking proprietary +applications with the library. If this is what you want to do, use the +[GNU Lesser General Public +License](https://www.gnu.org/licenses/lgpl.html) instead of this +License. + diff --git a/recipes/gametes/build.sh b/recipes/gametes/build.sh new file mode 100644 index 0000000000000..89d67ad13e340 --- /dev/null +++ b/recipes/gametes/build.sh @@ -0,0 +1,24 @@ +#create target directory +PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $PACKAGE_HOME + +#create bin +BINARY_HOME=$PREFIX/bin +mkdir -p $BINARY_HOME + +cd $SRC_DIR + +JAR_NAME=GAMETES_2.1.jar + +cp $JAR_NAME $PACKAGE_HOME/gametes.jar + +#mv wrapper script to package home +cp $RECIPE_DIR/gametes.py $PACKAGE_HOME + +#and symlink to $PREFIX/bin +#ln -s $PACKAGE_HOME/gametes.py ${BINARY_HOME} +ln -s $PACKAGE_HOME/gametes.py $BINARY_HOME/gametes + +#chmod +x ${BINARY_HOME} +chmod +x ${BINARY_HOME}/gametes + diff --git a/recipes/gametes/gametes.py b/recipes/gametes/gametes.py new file mode 100644 index 0000000000000..99dc779a47f50 --- /dev/null +++ b/recipes/gametes/gametes.py @@ -0,0 +1,88 @@ +#!/usr/bin/env python + +import os +import subprocess +import sys +from os import access, getenv, path, X_OK + + +# jar file +JAR_NAME = 'gametes.jar' +PKG_NAME = 'gametes' +PKG_VERSION = '2.1' +PKG_BUILDNUM = '0' + + +default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] + + + +def real_dirname(in_path): + """Return the path to the JAR file""" + #realPath = os.path.dirname(os.path.realpath(in_path)) + realPath = os.path.dirname(os.path.dirname(os.path.realpath(in_path))) + newPath = os.path.realpath(os.path.join(realPath, "..", "share", "{}-{}-{}".format(PKG_NAME, PKG_VERSION, PKG_BUILDNUM))) + return newPath + + + +def java_executable(): + """Returns the name of the Java executable.""" + java_home = getenv('JAVA_HOME') + java_bin = path.join('bin', 'java') + if java_home and access(os.path.join(java_home, java_bin), X_OK): + return os.path.join(java_home, java_bin) + else: + return "java" # Default to using 'java' command directly + + + +def jvm_opts(argv): + """Construct list of Java arguments based on our argument list. + + The argument list passed in argv must not include the script name. + The return value is a 3-tuple lists of strings of the form: + (memory_options, prop_options, passthrough_options) + """ + + + mem_opts, prop_opts, pass_args = [], [], [] + + for arg in argv: + if arg.startswith('-D') or arg.startswith('-XX'): + opts_list = prop_opts + elif arg.startswith('-Xm'): + opts_list = mem_opts + else: + opts_list = pass_args + opts_list.append(arg) + + if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: + mem_opts = default_jvm_mem_opts + + return (mem_opts, prop_opts, pass_args) + +def main(): + java = java_executable() + jar_dir = real_dirname(sys.argv[0]) + (mem_opts, prop_opts, pass_args) = jvm_opts(sys.argv[1:]) + + if pass_args != [] and pass_args[0].startswith('org'): + jar_arg = '-cp' + else: + jar_arg = '-jar' + + jar_path = os.path.join(jar_dir, JAR_NAME) + + if not os.path.isfile(jar_path): + sys.stderr.write('GAMETES jar file not found\n') + sys.exit(1) + + java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args + sys.exit(subprocess.call(java_args)) + + +if __name__ == '__main__': + main() + + diff --git a/recipes/gametes/meta.yaml b/recipes/gametes/meta.yaml new file mode 100644 index 0000000000000..6f6daf12580f6 --- /dev/null +++ b/recipes/gametes/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "gametes" %} +{% set version = "2.1" %} + +package: + name: {{ name }} + version: {{ version }} + +about: + home: https://sourceforge.net/projects/gametes/ + license: GPL-2.0-only + summary: Tool for the generation of complex single SNP models + license_file: LICENSE + + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("gametes", max_pin="x") }} + +source: + url: https://sourceforge.net/projects/gametes/files/GAMETES_2.1.jar + sha256: 5e38b0993f8915e3e3e4c225ce6b684455d02c6189877d6ae219d24ad69e27d7 + +requirements: + run: + - openjdk >=17 + - python + host: + - openjdk >=17 + - python + +test: + commands: + - $(echo $(gametes -h | grep Usage)) + + + From 853447f33ea9ba785dc7b07ad493641531b27408 Mon Sep 17 00:00:00 2001 From: Jeremy Volkening Date: Wed, 7 Feb 2024 04:08:07 -0600 Subject: [PATCH 0354/1813] Update perl-ms: add run_exports, bump version (#45116) * add run_exports to perl-ms; bump version * use SPDX version string --- recipes/perl-ms/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/perl-ms/meta.yaml b/recipes/perl-ms/meta.yaml index 818495bdd9743..8a00985087dc2 100644 --- a/recipes/perl-ms/meta.yaml +++ b/recipes/perl-ms/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-ms" %} -{% set version = "0.207002" %} -{% set sha256 = "86676202c44908eee77a7697a8ec73908707f3e5b68ba74932a375196850f1ad" %} +{% set version = "0.207003" %} +{% set sha256 = "29f1eb57200286c9e95b7f7251a3a3c7db9caf63eccdc7450467d8b77362c797" %} package: name: {{ name }} @@ -15,6 +15,8 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: @@ -90,6 +92,6 @@ test: about: home: http://metacpan.org/pod/MS - license: gpl_3 + license: GPL-3.0-or-later license_file: LICENSE summary: 'Namespace for mass spectrometry-related libraries' From 6f08b8b0e6b2cb227d5b32e41d14b4f946d7f7d7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 07:04:42 -0500 Subject: [PATCH 0355/1813] Update nanomotif to 0.1.14 (#45678) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index a9d41641151cb..6c85011e7505b 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.13" %} +{% set version = "0.1.14" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: 97a236a5f8d56f7150292c043af057e44c8625ab92cef5e1046f3ba40a84b5d7 + sha256: f8278b9102267bdb9e4f3e2aa46d6e9f4fb9a655525766b1bc31f6cf67f2e609 build: entry_points: From efc495898cc33d50dc5f0737115dd4165d46727f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 07:05:09 -0500 Subject: [PATCH 0356/1813] Update htsinfer to 0.11.0 (#45677) --- recipes/htsinfer/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/htsinfer/meta.yaml b/recipes/htsinfer/meta.yaml index 1a4e250b5331b..df57b6f70efa5 100644 --- a/recipes/htsinfer/meta.yaml +++ b/recipes/htsinfer/meta.yaml @@ -1,13 +1,13 @@ {% set name = "HTSinfer" %} -{% set version = "0.10.0" %} +{% set version = "0.11.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/zavolanlab/htsinfer/archive/refs/tags/v0.10.0.tar.gz - sha256: a851d00a47ef5a47e9c2540599ff2c16723dfac95c12ac85f7152b0ad4c295a7 + url: https://github.com/zavolanlab/htsinfer/archive/refs/tags/v0.11.0.tar.gz + sha256: f7225290e12bf129bdb654f06f1cb98da577be81d35f7d17844447fcdf058618 build: number: 0 From a2af164e319fd1fd8116bea86c591f0aedb8a0db Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 07:05:17 -0500 Subject: [PATCH 0357/1813] Update ena-webin-cli to 7.0.0 (#45676) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index aa7f4b8f4abec..b76445e0d12fe 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.10.0" %} -{% set sha256 = "3fd887d5fc5a1fbb28060f55e3903051aa9b15cc85cafd5bedb6e2c2645df1c4" %} +{% set version = "7.0.0" %} +{% set sha256 = "8b372aa08fe3e039f6d47d546ca18a20cbfcb1feb64748ea5a00527d81c7a418" %} package: name: ena-webin-cli From 5aee30851cd4e9af6bacd5c8865e2d428459d93c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 07:06:14 -0500 Subject: [PATCH 0358/1813] Update gimbleprep to 0.0.2b6 (#45667) * Update gimbleprep to 0.0.2b6 * Update gimbleprep to 0.0.2b6 --- recipes/gimbleprep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gimbleprep/meta.yaml b/recipes/gimbleprep/meta.yaml index dc28547728e74..1b3c4a90144e5 100644 --- a/recipes/gimbleprep/meta.yaml +++ b/recipes/gimbleprep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gimbleprep" %} -{% set version = "0.0.2b5" %} +{% set version = "0.0.2b6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/LohseLab/gimbleprep/archive/refs/tags/v{{ version }}.tar.gz - sha256: 6b9f893ba61fbd27577f87b561b7e2dad609589edfa62e63b6d2517b468bd953 + sha256: 5988eeb374d408f17b23cd3185e25e588c099e257357806979bea8e11e3ed272 build: noarch: python From 75dfdd68f1127370c52edae3145dfc7f4c5de3e3 Mon Sep 17 00:00:00 2001 From: Travis Wrightsman Date: Wed, 7 Feb 2024 07:11:28 -0500 Subject: [PATCH 0359/1813] Add peer (#45622) * Add peer * Add license for peer itself * Add make as dependency --- recipes/peer/build.sh | 10 +++++ recipes/peer/meta.yaml | 38 +++++++++++++++++++ ...0001-Comment-out-SWIG-package-search.patch | 31 +++++++++++++++ 3 files changed, 79 insertions(+) create mode 100644 recipes/peer/build.sh create mode 100644 recipes/peer/meta.yaml create mode 100644 recipes/peer/patches/0001-Comment-out-SWIG-package-search.patch diff --git a/recipes/peer/build.sh b/recipes/peer/build.sh new file mode 100644 index 0000000000000..1f1932d3cfc51 --- /dev/null +++ b/recipes/peer/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +set -eux + +mkdir build +cd build +cmake ../ -DBUILD_PYTHON_PACKAGE=OFF -DBUILD_PEERTOOL=ON +make -j $CPU_COUNT +mkdir -p "${PREFIX}/bin" +install src/peertool "${PREFIX}/bin" diff --git a/recipes/peer/meta.yaml b/recipes/peer/meta.yaml new file mode 100644 index 0000000000000..b24994dc6127a --- /dev/null +++ b/recipes/peer/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "peer" %} +{% set version = "1.3" %} +# no tags in upstream repository yet +{% set commit = "40bc4b2cd92459ce42f44dfe279717436395f3f6" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/PMBio/peer/archive/{{ commit }}.tar.gz + sha256: 80a549354569ae5ec7d4d92c78e7f8fa72da08fcd11322611f737044c34861ed + patches: + - patches/0001-Comment-out-SWIG-package-search.patch + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - cmake + - make + +test: + commands: + - peertool --help | grep -q USAGE + +about: + home: https://github.com/PMBio/peer + license: GPL-2.0-or-later + license_file: + - LICENSE + - External/yaml-cpp/license.txt + summary: 'A collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods' diff --git a/recipes/peer/patches/0001-Comment-out-SWIG-package-search.patch b/recipes/peer/patches/0001-Comment-out-SWIG-package-search.patch new file mode 100644 index 0000000000000..6628b8077e44a --- /dev/null +++ b/recipes/peer/patches/0001-Comment-out-SWIG-package-search.patch @@ -0,0 +1,31 @@ +From a66ffa0d4b5e0aca5a1de1ffad387eadef49447f Mon Sep 17 00:00:00 2001 +From: Travis Wrightsman +Date: Mon, 5 Feb 2024 12:21:17 -0500 +Subject: [PATCH] Comment out SWIG package search + +--- + CMakeLists.txt | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 80455af..0e0c66c 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -71,11 +71,11 @@ endif (BUILD_UNIVERSAL) + #for finding external libraries. + #see /usr/local/share/cmake-2.6/Modules/Find*.cmake for more examples + +-find_package(SWIG REQUIRED) +-include(${SWIG_USE_FILE}) ++#find_package(SWIG REQUIRED) ++#include(${SWIG_USE_FILE}) + + include_directories(${CMAKE_CURRENT_SOURCE_DIR}) +-set(CMAKE_SWIG_FLAGS "") ++#set(CMAKE_SWIG_FLAGS "") + + set(CMAKE_MODULE_PATH "${PEER_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH}) + include_directories(./include) +-- +2.39.2 + From e9d3da30f115fe43b8f5cfe6c4eec9f667120a0d Mon Sep 17 00:00:00 2001 From: Ryan James Kennedy <67742838+ryanjameskennedy@users.noreply.github.com> Date: Wed, 7 Feb 2024 15:02:34 +0100 Subject: [PATCH 0360/1813] Add git to virulencefinder (#45682) --- recipes/virulencefinder/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/virulencefinder/meta.yaml b/recipes/virulencefinder/meta.yaml index 0393ba33a0f8d..e57a9257fee59 100644 --- a/recipes/virulencefinder/meta.yaml +++ b/recipes/virulencefinder/meta.yaml @@ -11,8 +11,10 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic + run_exports: + - {{ pin_subpackage('virulencefinder', max_pin="x") }} requirements: run: @@ -22,10 +24,12 @@ requirements: - tabulate - cgecore - blast + - git test: commands: - virulencefinder.py --help + - git --help about: home: https://bitbucket.org/genomicepidemiology/virulencefinder From 46fa6ac57862105b73ec54646b9972fe30f71922 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 12:16:17 -0500 Subject: [PATCH 0361/1813] Update hmftools-sv-prep to 1.2.3 (#43434) * Update hmftools-sv-prep to 1.2 * Update hmftools-sv-prep to 1.2.1 * Update hmftools-sv-prep to 1.2.2 * add run_exports * Update hmftools-sv-prep to 1.2.3 * Use lowercasing for BASH script for consistency * Add required GRIDSS components, dependencies * Update test command * Update license family for consistency * Set correct GRIDSS package build * Remove quotes preventing BASH brace expansion --------- Co-authored-by: joshuazhuang7 Co-authored-by: Thanh Lee Co-authored-by: Stephen Watts Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/hmftools-sv-prep/build.sh | 10 +- .../gridss_shell_with_jar_entrypoint | 18 + recipes/hmftools-sv-prep/gridss_svprep.sh | 832 ++++++++++++++++++ recipes/hmftools-sv-prep/meta.yaml | 14 +- .../hmftools-sv-prep/{SvPrep.sh => svprep.sh} | 0 5 files changed, 865 insertions(+), 9 deletions(-) create mode 100644 recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint create mode 100755 recipes/hmftools-sv-prep/gridss_svprep.sh rename recipes/hmftools-sv-prep/{SvPrep.sh => svprep.sh} (100%) diff --git a/recipes/hmftools-sv-prep/build.sh b/recipes/hmftools-sv-prep/build.sh index 2089a1b4204e8..5b0bbef52c376 100644 --- a/recipes/hmftools-sv-prep/build.sh +++ b/recipes/hmftools-sv-prep/build.sh @@ -7,6 +7,10 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" cd "${SRC_DIR}" mv sv-prep*.jar $TGT/sv-prep.jar -cp $RECIPE_DIR/SvPrep.sh $TGT/SvPrep -ln -s $TGT/SvPrep $PREFIX/bin -chmod 0755 "${PREFIX}/bin/SvPrep" +cp $RECIPE_DIR/svprep.sh $TGT/svprep +cp $RECIPE_DIR/gridss_shell_with_jar_entrypoint $TGT/ +cp $RECIPE_DIR/gridss_svprep.sh $TGT/gridss_svprep + +ln -s $TGT/svprep $PREFIX/bin/ +ln -s $TGT/gridss_shell_with_jar_entrypoint $PREFIX/bin/gridss_svprep +chmod 0755 ${PREFIX}/bin/{gridss_,}svprep diff --git a/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint b/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint new file mode 100644 index 0000000000000..d9183aebce48e --- /dev/null +++ b/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint @@ -0,0 +1,18 @@ +#!/bin/bash +# Wrapper scripts that sets --jar gridss.jar command line argument +# so users don't need to know the path to the GRIDSS jar + +# Adapted from bioconda-recipes/picard/picard.sh +set -o pipefail +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +$DIR/$(basename $0) --jar "$DIR/gridss.jar" "$@" + diff --git a/recipes/hmftools-sv-prep/gridss_svprep.sh b/recipes/hmftools-sv-prep/gridss_svprep.sh new file mode 100755 index 0000000000000..9e0f9f0d519a4 --- /dev/null +++ b/recipes/hmftools-sv-prep/gridss_svprep.sh @@ -0,0 +1,832 @@ +#!/bin/bash +# GRIDSS execution script using SvPrep BAMs + +getopt --test +if [[ ${PIPESTATUS[0]} -ne 4 ]]; then + echo 'WARNING: "getopt --test"` failed in this environment.' 1>&2 + echo "WARNING: The version of getopt(1) installed on this system might not be compatible with the GRIDSS driver script." 1>&2 +fi +unset DISPLAY # Prevents errors attempting to connecting to an X server when starting the R plotting device +ulimit -n $(ulimit -Hn 2>/dev/null) 2>/dev/null # Reduce likelihood of running out of open file handles +set -o errexit -o pipefail -o noclobber -o nounset +last_command="" +current_command="" +trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG +trap 'echo "\"${last_command}\" command completed with exit code $?."' EXIT +#253 forcing C locale for everything +export LC_ALL=C + +EX_USAGE=64 +EX_NOINPUT=66 +EX_CANTCREAT=73 +EX_CONFIG=78 + +workingdir="." +reference="" +output_vcf="" +assembly="" +threads=8 +jvmheap="30g" +otherjvmheap="4g" +blacklist="" +metricsrecords=10000000 +maxcoverage=50000 +config_file="" +labels="" +bams="" +filtered_bams="" +full_bams="" +keepTempFiles="false" + +steps="all" +do_preprocess=false +do_assemble=false +do_call=false + +USAGE_MESSAGE=" +Usage: gridss [options] -r -o -a input1.bam [input2.bam [...]] + + -r/--reference: reference genome to use. + -o/--output: output VCF. + -a/--assembly: location of the GRIDSS assembly BAM. This file will be + created by GRIDSS. + -t/--threads: number of threads to use. (Default: $threads) + -j/--jar: location of GRIDSS jar + -w/--workingdir: directory to place GRIDSS intermediate and temporary files + .gridss.working subdirectories will be created. (Default: $workingdir) + -s/--steps: processing steps to run. Defaults to all steps. + Multiple steps are specified using comma separators. Possible steps are: + preprocess, assemble, call, all + -e/--blacklist: BED file containing regions to ignore + -c/--configuration: configuration file use to override default GRIDSS + settings. + -l/--labels: comma separated labels to use in the output VCF for the input + files. Supporting read counts for input files with the same label are + aggregated (useful for multiple sequencing runs of the same sample). + Labels default to input filenames, unless a single read group with a + non-empty sample name exists in which case the read group sample name + is used (which can be disabled by \"useReadGroupSampleNameCategoryLabel=false\" + in the configuration file). If labels are specified, they must be + specified for all input files. + -b/bams: comma separated full-path BAM files + -f/filtered_bams: comma separated full-path filtered BAM files + --jvmheap: size of JVM heap for the high-memory component of assembly and variant calling. (Default: $jvmheap) + --otherjvmheap: size of JVM heap for everything else. Useful to prevent + java out of memory errors when using large (>4Gb) reference genomes. + Note that some parts of assembly and variant calling use this heap + size. (Default: $otherjvmheap) + " + +OPTIONS=r:o:a:t:j:w:e:s:c:l:b:f: +LONGOPTS=reference:,output:,assembly:,threads:,jar:,workingdir:,jvmheap:,otherjvmheap:,blacklist:,steps:,configuration:,labels:,bams:,filtered_bams: +! PARSED=$(getopt --options=$OPTIONS --longoptions=$LONGOPTS --name "$0" -- "$@") +if [[ ${PIPESTATUS[0]} -ne 0 ]]; then + # e.g. return value is 1 + # then getopt has complained about wrong arguments to stdout + echo "$USAGE_MESSAGE" 1>&2 + exit $EX_USAGE +fi +eval set -- "$PARSED" + +POSITIONAL_ARGS=() + +#while true; do +while [[ $# -gt 0 ]]; do + case "$1" in + -r|--reference) + reference="$2" + shift 2 + ;; + -l|--labels) + labels="$2" + shift 2 + ;; + -b|--bams) + bams="$2" + shift 2 + ;; + -f|--filtered_bams) + filtered_bams="$2" + shift 2 + ;; + -s|--steps) + steps="$2" + shift 2 + ;; + -w|--workingdir) + workingdir="$2" + shift 2 + ;; + -o|--output) + output_vcf="$2" + shift 2 + ;; + -a|--assembly) + if [[ "$assembly" == "" ]] ; then + assembly="$2" + else + assembly="$assembly $2" + fi + # TODO: support multiple assembly files + shift 2 + ;; + -e|--blacklist) + blacklist="$2" + shift 2 + ;; + -j|--jar) + GRIDSS_JAR="$2" + shift 2 + ;; + --jvmheap) + jvmheap="$2" + shift 2 + ;; + --otherjvmheap) + otherjvmheap="$2" + shift 2 + ;; + -t|--threads) + printf -v threads '%d\n' "$2" 2>/dev/null + printf -v threads '%d' "$2" 2>/dev/null + shift 2 + ;; + -c|--configuration) + config_file=$2 + shift 2 + ;; + *) + POSITIONAL_ARGS+=("$1") # save positional arg + # echo "Unparsed param" + shift + ;; + esac +done + +##### --workingdir +echo "Using working directory \"$workingdir\"" 1>&2 +if [[ "$workingdir" == "" ]] ; then + echo "$USAGE_MESSAGE" 1>&2 + echo "Working directory must be specified. Specify using the --workingdir command line argument" 1>&2 + exit $EX_USAGE +fi +if [[ "$(tr -d ' \n' <<< "$workingdir")" != "$workingdir" ]] ; then + echo "workingdir cannot contain whitespace" 1>&2 + exit $EX_USAGE + fi +if [[ ! -d $workingdir ]] ; then + mkdir -p $workingdir + if [[ ! -d $workingdir ]] ; then + echo Unable to create working directory $workingdir 1>&2 + exit $EX_CANTCREAT + fi +fi +workingdir=$(dirname $workingdir/placeholder) +timestamp=$(date +%Y%m%d_%H%M%S) +# Logging +logfile=$workingdir/gridss.full.$timestamp.$HOSTNAME.$$.log +# $1 is message to write +write_status() { + echo "$(date): $1" | tee -a $logfile 1>&2 +} +write_status "Full log file is: $logfile" +trap 'echo "\"${last_command}\" command completed with exit code $?. +***** +The underlying error message can be found in $logfile +*****"' EXIT +# Timing instrumentation +timinglogfile=$workingdir/gridss.timing.$timestamp.$HOSTNAME.$$.log +if which /usr/bin/time >/dev/null ; then + timecmd="/usr/bin/time" + write_status "Found /usr/bin/time" +else + timecmd="" + write_status "Not found /usr/bin/time" +fi +if [[ "$timecmd" != "" ]] ; then + timecmd="/usr/bin/time --verbose -a -o $timinglogfile" + if ! $timecmd echo 2>&1 > /dev/null; then + timecmd="/usr/bin/time -a -o $timinglogfile" + fi + if ! $timecmd echo 2>&1 > /dev/null ; then + timecmd="" + write_status "Unexpected /usr/bin/time version. Not logging timing information." + fi + # We don't need timing info of the echo + rm -f $timinglogfile +fi + +### Find the jars +find_jar() { + env_name=$1 + if [[ -f "${!env_name:-}" ]] ; then + echo "${!env_name}" + else + write_status "Unable to find $2 jar. Specify using the environment variant $env_name, or the --jar command line parameter." + exit $EX_NOINPUT + fi +} +gridss_jar=$(find_jar GRIDSS_JAR gridss) +write_status "Using GRIDSS jar $gridss_jar" + +# Check all key inputs: + +if [[ "$labels" == "" ]] ; then + write_status "Labels must be specified" + exit $EX_USAGE +fi + +if [[ "$bams" == "" ]] ; then + write_status "Full BAMs must be specified" + exit $EX_USAGE +fi + +if [[ "$filtered_bams" == "" ]] ; then + write_status "Filtered BAMs must be specified" + exit $EX_USAGE +fi + +##### --reference +if [[ "$reference" == "" ]] ; then + write_status "$USAGE_MESSAGE" + write_status "Reference genome must be specified. Specify using the --reference command line argument" + exit $EX_USAGE +fi + +if [ ! -f $reference ] ; then + write_status "$USAGE_MESSAGE" + write_status "Missing reference genome $reference. Specify reference location using the --reference command line argument" + exit $EX_USAGE +fi +write_status "Using reference genome \"$reference\"" + +##### --output +if [[ $do_call == "true" ]] ; then + if [[ "$output_vcf" == "" ]] ; then + write_status "$USAGE_MESSAGE" + write_status "Output VCF not specified. Use --output to specify output file." + exit $EX_USAGE + fi + mkdir -p $(dirname $output_vcf) + if [[ ! -d $(dirname $output_vcf) ]] ; then + write_status "Unable to create directory for $output_vcf for output VCF." + exit $EX_CANTCREAT + fi + write_status "Using output VCF $output_vcf" +fi + +##### --assembly +if [[ $do_assemble == "true" ]] || [[ $do_call == "true" ]]; then + if [[ "$assembly" == "" ]] ; then + if [[ "$output_vcf" == "" ]] ; then + write_status "Either the assembly output file must explicitly specified with -a, or the output VCF specified with -o" + exit $EX_USAGE + fi + assembly=$output_vcf.assembly.bam + fi + write_status "Using assembly bam $assembly" + if [[ $do_assemble == "true" ]] ; then + mkdir -p $(dirname $assembly) + if [[ ! -d $(dirname $assembly) ]] ; then + write_status "Unable to parent create directory for $assembly" + exit $EX_CANTCREAT + fi + else + if [[ ! -f $assembly ]] ; then + write_status "Missing assembly file $assembly" + write_status "Ensure the GRIDSS assembly step has been run" + exit $EX_NOINPUT + fi + fi +fi + +##### --threads +if [[ "$threads" -lt 1 ]] ; then + write_status "$USAGE_MESSAGE" + write_status "Illegal thread count: $threads. Specify an integer thread count using the --threads command line argument" + exit $EX_USAGE +fi +if [[ "$threads" -gt 8 ]] ; then + write_status "WARNING: GRIDSS scales sub-linearly at high thread count. Up to 8 threads is the recommended level of parallelism." +fi +write_status "Using $threads worker threads." + +if [[ "$blacklist" == "" ]] ; then + blacklist_arg="" + write_status "Using no blacklist bed. The encode DAC blacklist is recommended for hg19." +elif [[ ! -f $blacklist ]] ; then + write_status "$USAGE_MESSAGE" + write_status "Missing blacklist file $blacklist" + exit $EX_NOINPUT +else + blacklist_arg="BLACKLIST=$blacklist" + write_status "Using blacklist $blacklist" + if [[ "$(tr -d ' \n' <<< "$blacklist_arg")" != "$blacklist_arg" ]] ; then + write_status "blacklist cannot contain whitespace" + exit $EX_USAGE + fi +fi + +if [[ "$jvmheap" == "" ]] ; then + if [[ $threads -gt 8 ]] ; then + write_status "Warning: GRIDSS assembly may stall and run out of memory. with $threads and $jvmheap heap size." + fi +fi + +write_status "Using JVM maximum heap size of $jvmheap for assembly and variant calling." + +config_args="" +if [[ "$config_file" != "" ]] ; then + if [[ ! -f $config_file ]] ; then + write_status "Configuration file $config_file does not exist" + exit $EX_NOINPUT + fi + config_args="CONFIGURATION_FILE=$config_file" +fi + +input_args="" +input_filtered_args="" + +# no longer read in the BAM file list from the end of the arguments list + +nows_labels=$(tr -d ' \n' <<< "$labels") +if [[ "$nows_labels" != "$labels" ]] ; then + write_status "input labels cannot contain whitespace" + exit $EX_USAGE +fi +IFS=',' read -ra LABEL_ARRAY <<< "$nows_labels" +label_count=${#LABEL_ARRAY[@]} + +for label in "${LABEL_ARRAY[@]}" ; do + input_args="$input_args INPUT_LABEL=$label" + input_filtered_args="$input_filtered_args INPUT_LABEL=$label" + #write_status "label is $label" +done + +nows_bams=$(tr -d ' \n' <<< "$bams") +if [[ "$nows_bams" != "$bams" ]] ; then + write_status "input filtered BAMs cannot contain whitespace" + exit $EX_USAGE +fi +IFS=',' read -ra BAM_ARRAY <<< "$nows_bams" +for bam_file in "${BAM_ARRAY[@]}" ; do + + if [[ "$(basename $bam_file)" == "$(basename $assembly)" ]] ; then + write_status "assembly and input filtered bam files must have different filenames" + exit $EX_USAGE + fi + + input_args="$input_args INPUT=$bam_file" + # write_status "full bam file is $bam_file" +done + +nows_bams=$(tr -d ' \n' <<< "$filtered_bams") +if [[ "$nows_bams" != "$filtered_bams" ]] ; then + write_status "input filtered BAMs cannot contain whitespace" + exit $EX_USAGE +fi +IFS=',' read -ra FILT_BAM_ARRAY <<< "$nows_bams" +for filtered_bam_file in "${FILT_BAM_ARRAY[@]}" ; do + + if [[ "$(basename $filtered_bam_file)" == "$(basename $assembly)" ]] ; then + write_status "assembly and input filtered bam files must have different filenames" + exit $EX_USAGE + fi + + input_filtered_args="$input_filtered_args INPUT=$filtered_bam_file" + # write_status "filtered bam file is $filtered_bam_file" +done + +for (( i=0; i < $label_count; ++i )) +do + write_status "Label $i: name=${LABEL_ARRAY[$i]} full-bam=${BAM_ARRAY[$i]} filtered-bam=${FILT_BAM_ARRAY[$i]}" +done + +write_status "Full BAM args: $input_args" +write_status "Filtered BAM args: $input_filtered_args" + + +# Validate tools exist on path +for tool in Rscript samtools java bwa ; do #minimap2 + if ! which $tool >/dev/null; then + write_status "Error: unable to find $tool on \$PATH" + exit $EX_CONFIG + fi + write_status "Found $(which $tool)" +done +if $(samtools --version-only >/dev/null) ; then + write_status "samtools version: $(samtools --version-only 2>&1)" +else + write_status "Your samtools version does not support --version-only. Update samtools." + exit $EX_CONFIG +fi +if [[ "$(samtools --version-only)" =~ ^([0-9]+)[.]([0-9]+) ]] ; then + samtools_major_version=${BASH_REMATCH[1]} + samtools_minor_version=${BASH_REMATCH[2]} + if [[ "$samtools_major_version" -le 1 ]] && [[ "$samtools_minor_version" -lt 10 ]] ; then + write_status "samtools 1.13 or later is required." + exit $EX_CONFIG + fi +else + write_status "Unable to determine samtools version" + exit $EX_CONFIG +fi + +# write_status "R version: $(Rscript --version 2>&1)" + +write_status "bwa $(bwa 2>&1 | grep Version || echo -n)" + +if [[ "$timecmd" != "" ]] ; then + if which /usr/bin/time >/dev/null ; then + write_status "time version: $(/usr/bin/time --version 2>&1)" + fi +fi +write_status "bash version: $(/bin/bash --version 2>&1 | head -1)" + +# check java version is ok using the gridss.Echo entry point +if java -cp $gridss_jar gridss.Echo ; then + write_status "java version: $(java -version 2>&1 | tr '\n' '\t')" +else + write_status "Unable to run GRIDSS jar - requires java 1.8 or later" + write_status "java version: $(java -version 2>&1)" + exit $EX_CONFIG +fi + +if ! java -Xms$jvmheap -cp $gridss_jar gridss.Echo ; then + write_status "Failure invoking java with --jvmheap parameter of \"$jvmheap\". Specify a JVM heap size (e.g. \"31g\") that is valid for this machine." + exit 1 +fi + +write_status "Max file handles: $(ulimit -n)" 1>&2 + +steps_message="Running GRIDSS steps:" + +for step in $(echo $steps | tr ',' ' ' ) ; do + if [[ "$step" == "all" ]] ; then + do_preprocess=true + do_assemble=true + do_call=true + steps_message="$steps_message all" + elif [[ "$step" == "preprocess" ]] ; then + do_preprocess=true + steps_message="$steps_message pre-process" + elif [[ "$step" == "assemble" ]] ; then + do_assemble=true + steps_message="$steps_message assembly" + elif [[ "$step" == "call" ]] ; then + do_call=true + steps_message="$steps_message call" + else + write_status "Unknown step \"$step\"" + exit $EX_USAGE + fi +done + +write_status "$steps_message" + +# don't keep files +if [[ $keepTempFiles == "true" ]] ; then + rmcmd="echo rm disabled:" + jvm_args="-Dgridss.keepTempFiles=true" +else + rmcmd="rm" + jvm_args="" +fi + +jvm_args="$jvm_args \ + -XX:ParallelGCThreads=$threads \ + -Dsamjdk.reference_fasta=$reference \ + -Dsamjdk.use_async_io_read_samtools=true \ + -Dsamjdk.use_async_io_write_samtools=true \ + -Dsamjdk.use_async_io_write_tribble=true \ + -Dsamjdk.buffer_size=4194304 \ + -Dsamjdk.async_io_read_threads=$threads" + +aligner_args=' + ALIGNER_COMMAND_LINE=null + ALIGNER_COMMAND_LINE=bwa + ALIGNER_COMMAND_LINE=mem + ALIGNER_COMMAND_LINE=-K + ALIGNER_COMMAND_LINE=10000000 + ALIGNER_COMMAND_LINE=-L + ALIGNER_COMMAND_LINE=0,0 + ALIGNER_COMMAND_LINE=-t + ALIGNER_COMMAND_LINE=%3$d + ALIGNER_COMMAND_LINE=%2$s + ALIGNER_COMMAND_LINE=%1$s' + +samtools_sort="samtools sort --no-PG -@ $threads" + +readpairing_args="READ_PAIR_CONCORDANT_PERCENT=null" + + +# set-up reference has been removed since can assume to exist + +#### +# Pre-process for each filtered BAM file +#### + +if [[ $do_preprocess == true ]] ; then + write_status "*** PRE-PROCESS ***" + + for (( i=0; i < $label_count; ++i )) + do + label=${LABEL_ARRAY[$i]} + bam_file=${FILT_BAM_ARRAY[$i]} + write_status "Processing: sample ${LABEL_ARRAY[$i]}, filtered-bam ${FILT_BAM_ARRAY[$i]}" + + dir=$workingdir/$(basename $bam_file).gridss.working + prefix=$dir/$(basename $bam_file) + write_status "Start pre-processing: $bam_file, working dir: $dir, prefix: $prefix" + + tmp_prefix=$workingdir/$(basename $bam_file).gridss.working/tmp.$(basename $bam_file) + mkdir -p $dir + if [[ ! -d $dir ]] ; then + write_status "Unable to create directory $dir" + exit $EX_CANTCREAT + fi + + name_sorted_bam=$tmp_prefix.namedsorted.bam + write_status "Creating name-sorted BAM from $bam_file, writing to $name_sorted_bam" + + $timecmd $samtools_sort -l 1 -n \ + -T $tmp_prefix.namedsorted-tmp \ + -Obam \ + -o ${name_sorted_bam} \ + ${bam_file} + + write_status "Running ComputeSamTags|samtools: $bam_file" + + rm -f $tmp_prefix.coordinate-tmp* + + { $timecmd java -Xmx$otherjvmheap $jvm_args \ + -cp $gridss_jar gridss.ComputeSamTags \ + TMP_DIR=$dir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + COMPRESSION_LEVEL=0 \ + I=$name_sorted_bam \ + O=/dev/stdout \ + WORKER_THREADS=$threads \ + ASSUME_SORTED=true \ + REMOVE_TAGS=aa \ + MODIFICATION_SUMMARY_FILE=$prefix.computesamtags.changes.tsv \ + | $timecmd $samtools_sort \ + -l 1 \ + -T $tmp_prefix.coordinate-tmp \ + -Obam \ + -o $tmp_prefix.coordinate.bam \ + /dev/stdin \ + ; } 1>&2 2>> $logfile + + write_status "Removing name-sorted bam: $tmp_prefix.namedsorted.bam" + $rmcmd $tmp_prefix.namedsorted.bam + + write_status "Running SoftClipsToSplitReads: sample $label, input: $tmp_prefix.coordinate.bam, output: $tmp_prefix.sc2sr.primary.sv.bam" + rm -f $tmp_prefix.sc2sr.suppsorted.sv-tmp* + { $timecmd java -Xmx$otherjvmheap $jvm_args \ + -Dsamjdk.create_index=false \ + -cp $gridss_jar gridss.SoftClipsToSplitReads \ + TMP_DIR=$workingdir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + I=$tmp_prefix.coordinate.bam \ + O=$tmp_prefix.sc2sr.primary.sv.bam \ + COMPRESSION_LEVEL=1 \ + OUTPUT_UNORDERED_RECORDS=$tmp_prefix.sc2sr.supp.sv.bam \ + WORKER_THREADS=$threads \ + $aligner_args \ + && $rmcmd $tmp_prefix.coordinate.bam \ + && $timecmd $samtools_sort \ + -l 1 \ + -T $tmp_prefix.sc2sr.suppsorted.sv-tmp \ + -Obam \ + -o $tmp_prefix.sc2sr.suppsorted.sv.bam \ + $tmp_prefix.sc2sr.supp.sv.bam \ + && $rmcmd $tmp_prefix.sc2sr.supp.sv.bam \ + && $rmcmd -f $prefix.sv.tmp.bam $prefix.sv.tmp.bam.bai \ + && $timecmd samtools merge \ + -c \ + -p \ + --write-index \ + -@ $threads \ + $prefix.sv.tmp.bam \ + $tmp_prefix.sc2sr.primary.sv.bam \ + $tmp_prefix.sc2sr.suppsorted.sv.bam \ + && $rmcmd $tmp_prefix.sc2sr.primary.sv.bam \ + && $rmcmd $tmp_prefix.sc2sr.suppsorted.sv.bam \ + && mv $prefix.sv.tmp.bam $prefix.sv.bam \ + && mv $prefix.sv.tmp.bam.csi $prefix.sv.bam.csi \ + ; } 1>&2 2>> $logfile + + write_status "Produced SV bam:: $prefix.sv.bam" + + # create metrics on the full BAM and then copy these over the metrics made from the filtered BAMs + full_bam_file=${BAM_ARRAY[$i]} + write_status "Running CollectGridssMetrics on $label full BAM $full_bam_file" + + # test_prefix=$prefix.cp + + { $timecmd java -Xmx$otherjvmheap $jvm_args \ + -cp $gridss_jar gridss.analysis.CollectGridssMetrics \ + REFERENCE_SEQUENCE=$reference \ + TMP_DIR=$dir \ + ASSUME_SORTED=true \ + I=$full_bam_file \ + O=$prefix \ + THRESHOLD_COVERAGE=$maxcoverage \ + FILE_EXTENSION=null \ + GRIDSS_PROGRAM=null \ + GRIDSS_PROGRAM=CollectCigarMetrics \ + GRIDSS_PROGRAM=CollectMapqMetrics \ + GRIDSS_PROGRAM=CollectTagMetrics \ + GRIDSS_PROGRAM=CollectIdsvMetrics \ + PROGRAM=null \ + PROGRAM=CollectInsertSizeMetrics \ + STOP_AFTER=$metricsrecords \ + ; } 1>&2 2>> $logfile + + write_status "Complete pre-processing sample: $label" + done + + write_status "*** PRE-PROCESS COMPLETE ***" +fi + +##### +# ASSEMBLY +#### + +assembly_args="ASSEMBLY=$assembly" + +if [[ $do_assemble == true ]] ; then + + write_status "*** ASSEMBLY ***" + write_status "Running AssembleBreakends: writing output to dir $assembly" + { $timecmd java -Xmx$jvmheap $jvm_args \ + -Dgridss.output_to_temp_file=true \ + -cp $gridss_jar gridss.AssembleBreakends \ + JOB_INDEX=0 \ + JOB_NODES=1 \ + TMP_DIR=$workingdir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + WORKER_THREADS=$threads \ + $input_filtered_args \ + $blacklist_arg \ + $config_args \ + $readpairing_args \ + O=$assembly \ + ; } 1>&2 2>> $logfile + + write_status "AssemblyBreakends complete" + + dir=$workingdir/$(basename $assembly).gridss.working/ + prefix=$dir/$(basename $assembly) + tmp_prefix=$dir/tmp.$(basename $assembly) + + write_status "RunningSoftClipsToSplitReads: running on assembly output dir $assembly" + rm -f $tmp_prefix.sc2sr.suppsorted.sv-tmp* + { $timecmd java -Xmx$otherjvmheap $jvm_args \ + -Dgridss.async.buffersize=16 \ + -Dsamjdk.create_index=false \ + -Dgridss.output_to_temp_file=true \ + -cp $gridss_jar gridss.SoftClipsToSplitReads \ + TMP_DIR=$dir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + WORKER_THREADS=$threads \ + I=$assembly \ + O=$tmp_prefix.sc2sr.primary.sv.bam \ + OUTPUT_UNORDERED_RECORDS=$tmp_prefix.sc2sr.supp.sv.bam \ + REALIGN_ENTIRE_READ=true \ + READJUST_PRIMARY_ALIGNMENT_POSITION=true \ + $aligner_args \ + && $timecmd $samtools_sort \ + -T $tmp_prefix.sc2sr.suppsorted.sv-tmp \ + -Obam \ + -o $tmp_prefix.sc2sr.suppsorted.sv.bam \ + $tmp_prefix.sc2sr.supp.sv.bam \ + && $rmcmd $tmp_prefix.sc2sr.supp.sv.bam \ + && $rmcmd -f $prefix.sv.tmp.bam $prefix.sv.tmp.bam.bai \ + && $timecmd samtools merge \ + -c \ + -p \ + -@ $threads \ + $prefix.sv.tmp.bam \ + $tmp_prefix.sc2sr.primary.sv.bam \ + $tmp_prefix.sc2sr.suppsorted.sv.bam \ + && $timecmd samtools index $prefix.sv.tmp.bam \ + && $rmcmd $tmp_prefix.sc2sr.primary.sv.bam \ + && $rmcmd $tmp_prefix.sc2sr.suppsorted.sv.bam \ + && mv $prefix.sv.tmp.bam $prefix.sv.bam \ + && mv $prefix.sv.tmp.bam.bai $prefix.sv.bam.bai \ + ; } 1>&2 2>> $logfile + + write_status "Produced assembly BAM: $prefix.sv.bam" + + write_status "Complete Assembly" + + # no idea why this is a for loop, could just be: ASSEMBLY=$assembly + #assembly_args="" + #for ass in $assembly ; do + # assembly_args="$assembly_args ASSEMBLY=$ass" + #done + write_status "Assembly args: $assembly_args" + + write_status "*** ASSEMBLY COMPLETE ***" +fi + +#### +# VARIANT CALLING +#### + +if [[ $do_call == true ]] ; then + write_status "*** VARIANT CALLING ***" + + write_status "Creating variant VCF: $output_vcf" + + dir=$workingdir/$(basename $output_vcf).gridss.working + prefix=$dir/$(basename $output_vcf) + mkdir -p $dir + if [[ ! -d $dir ]] ; then + write_status "Unable to create directory $dir" + exit $EX_CANTCREAT + fi + + # create symbolic links to the full BAM as though they were produced by the pre-process step + # eg: ./gridss_02/COLO829R.bam.gridss.working/COLO829R.bam.sv.bam + for (( i=0; i < $label_count; ++i )) + do + bam_file=${BAM_ARRAY[$i]} + bam_dir=$workingdir/$(basename $bam_file).gridss.working + + if [[ ! -d $bam_dir ]] ; then + mkdir -p $bam_dir + fi + + sv_bam_file=$bam_dir/$(basename $bam_file).sv.bam + # write_status "Making soft-link to ${sv_bam_file}" + #ln -sfr ${bam_file} ${sv_bam_file} + #ln -sfr ${bam_file}.bai ${sv_bam_file}.bai + done + + write_status "Running IdentifyVariants" + { $timecmd java -Xmx$jvmheap $jvm_args \ + -Dgridss.output_to_temp_file=true \ + -cp $gridss_jar gridss.IdentifyVariants \ + TMP_DIR=$workingdir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + WORKER_THREADS=$threads \ + $input_filtered_args \ + $blacklist_arg \ + $config_args \ + $assembly_args \ + OUTPUT_VCF=$prefix.unallocated.vcf \ + $readpairing_args \ + ; } 1>&2 2>> $logfile + write_status "IdentifyVariants complete, produced $prefix.unallocated.vcf" + + write_status "Running AnnotateVariants" + { $timecmd java -Xmx$jvmheap $jvm_args \ + -Dgridss.output_to_temp_file=true \ + -Dgridss.async.buffersize=2048 \ + -cp $gridss_jar gridss.AnnotateVariants \ + TMP_DIR=$workingdir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + WORKER_THREADS=$threads \ + $input_filtered_args \ + $blacklist_arg \ + $config_args \ + $assembly_args \ + INPUT_VCF=$prefix.unallocated.vcf \ + OUTPUT_VCF=$prefix.allocated.vcf \ + $readpairing_args \ + ; } 1>&2 2>> $logfile + $rmcmd $prefix.unallocated.vcf + write_status "AnnotateVariants complete, produced $prefix.allocated.vcf" + + write_status "Running AnnotateInsertedSequence" + + { $timecmd java -Xmx$otherjvmheap $jvm_args \ + -Dgridss.output_to_temp_file=true \ + -cp $gridss_jar gridss.AnnotateInsertedSequence \ + TMP_DIR=$workingdir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + WORKER_THREADS=$threads \ + INPUT=$prefix.allocated.vcf \ + OUTPUT=$output_vcf \ + && $rmcmd $prefix.allocated.vcf \ + ; } 1>&2 2>> $logfile + write_status "AnnotateInsertedSequence complete, produced $output_vcf" + + write_status "*** VARIANT CALLING COMPLETE ***" +fi + +if [[ -f $logfile ]] ; then + write_status "Run complete with $(grep WARNING $logfile | wc -l) warnings and $(grep ERROR $logfile | wc -l) errors." +fi +trap - EXIT +exit 0 # success! diff --git a/recipes/hmftools-sv-prep/meta.yaml b/recipes/hmftools-sv-prep/meta.yaml index c81ed9c3f6a43..2af81c748ca39 100644 --- a/recipes/hmftools-sv-prep/meta.yaml +++ b/recipes/hmftools-sv-prep/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "1.1" %} -{% set sha256 = "e7487a16c609ad4d9f3b2d29ebada02b04fbd3bef3dacd26f228bb1928d5606e" %} +{% set version = "1.2.3" %} +{% set sha256 = "8f42be297e1ece6d070324f8b12b0a30106291731ac89f5d3c0fc2d82fd887ab" %} package: name: hmftools-sv-prep version: '{{ version }}' source: - url: 'https://github.com/hartwigmedical/hmftools/releases/download/sv-prep-v{{ version }}/sv-prep_v{{ version }}.jar' + url: https://github.com/hartwigmedical/hmftools/releases/download/sv-prep-v{{ version }}/sv-prep_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('hmftools-sv-prep', max_pin="x") }} requirements: run: - zlib - openjdk >=8 - - samtools + - gridss =2.13.2=h50ea8bc_3 test: commands: - - 'SvPrep 2>&1 | grep -q "SvPrep version"' + - 'svprep -version | grep SvPrep' about: home: https://github.com/hartwigmedical/hmftools/tree/master/sv-prep diff --git a/recipes/hmftools-sv-prep/SvPrep.sh b/recipes/hmftools-sv-prep/svprep.sh similarity index 100% rename from recipes/hmftools-sv-prep/SvPrep.sh rename to recipes/hmftools-sv-prep/svprep.sh From 24f76761757b424e960c797b301f34cbb15ab812 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 12:22:43 -0500 Subject: [PATCH 0362/1813] Update capcruncher to 0.3.12 (#45679) --- recipes/capcruncher/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/capcruncher/meta.yaml b/recipes/capcruncher/meta.yaml index 39a98b445fdb9..f65c123600dbe 100644 --- a/recipes/capcruncher/meta.yaml +++ b/recipes/capcruncher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "capcruncher" %} -{% set version = "0.3.11" %} +{% set version = "0.3.12" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/capcruncher-{{ version }}.tar.gz - sha256: 1baee46dc9eaab97125796292bc7d6a24821c69538d43f205a344f550db14a7a + sha256: 43b1e634dac4eee5f801b69b2adafb07b61c72556cc32b1cd5e03518ed2e407b build: number: 0 From d9e3cb351c5b5ba69ad4a5fc20f41188c625957b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 12:23:28 -0500 Subject: [PATCH 0363/1813] Update hmftools-purple to 4.0.1 (#45685) --- recipes/hmftools-purple/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-purple/meta.yaml b/recipes/hmftools-purple/meta.yaml index a5aa250c79fa7..ec2fb71d6ffb2 100644 --- a/recipes/hmftools-purple/meta.yaml +++ b/recipes/hmftools-purple/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "4.0" %} -{% set sha256 = "58b2457143f77e7752a907a59f1fdd9550fae7483def373ad39ea4ac8fdbc383" %} +{% set version = "4.0.1" %} +{% set sha256 = "e52e98b04dd22ae5b785257f9decb16d4ea270a8de7aaa124ad07e5653b4713c" %} package: name: hmftools-purple From 22d75800c408cc2bf5510733a5930ad239612723 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 12:23:55 -0500 Subject: [PATCH 0364/1813] Update nanomotif to 0.1.15 (#45688) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index 6c85011e7505b..300d48d2bebe0 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.14" %} +{% set version = "0.1.15" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: f8278b9102267bdb9e4f3e2aa46d6e9f4fb9a655525766b1bc31f6cf67f2e609 + sha256: d218e3ea6822891c17225800849944ba87b64da3dff75526aa0c5f09d43f2234 build: entry_points: From d4d1be04eea80f44e82be9ab8d6a6ec30f1cbabd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 15:50:36 -0500 Subject: [PATCH 0365/1813] Update snakemake to 8.4.7 (#45684) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 4a8831860540c..c1aeb3dbbadc4 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.6" %} +{% set version = "8.4.7" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 173df5ef2674191fe61c67f9a9e13fc7cbcca318d470a1d8e652f556ce706545 + sha256: 030f299937a09d328254a0705b87b91ecaf7d3bce51f3c4cee16df2a3718158f build: number: 0 From d51f702992a7fe96c9b40a59043884f405b372e2 Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Wed, 7 Feb 2024 15:51:06 -0500 Subject: [PATCH 0366/1813] Update gsearch v0.1.9 (#45690) * Update annembed v0.1.4 * Update gsearch v0.1.9 --- recipes/gsearch/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gsearch/meta.yaml b/recipes/gsearch/meta.yaml index b378ec2e3aee7..3149d4081ee0d 100644 --- a/recipes/gsearch/meta.yaml +++ b/recipes/gsearch/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.8" %} +{% set version = "0.1.9" %} package: name: gsearch @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/gsearch/archive/v{{ version }}.tar.gz - sha256: bdb954e52c61baf94f7de574b4a578df19f12508af89996d461aeebb43a39a8f + sha256: 21d87192f55a0826744e474c5e22add204b7d2b634bdc692d29ab88175a34c36 requirements: build: @@ -23,7 +23,7 @@ requirements: test: commands: - - gsearchbin -h + - gsearch -h about: home: https://github.com/jean-pierreBoth/gsearch From ea202d1b70fb2b4345688243fb2f7007fa014461 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino <62253982+AndreaGuarracino@users.noreply.github.com> Date: Wed, 7 Feb 2024 21:51:40 +0100 Subject: [PATCH 0367/1813] add pyhon3 as `run` requirement to `wfmash` recipe (#45687) * add pyhon3 as `run` requirement * increment number --- recipes/wfmash/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/wfmash/meta.yaml b/recipes/wfmash/meta.yaml index ac6ba6133b387..c01b522985de1 100644 --- a/recipes/wfmash/meta.yaml +++ b/recipes/wfmash/meta.yaml @@ -13,7 +13,7 @@ build: skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} - number: 0 + number: 1 requirements: build: @@ -30,6 +30,7 @@ requirements: - libblas run: - llvm-openmp # [osx] + - python >=3.7 test: commands: From 52588d01d09f4649bece312d11f486d3121a6b55 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 21:53:07 -0500 Subject: [PATCH 0368/1813] Update snaketool-utils to 0.0.5 (#45695) --- recipes/snaketool-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snaketool-utils/meta.yaml b/recipes/snaketool-utils/meta.yaml index 36bc8b6314b9f..2d9130b89bfb3 100644 --- a/recipes/snaketool-utils/meta.yaml +++ b/recipes/snaketool-utils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snaketool-utils" %} -{% set version = "0.0.4" %} +{% set version = "0.0.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snaketool_utils-{{ version }}.tar.gz - sha256: 75a35ba887be3ead290087241d1222dc8ef79e36cb3ccb395d9c7059b72cbe06 + sha256: a686300efcec715fba806479b10dde0f98781a90600c7bf7cadcca1ebb655305 build: noarch: python From fb4357c451a9e2aff00a7af4ae47792e012f5dea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 00:16:32 -0500 Subject: [PATCH 0369/1813] Update koverage to 0.1.11 (#45697) --- recipes/koverage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/koverage/meta.yaml b/recipes/koverage/meta.yaml index d7047f608650d..fb97ab5265ccd 100644 --- a/recipes/koverage/meta.yaml +++ b/recipes/koverage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "koverage" %} -{% set version = "0.1.10" %} +{% set version = "0.1.11" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 46d7d444350932a88f6d0158c946671f2f0a6b4769f3c9c68e4b13fa76ecefc2 + sha256: 24d785d654524a59c109f6fb3b3f6fc211b5f7177d643597f144fc6954a74d57 build: noarch: python From 76e1897ab1395c2f443dcc286d92e285a19ce6ef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 00:16:56 -0500 Subject: [PATCH 0370/1813] Update trimnami to 0.1.3 (#45698) --- recipes/trimnami/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/trimnami/meta.yaml b/recipes/trimnami/meta.yaml index 74c441bf5757e..f1153c947bca4 100644 --- a/recipes/trimnami/meta.yaml +++ b/recipes/trimnami/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trimnami" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 5a045d74b3a3e388d32ef2b43429f3742adaa90566d44a52f7cd9bb70d428e69 + sha256: 37e15eec675d7cc65d75b49e0d6151ceceee53ea043f854ffad05b5895ce8d78 build: noarch: python From b45bdc458b302748b671d3a50ae6d010d9b4dfff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 05:39:21 -0500 Subject: [PATCH 0371/1813] Update nanomotif to 0.1.17 (#45699) * Update nanomotif to 0.1.16 * Update nanomotif to 0.1.17 --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index 300d48d2bebe0..8bf32fe611950 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.15" %} +{% set version = "0.1.17" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: d218e3ea6822891c17225800849944ba87b64da3dff75526aa0c5f09d43f2234 + sha256: 48bd357472e36ed6336ff555fc55a81779d05ea3cf0e1b25f6a5d1cadf0763f5 build: entry_points: From 6916ecf9c3b76af48532d28338afbd0615281e02 Mon Sep 17 00:00:00 2001 From: Ryan James Kennedy <67742838+ryanjameskennedy@users.noreply.github.com> Date: Thu, 8 Feb 2024 14:44:57 +0100 Subject: [PATCH 0372/1813] Add git to resfinder (#45686) --- recipes/resfinder/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/resfinder/meta.yaml b/recipes/resfinder/meta.yaml index 53c3e5a68befa..4f4e2bcf04abe 100644 --- a/recipes/resfinder/meta.yaml +++ b/recipes/resfinder/meta.yaml @@ -12,7 +12,7 @@ source: - python_path.patch build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage('resfinder', max_pin="x") }} @@ -33,10 +33,13 @@ requirements: - python-dateutil - kma - blast >=2.8.1 + - git test: imports: - resfinder + commands: + - python -m resfinder --help about: home: https://bitbucket.org/genomicepidemiology/resfinder From 70eca7527a37e0502432afa1e80034f1fee60e0a Mon Sep 17 00:00:00 2001 From: Andrei Prodan Date: Thu, 8 Feb 2024 15:29:56 +0100 Subject: [PATCH 0373/1813] Add Scevan R package recipe (#45649) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * receipt for SCEVAN R package * add LICENSE and fix linting errors * fix build errors * fix linting error * add devtools and other dependencies as conda installs * add tag for SCEVAN; use "host" instead of "build" requirements * Update recipes/scevan/meta.yaml Co-authored-by: Pablo Moreno * bump rename to r-scevan; bump version to v1.0.1 * rename recipe subfolder to r-scevan * fix typo in tag URL * fix type in SCEVAN devtools::install_github() command * Update recipes/r-scevan/meta.yaml Co-authored-by: Björn Grüning * Update recipes/r-scevan/meta.yaml Co-authored-by: Björn Grüning * update license identifier * Update recipes/r-scevan/meta.yaml Co-authored-by: Christian Brueffer * solve conflict * edit "script:" * re-add yaGST installation * re-add ${R} CMD INSTALL --build . * fix order in "script:" * build using a build.sh file and devtools * fix dependencies --------- Co-authored-by: Pablo Moreno Co-authored-by: Björn Grüning Co-authored-by: Christian Brueffer --- recipes/r-scevan/build.sh | 4 +++ recipes/r-scevan/meta.yaml | 64 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 recipes/r-scevan/build.sh create mode 100644 recipes/r-scevan/meta.yaml diff --git a/recipes/r-scevan/build.sh b/recipes/r-scevan/build.sh new file mode 100644 index 0000000000000..c3ea0d7102a89 --- /dev/null +++ b/recipes/r-scevan/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +R -e "library(devtools)" +R -e "devtools::install_github('miccec/yaGST')" +R CMD INSTALL --build . diff --git a/recipes/r-scevan/meta.yaml b/recipes/r-scevan/meta.yaml new file mode 100644 index 0000000000000..bb1703e201397 --- /dev/null +++ b/recipes/r-scevan/meta.yaml @@ -0,0 +1,64 @@ +package: + name: r-scevan + version: 1.0.1 + +source: + url: https://github.com/AntonioDeFalco/SCEVAN/archive/refs/tags/v1.0.1.tar.gz + sha256: 7558d31282c36418db3960b3edb9cb9815db14b0a48d8882287e11f752dfeab1 + +build: + number: 0 + noarch: generic # Specify that the package is noarch + run_exports: '{{ pin_compatible("r-scevan", max_pin="x.x") }}' + rpaths: + - lib/R/lib + - lib + +requirements: + host: + - r-base + - r-remotes + - r-devtools + - r-rcpp + - r-paralleldist + - r-pheatmap + - r-forcats + - r-dplyr + - bioconductor-fgsea + - r-cluster + - r-ggplot2 + - r-Rtsne + - bioconductor-scran + - r-ape + - bioconductor-ggtree + - r-tidytree + - r-ggrepel + - r-optparse + run: + - r-base + - r-devtools + - r-paralleldist + - r-pheatmap + - r-forcats + - r-dplyr + - bioconductor-fgsea + - r-cluster + - r-ggplot2 + - r-Rtsne + - bioconductor-scran + - r-ape + - bioconductor-ggtree + - r-tidytree + - r-ggrepel + - r-optparse + +test: + commands: + - $R -e "library(SCEVAN)" + +about: + home: https://github.com/AntonioDeFalco/SCEVAN/ + license: GPL-3.0-only + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single CEll Variational Aneuploidy aNalysis From 4c94c0efbbcae7d0a04079aaf3655ee4335c8835 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ozan=20=C3=96z=C4=B1=C5=9F=C4=B1k?= Date: Thu, 8 Feb 2024 16:59:45 +0100 Subject: [PATCH 0374/1813] Update orsum (#45701) --- recipes/orsum/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/orsum/meta.yaml b/recipes/orsum/meta.yaml index 3591a34be072a..914af7c1fb195 100644 --- a/recipes/orsum/meta.yaml +++ b/recipes/orsum/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.6.0" %} -{% set sha256hash = "b44f9d5a68e4983da93c41cf5e4053c77ac550e0482601c1da6a83b039328da9" %} +{% set version = "1.7.0" %} +{% set sha256hash = "ba228a3d1ca6aa6269a624ab109c1a6c41c58dd392abcf46f8edc2e52760c1a8" %} package: name: orsum version: {{ version }} @@ -11,6 +11,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('orsum', max_pin="x.x") }} requirements: run: From 3f1ee483322076a8e32c43e35d99ba6c01e29186 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Thu, 8 Feb 2024 08:00:21 -0800 Subject: [PATCH 0375/1813] Add ntsynt (#45692) --- recipes/ntsynt/build.sh | 9 ++++++++ recipes/ntsynt/meta.yaml | 49 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 recipes/ntsynt/build.sh create mode 100644 recipes/ntsynt/meta.yaml diff --git a/recipes/ntsynt/build.sh b/recipes/ntsynt/build.sh new file mode 100644 index 0000000000000..c0ea64c9342bc --- /dev/null +++ b/recipes/ntsynt/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" + +# Build ntSynt +mkdir -p ${PREFIX}/bin +meson setup build --prefix ${PREFIX} +cd build +ninja install diff --git a/recipes/ntsynt/meta.yaml b/recipes/ntsynt/meta.yaml new file mode 100644 index 0000000000000..0fa8488dc1a91 --- /dev/null +++ b/recipes/ntsynt/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "ntSynt" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/bcgsc/ntSynt/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.gz + sha256: db3fe491233d93967120d091a19abbef1fa5dfa637814bb617814a1b3e3f1331 + +build: + number: 0 + run_exports: + - {{ pin_subpackage("ntsynt", max_pin="x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - cmake + host: + - python + - meson + - ninja + - llvm-openmp # [osx] + - libgomp # [linux] + - btllib + run: + - python + - btllib + - intervaltree + - pybedtools + - ncls + - python-igraph + - snakemake + - samtools + - seqtk + +test: + commands: + - ntSynt -h + imports: + - btllib + +about: + home: https://github.com/bcgsc/ntsynt + license: GPL-3.0 + license_file: LICENSE + summary: 'Detecting multi-genome synteny blocks using minimizer graph mapping' From c7003c79932a9f69a1fde479b8987810e71664d2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:16:29 -0500 Subject: [PATCH 0376/1813] Update pango-designation to 1.25 (#45717) --- recipes/pango-designation/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pango-designation/meta.yaml b/recipes/pango-designation/meta.yaml index 3c559b4e5981f..7dcdda6f72e20 100644 --- a/recipes/pango-designation/meta.yaml +++ b/recipes/pango-designation/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.24" %} +{% set version = "1.25" %} package: name: pango-designation @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pango-designation/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9b84365c503a71ac5aadf47b977aa022450457492b24955149f26469f733f898 + sha256: f57bc2dee34d39ac73d27782357a4332f899bf45a495c8c279c6905c8b0130be build: number: 0 From 7cd528a1d141697d37d189fb04c891932621a16d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:18:56 -0500 Subject: [PATCH 0377/1813] Update planemo to 0.75.21 (#45713) --- recipes/planemo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 2fa68f4e4e03e..6ac4349111683 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.20" %} -{% set sha256 = "de61edcb2496c9301b751ac12d0c83441dfcb36cff3a279db3e7942e3fc4b873" %} +{% set version = "0.75.21" %} +{% set sha256 = "c8b238d258ee85244a2a7d067452ef14f191c78e1e0923945bdd5e759682716e" %} package: name: {{ name|lower }} From 615d282c6badfff1cb4aacecf70ca5676868d3c7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:19:32 -0500 Subject: [PATCH 0378/1813] Update annonars to 0.35.0 (#45712) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 49388dd1ed49a..7cfa355bc6dbb 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.34.1" %} +{% set version = "0.35.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 55f4d7fff2f94eaf94e7752a426ee2532f88ffb25a0d2bb0cf0b4127212bf3e1 + sha256: cdea1de0bdcc1d223093fcf8d629af5c24bc788900a0cc47256e42fba587c2c8 requirements: build: From 290da9e9839bc247e8914dd1088045f58354b5ce Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:49:36 -0500 Subject: [PATCH 0379/1813] Update cramino to 0.14.1 (#45710) * Update cramino to 0.14.0 * Update cramino to 0.14.1 --------- Co-authored-by: Wouter De Coster --- recipes/cramino/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cramino/meta.yaml b/recipes/cramino/meta.yaml index 0d07842df6aad..5647f84ea1049 100644 --- a/recipes/cramino/meta.yaml +++ b/recipes/cramino/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.13.1" %} +{% set version = "0.14.1" %} package: name: cramino @@ -12,7 +12,7 @@ build: source: url: https://github.com/wdecoster/cramino/archive/v{{ version }}.tar.gz - sha256: 92e60915b2fccacb21f2c5b71253b667615e1a99f964f232569122458cf64c40 + sha256: 57e15afb113808c327a4ec843ae1677f37c35f692e04927cfcc3823affac6cff requirements: build: From 5374257f95b5246716c2ad1ade6a63f9e2002237 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:50:45 -0500 Subject: [PATCH 0380/1813] Update vcfsim to 1.0.9.alpha (#45719) --- recipes/vcfsim/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vcfsim/meta.yaml b/recipes/vcfsim/meta.yaml index 96d58274dcb6d..5883749ef127a 100644 --- a/recipes/vcfsim/meta.yaml +++ b/recipes/vcfsim/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcfsim" %} -{% set version = "1.0.8.alpha" %} +{% set version = "1.0.9.alpha" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Pie115/VCFSimulator-SamukLab/archive/{{ version }}.tar.gz - sha256: 67a2be52bb06b44dfb3cb96cff766cae866181b0b1e136d1d8737a229438068c + sha256: 364eb81f21b5071450b553649c5be1e2c273a63bb04e9a6e4af2e1455bb8c48e build: noarch: python From 0500d94f5f693fc079dd73bde43baad0197638fd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:16:10 -0500 Subject: [PATCH 0381/1813] Update dfast to 1.2.21 (#45702) * Update dfast to 1.2.21 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/dfast/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/dfast/meta.yaml b/recipes/dfast/meta.yaml index bee44b4572a7a..b57da8b83f70f 100644 --- a/recipes/dfast/meta.yaml +++ b/recipes/dfast/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.20" %} +{% set version = "1.2.21" %} package: name: dfast @@ -6,11 +6,13 @@ package: source: url: https://github.com/nigyta/dfast_core/archive/{{ version }}.tar.gz - sha256: 57f24e8bc20f412b73612ba710e14a009f77381f415f3ee47d69b5c7411ef71d + sha256: 70283cbfc756f5033cc92d1c721b9f7b5d5ba521a6da6e36e2bed794267c8a7b build: number: 0 binary_relocation: False # [osx] + run_exports: + - {{ pin_subpackage("dfast", max_pin="x.x") }} requirements: build: From 03b984b680404a6ecb450884abf90fa9e13f9348 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:16:18 -0500 Subject: [PATCH 0382/1813] Update oakvar to 2.9.87 (#45696) * Update oakvar to 2.9.86 * Update oakvar to 2.9.87 --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 15f40af72b4d6..2054f16001ab9 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.85" %} -{% set sha256 = "ff8f8f8a6ab8cd9c9307edf2cb710a9ccdb9649f3c46ff656f336678419e514b" %} +{% set version = "2.9.87" %} +{% set sha256 = "3ee4c24b0d1f8995b7f41ec2ba2c6948c9bd6bed4166715a1fe3b0e4436fba44" %} package: name: {{ name|lower }} From a4e82d7f38830bd81aafd000e2b00ab38bb52eff Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Fri, 9 Feb 2024 01:16:43 +0100 Subject: [PATCH 0383/1813] Fix pydantic dependency of varfish-cli more strictly. (#45703) --- recipes/varfish-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml index f65d88b9dd723..909078b89013b 100644 --- a/recipes/varfish-cli/meta.yaml +++ b/recipes/varfish-cli/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - varfish-cli = varfish_cli.__main__:main @@ -33,7 +33,7 @@ requirements: - tqdm - tabulate - polyleven - - pydantic + - pydantic >=2.0,<3.0 - python-dateutil - simplejson - typeguard From 2099a9b354f510d914d2b6d31f860d21e9163bfb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:17:31 -0500 Subject: [PATCH 0384/1813] Update assemblycomparator2 to 2.5.18 (#45706) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index 6c929a7075290..1558758fef16b 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.17" %} +{% set version = "2.5.18" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5c15c4882529d33d56678eb3b710e243e3f5adc49b7d0ad1871f26ecab69d97e + sha256: 74d1f4959405c8ad01dd2cb2ad842c8ac71211b9ae8a125f4e58e44016cfd4a6 build: From 434604dcc7510790ee6ec9d1a69ae10dc09e2116 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:17:44 -0500 Subject: [PATCH 0385/1813] Update centrifuger to 1.0.1 (#45711) --- recipes/centrifuger/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/centrifuger/meta.yaml b/recipes/centrifuger/meta.yaml index a25ea6d2ebf32..dbb8ff62c7d69 100644 --- a/recipes/centrifuger/meta.yaml +++ b/recipes/centrifuger/meta.yaml @@ -1,5 +1,5 @@ {% set name = "centrifuger" %} -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ build: source: url: https://github.com/mourisl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 88d8e9031caa9298a2ea0c3a7a4d4a8a2a569dcc32cf6f795a13cdf03612aa49 + sha256: 4ce9a20d786a39ef26b1ef31851c180e0b1baae1efc2d9ad8442bec6203d04bb requirements: build: From 6f6d2632a1ab9c3a226365641d2e396300f64e82 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:18:04 -0500 Subject: [PATCH 0386/1813] Update igv-reports to 1.12.0 (#45720) --- recipes/igv-reports/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/igv-reports/meta.yaml b/recipes/igv-reports/meta.yaml index 8b464c54de237..1e69cef3c08a1 100644 --- a/recipes/igv-reports/meta.yaml +++ b/recipes/igv-reports/meta.yaml @@ -1,5 +1,5 @@ {% set name = "igv-reports" %} -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8a524c53f4bbcf93d58a2b2246d8473b22bea1955a492f81365c4c27164efe86 + sha256: 2a4bb08945e7872108a83037468249581b2fb42b2934cf33446971443175611d build: noarch: python From b83cbb4ba24c810ba234af44584af949e4b0a7c0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:18:17 -0500 Subject: [PATCH 0387/1813] Update ndex2 to 3.8.0 (#45721) --- recipes/ndex2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ndex2/meta.yaml b/recipes/ndex2/meta.yaml index 223be915ae200..b3b3536e16221 100644 --- a/recipes/ndex2/meta.yaml +++ b/recipes/ndex2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ndex2" %} -{% set version = "3.7.0" %} +{% set version = "3.8.0" %} package: @@ -8,7 +8,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ndex2-{{ version }}.tar.gz" - sha256: "5fed3b6c204275fd75724f7d609823f9f6e249b3d468fdd8b0a1f7a9be7a294f" + sha256: "9f4d7f4b9594664191fba5c6512e315ed47b13bc416df5769802f87a7c22d1c8" build: noarch: python From e0b145f6b921aa1937bed57945a8c1b21be7c31e Mon Sep 17 00:00:00 2001 From: Catherine Chahrour <74187550+CChahrour@users.noreply.github.com> Date: Fri, 9 Feb 2024 00:23:39 +0000 Subject: [PATCH 0388/1813] Add seqnado (#45705) * add seqnado * add seqnado * add alsmith as maintainer * edit recipe * add singularity * require wget for testing * update recipe * fix license SPDX identifier --- recipes/seqnado/meta.yaml | 66 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 recipes/seqnado/meta.yaml diff --git a/recipes/seqnado/meta.yaml b/recipes/seqnado/meta.yaml new file mode 100644 index 0000000000000..c9914ff336c16 --- /dev/null +++ b/recipes/seqnado/meta.yaml @@ -0,0 +1,66 @@ +{% set name = "seqnado" %} +{% set version = "0.4.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqnado-{{ version }}.tar.gz + sha256: 171d551baf6eb3e6b7402510826688804f9fab0d3dba0db9907da92a1059dc47 + +build: + number: 0 + noarch: python + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} + script: {{ PYTHON }} -m pip install . --no-deps -vvv + entry_points: + - seqnado = seqnado.cli:cli_pipeline + - seqnado-design = seqnado.cli:cli_design + - seqnado-config = seqnado.cli:cli_config + run_exports: + - {{ pin_subpackage('seqnado', max_pin="x.x") }} + +requirements: + host: + - python >=3.10 + - setuptools >=61.0 + - wheel + - setuptools-scm >=6.2 + - pip + run: + - click + - cookiecutter + - drmaa + - pandas + - pulp <=2.7.0 + - pydantic + - python >=3.10 + - pyyaml + - seaborn + - setuptools-scm + - singularity + - snakemake <=7.3.2 + - snakemake-wrapper-utils + - tracknado + - wget + +test: + imports: + - seqnado + commands: + - seqnado --help + - seqnado-design --help + - seqnado-config --help + +about: + home: https://alsmith151.github.io/SeqNado/ + summary: Pipelines for genomics analysis + license: GPL-3.0-or-later + license_file: LICENSE + +extra: + recipe-maintainers: + - alsmith151 + - CChahrour From 0e81bc99e805d3cf9f7e3a125fe6457bf8545095 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:24:32 -0500 Subject: [PATCH 0389/1813] Update pangu to 0.2.4 (#45496) * Update pangu to 0.2.3 * add run_exports * Update pangu to 0.2.4 --------- Co-authored-by: mencian --- recipes/pangu/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/pangu/meta.yaml b/recipes/pangu/meta.yaml index cabad42e5e79a..dbf8e578c4815 100644 --- a/recipes/pangu/meta.yaml +++ b/recipes/pangu/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.2" %} -{% set sha256 = "91133019717eb8becc6f9345257891206bea57c5b3706b18440cfe3c393fd07c" %} +{% set version = "0.2.4" %} +{% set sha256 = "1437175d891a76f71a19dc86121c08b19d81a61273cbbd09bbab6e090c42e3f2" %} package: name: pangu @@ -14,7 +14,9 @@ build: noarch: python entry_points: - pangu = pangu.__main__:main_cli - script: python -m pip install --no-deps -vv . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation -vvv . + run_exports: + - {{ pin_subpackage('pangu', max_pin="x.x") }} requirements: host: From 31d4ad95cd0bd282aac6bf9f3084b1f445b1e8aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= <51365402+balajtimate@users.noreply.github.com> Date: Fri, 9 Feb 2024 01:25:28 +0100 Subject: [PATCH 0390/1813] Update htsinfer (#45633) * update htsinfer * update sha256 * update tests * update version and sha * reset build number * increase build number --- recipes/htsinfer/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/htsinfer/meta.yaml b/recipes/htsinfer/meta.yaml index df57b6f70efa5..b853db128b352 100644 --- a/recipes/htsinfer/meta.yaml +++ b/recipes/htsinfer/meta.yaml @@ -10,7 +10,7 @@ source: sha256: f7225290e12bf129bdb654f06f1cb98da577be81d35f7d17844447fcdf058618 build: - number: 0 + number: 1 noarch: python entry_points: - htsinfer = htsinfer.cli:main @@ -26,7 +26,7 @@ requirements: - numpy >=1.22, <1.25 - pandas >=1.3.5, <1.4.0 - biopython >=1.78 - - pydantic >=1.8.1, <2 + - pydantic >=2, <3 - pysam >=0.16.0 - pyahocorasick >=1.4.0 run: @@ -36,7 +36,7 @@ requirements: - numpy >=1.22, <1.25 - pandas >=1.3.5, <1.4.0 - pyahocorasick >=1.4.0 - - pydantic >=1.8.1, <2 + - pydantic >=2, <3 - pysam >=0.16.0 - python >=3.8, <=3.10 - star >=2.7.6 From 08d17ebc9f04bfdc00fceb243e342ba33d9e104c Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 9 Feb 2024 11:27:42 +1100 Subject: [PATCH 0391/1813] Patch hmftools-sv-prep 1.2.3 (#45694) * Enable SvPrep to discover GRIDSS JAR * Bump build number * Fix class-path detection in BASH script --- .../gridss_shell_with_jar_entrypoint | 32 +++++++++++++------ recipes/hmftools-sv-prep/meta.yaml | 2 +- recipes/hmftools-sv-prep/svprep.sh | 2 +- 3 files changed, 24 insertions(+), 12 deletions(-) diff --git a/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint b/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint index d9183aebce48e..1b8d632b76499 100644 --- a/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint +++ b/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint @@ -4,15 +4,27 @@ # Adapted from bioconda-recipes/picard/picard.sh set -o pipefail -# Find original directory of bash script, resolving symlinks -# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 -SOURCE="${BASH_SOURCE[0]}" -while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink - DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located -done -DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" -$DIR/$(basename $0) --jar "$DIR/gridss.jar" "$@" +resolve_source_directory() { + # Find original directory of bash script, resolving symlinks + # http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 + local SOURCE="${1}" + while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located + done + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + echo $DIR +} +# Sanity check for GRIDSS dependency +if ! hash gridss 2>/dev/null; then + echo "Could not find 'gridss' in PATH, exiting"; + exit 1; +fi + +SCRIPT_DIR=$(resolve_source_directory ${BASH_SOURCE[0]}) +JAR_DIR=$(resolve_source_directory $(which gridss)) + +$SCRIPT_DIR/$(basename $0) --jar "$JAR_DIR/gridss.jar" "$@" diff --git a/recipes/hmftools-sv-prep/meta.yaml b/recipes/hmftools-sv-prep/meta.yaml index 2af81c748ca39..17301d9a6a0ec 100644 --- a/recipes/hmftools-sv-prep/meta.yaml +++ b/recipes/hmftools-sv-prep/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('hmftools-sv-prep', max_pin="x") }} diff --git a/recipes/hmftools-sv-prep/svprep.sh b/recipes/hmftools-sv-prep/svprep.sh index 053fdd8f1f5e2..6cd23a12769db 100755 --- a/recipes/hmftools-sv-prep/svprep.sh +++ b/recipes/hmftools-sv-prep/svprep.sh @@ -60,7 +60,7 @@ if [ "$jvm_mem_opts" == "" ]; then fi pass_arr=($pass_args) -if [[ ${pass_arr[0]:=} == org* ]] +if [[ ${pass_arr[0]:=} == com.hartwig.* ]] then eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/sv-prep.jar" $pass_args else From 8a631db0b86d9546a6e03bb71b2b7e7bc0e3b33c Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 9 Feb 2024 01:53:31 +0100 Subject: [PATCH 0392/1813] Update sepp (#44721) * using latest release of upstream * use recent gapc update with hopes to compile on OSX * add subrecipe for older version 4.3.10 (pinned in qiime2) which shall additionally expose upp.config * fix breaking changes in recipe, no changes in upstream * remove sub-recipe (for now) --- recipes/sepp/build.sh | 15 ++++++++++++++- recipes/sepp/meta.yaml | 6 +++--- 2 files changed, 17 insertions(+), 4 deletions(-) diff --git a/recipes/sepp/build.sh b/recipes/sepp/build.sh index 679123229a05e..925564b6363c6 100644 --- a/recipes/sepp/build.sh +++ b/recipes/sepp/build.sh @@ -5,13 +5,26 @@ python setup.py upp -c # ensure SEPP's configuration file is at the correct location ... echo "${PREFIX}/share/sepp/sepp" > home.path -cp home.path ${PREFIX}/lib/python*/site-packages/ +# ensure directory is created ... ($SP_DIR = Python's site-packages location, see https://docs.conda.io/projects/conda-build/en/stable/user-guide/environment-variables.html#environment-variables-set-during-the-build-process) +mkdir -p $SP_DIR/ +# ... before we copy content into it +cp -rv home.path $SP_DIR/ mkdir -p $PREFIX/share/sepp/sepp # ... and holds correct path names mv -v sepp-package/sepp/default.main.config $PREFIX/share/sepp/sepp/main.config # copy upp config, as it's still needed cp ./.sepp/upp.config $PREFIX/share/sepp/sepp/upp.config +# replace $PREFIX with /opt/anaconda1anaconda2anaconda3 for later replacement of concrete build PREFIX +# note: can't apply a patch here, as upp.config is not part of upstream but gets generated during python setup +if [ $unamestr == 'Linux' ]; +then + sed -i 's@'"$PREFIX"'@/opt/anaconda1anaconda2anaconda3@g' $PREFIX/share/sepp/sepp/upp.config +elif [ $unamestr == 'Darwin' ]; +then + gsed -i 's@'"$PREFIX"'@/opt/anaconda1anaconda2anaconda3@g' $PREFIX/share/sepp/sepp/upp.config +fi + $PYTHON -m pip install . --ignore-installed --no-deps -vv # copy bundled binaries, but hmmer which should be provided by conda, into $PREFIX/bin/ diff --git a/recipes/sepp/meta.yaml b/recipes/sepp/meta.yaml index 731db6eeaceb8..980e754e11f8c 100644 --- a/recipes/sepp/meta.yaml +++ b/recipes/sepp/meta.yaml @@ -15,13 +15,13 @@ source: - nodeps.setup.py.patch build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('sepp', max_pin="x") }} requirements: host: - - python 3.7 + - python <=3.9 - setuptools - pip - dendropy <=4.5.1 @@ -29,7 +29,7 @@ requirements: - hmmer ==3.1b2 run: - - python 3.7 + - python <=3.9 - dendropy <=4.5.1 - openjdk - hmmer ==3.1b2 From 252b37eb50c8fc52429d9fddb986b704eb12daf8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 20:16:48 -0500 Subject: [PATCH 0393/1813] Update r-jackstraw to 1.3.9 (#45683) * Update r-jackstraw to 1.3.9 * add run_exports --------- Co-authored-by: mencian --- recipes/r-jackstraw/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/r-jackstraw/meta.yaml b/recipes/r-jackstraw/meta.yaml index 5bb00456a1c3e..87c8d069725c3 100644 --- a/recipes/r-jackstraw/meta.yaml +++ b/recipes/r-jackstraw/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.3.8' %} +{% set version = '1.3.9' %} package: name: r-jackstraw @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/jackstraw_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/jackstraw/jackstraw_{{ version }}.tar.gz - sha256: 897146888be7f7962a038939fa88005de729f4fcbf4291f6577d59f456cca011 + sha256: 6a599ec3803c64884973eeab44aaf5a78ec44406ef4f536993406e4b6c90f871 build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-jackstraw', max_pin="x") }} requirements: host: From 52504e41c56f0ebbea63d3672295eca29aee4cd5 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Fri, 9 Feb 2024 01:17:44 +0000 Subject: [PATCH 0394/1813] Re-points LD_LIBRARY_PATH to dynamically linked library when loading environment (#45716) * Re-points LD_LIBRARY_PATH to static library when loading environment * Bump aster build number --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/aster/activate.sh | 3 +++ recipes/aster/build.sh | 6 ++++++ recipes/aster/deactivate.sh | 3 +++ recipes/aster/meta.yaml | 2 +- 4 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 recipes/aster/activate.sh create mode 100644 recipes/aster/deactivate.sh diff --git a/recipes/aster/activate.sh b/recipes/aster/activate.sh new file mode 100644 index 0000000000000..8b7e185b7e5ce --- /dev/null +++ b/recipes/aster/activate.sh @@ -0,0 +1,3 @@ +export OLD_LD_LIBRARY_PATH=${LD_LIBRARY_PATH} +export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib/:${LD_LIBRARY_PATH} +export SINGULARITYENV_LD_LIBRARY_PATH=${LD_LIBRARY_PATH} \ No newline at end of file diff --git a/recipes/aster/build.sh b/recipes/aster/build.sh index 786e3a99cae85..ef017cb87c7ae 100644 --- a/recipes/aster/build.sh +++ b/recipes/aster/build.sh @@ -1,5 +1,11 @@ #!/bin/bash +for CHANGE in "activate" "deactivate" +do + mkdir -p "${PREFIX}/etc/conda/${CHANGE}.d" + cp "${RECIPE_DIR}/${CHANGE}.sh" "${PREFIX}/etc/conda/${CHANGE}.d/${PKG_NAME}_${CHANGE}.sh" +done + sed -i.bak1 's/-march=native/-march=x86-64 -mtune=generic/g' makefile if [ "$(uname)" == "Darwin" ]; then diff --git a/recipes/aster/deactivate.sh b/recipes/aster/deactivate.sh new file mode 100644 index 0000000000000..3b8e36f330814 --- /dev/null +++ b/recipes/aster/deactivate.sh @@ -0,0 +1,3 @@ +export LD_LIBRARY_PATH=${OLD_LD_LIBRARY_PATH} +unset OLD_LD_LIBRARY_PATH +unset SINGULARITYENV_LD_LIBRARY_PATH \ No newline at end of file diff --git a/recipes/aster/meta.yaml b/recipes/aster/meta.yaml index 30d17f22be13c..261c0d86b4a8b 100644 --- a/recipes/aster/meta.yaml +++ b/recipes/aster/meta.yaml @@ -7,7 +7,7 @@ package: version: "{{ version }}" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('aster', max_pin="x") }} From 9e22007aafcf2648104a47fb5ddc1167a279dd67 Mon Sep 17 00:00:00 2001 From: Jens-Uwe Ulrich <46562264+JensUweUlrich@users.noreply.github.com> Date: Fri, 9 Feb 2024 02:29:29 +0100 Subject: [PATCH 0395/1813] Add taxor (#45392) * initial taxor commit * skip osx build * add requirement libgomp * build taxor instead of using prebuild binary * md5sum correction * change cmake minimum version to 3.28 * use taxor version 0.1.1 * removed chopper tests * add requirement cxxopts * remove chopper install command * update seqan3 platform.hpp * upgrade to seqan 3.3 * change build directories * change source directories * removed seqan dependencies * use dynamic zlib and bzip2 * libdirsuffix for ankerl * check existing libdir for ankerl * add requirement sdsl-lite * try again with precompiled binary * rollback * syncmer preprocessor directive added * preprocessor directive added to insert_into_ixf * preprocessor directive added to ixf * updated IXF code in seqan3 * updated xxhash.h * updated xxhash.h and release * edit dependencies and use SPDX identifier --------- Co-authored-by: Jens-Uwe Ulrich Co-authored-by: mencian --- recipes/taxor/build.sh | 10 +++++++++ recipes/taxor/meta.yaml | 47 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100755 recipes/taxor/build.sh create mode 100755 recipes/taxor/meta.yaml diff --git a/recipes/taxor/build.sh b/recipes/taxor/build.sh new file mode 100755 index 0000000000000..92946f0a50a31 --- /dev/null +++ b/recipes/taxor/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +mkdir ${SRC_DIR}/build/ +cd ${SRC_DIR}/build/ +cmake ${SRC_DIR}/src +cmake --build . --config Release + +cp ${SRC_DIR}/build/main/taxor $PREFIX/bin +chmod +x $PREFIX/bin/taxor + diff --git a/recipes/taxor/meta.yaml b/recipes/taxor/meta.yaml new file mode 100755 index 0000000000000..cc994c4012da7 --- /dev/null +++ b/recipes/taxor/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "0.1.1" %} + +package: + name: taxor + version: {{ version }} + +source: + url: https://github.com/JensUweUlrich/Taxor/archive/refs/tags/{{ version }}.tar.gz # [linux] + md5: ad6a34b6c3d2c114bed5181af8f69ad3 # [linux] + +build: + number: 0 + run_exports: + - {{ pin_subpackage('taxor', max_pin='x.x.x') }} + skip: true # [osx] + +requirements: + build: + - make + - {{ compiler('cxx') }} + - {{ compiler('c') }} + - cmake >=3.21 + host: + - zlib + - bzip2 + - libgomp # [linux] + - cxxopts >=2.2.0 + - grep + - coreutils + - curl + - diffutils + run: + - grep + - coreutils + - curl + - diffutils + +test: + commands: + - taxor --help + +about: + home: https://github.com/JensUweUlrich/Taxor + summary: Fast and space-efficient taxonomic classification of long reads + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE.md From 853e13040298ca11fbef1c38632ea7dab247a973 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 8 Feb 2024 21:17:23 -0600 Subject: [PATCH 0396/1813] Add recipe for gffpandas v1.2.2 (#45724) * Add recipe for gffpandas v1.2.2 * add summary --- recipes/gffpandas/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 recipes/gffpandas/meta.yaml diff --git a/recipes/gffpandas/meta.yaml b/recipes/gffpandas/meta.yaml new file mode 100644 index 0000000000000..0d3f2ead2c06e --- /dev/null +++ b/recipes/gffpandas/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "gffpandas" %} +{% set version = "1.2.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/foerstner-lab/gffpandas/archive/v{{ version }}.tar.gz + sha256: bf58757e8d0eb4c2aa800864d2ab6e8ee3d499862473417435b57a05d9bf00b2 + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('gffpandas', max_pin="x") }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - pandas + +test: + imports: + - gffpandas + +about: + home: https://github.com/foerstner-lab/gffpandas + summary: "Parse GFF3 into Pandas dataframes" + license: MIT + license_family: MIT + license_file: LICENSE + doc_url: https://gffpandas.readthedocs.io/en/latest/ From e8f7ba30e6853fd5f3bc5f606bce15e449913e62 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 22:17:45 -0500 Subject: [PATCH 0397/1813] Update liftover to 1.1.18 (#45723) --- recipes/liftover/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/liftover/meta.yaml b/recipes/liftover/meta.yaml index 8c82c1069fba5..13f38da8679fa 100644 --- a/recipes/liftover/meta.yaml +++ b/recipes/liftover/meta.yaml @@ -1,6 +1,6 @@ {% set name = "liftover" %} -{% set version = "1.1.17" %} -{% set sha256 = "cb06a3843b570ec554fbc0dd871c0b87d3645200e2c65f6cc97cd4b6146efaf9" %} +{% set version = "1.1.18" %} +{% set sha256 = "a4bf896c5dd59a284929d68f446a78c426827efbec430d35da1ec7bcd29eac44" %} package: name: {{ name|lower }} From 04fedb7859b1182d44f1785ed3ccff511a9a236f Mon Sep 17 00:00:00 2001 From: Michael Roach Date: Fri, 9 Feb 2024 15:40:43 +1030 Subject: [PATCH 0398/1813] Update purge_haplotigs to 1.1.3 (#45726) * Update purge_haplotigs to 1.1.3 * Update maintainer information --- recipes/purge_haplotigs/meta.yaml | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/recipes/purge_haplotigs/meta.yaml b/recipes/purge_haplotigs/meta.yaml index c8cde29e6dec1..583dc731bed0f 100644 --- a/recipes/purge_haplotigs/meta.yaml +++ b/recipes/purge_haplotigs/meta.yaml @@ -1,15 +1,18 @@ -{% set version = "1.1.2" %} +{% set name = "purge_haplotigs" %} +{% set version = "1.1.3" %} package: - name: purge_haplotigs - version: '{{ version }}' + name: {{ name }} + version: {{ version }} source: - url: https://bitbucket.org/mroachawri/purge_haplotigs/get/v{{ version }}.tar.gz - sha256: 14daf0454606232c5adbc5ca42cd873a0c4eb8b7f52d22edd434027d5e8fdca0 + url: https://bitbucket.org/mroachawri/{{ name }}/get/v{{ version }}.tar.gz + sha256: 68d9bc8464f6d53281127576eab67068fbc1c45d37a60dffdc344b2c0be4ff84 build: number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} noarch: generic requirements: @@ -40,3 +43,7 @@ about: license_family: MIT license_file: LICENSE summary: Pipeline to help with curating heterozygous diploid genome assemblies. + +extra: + recipe-maintainers: + - beardymcjohnface From b47bc36783dfdfa49c46be3ecf7ca41e7424b406 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 9 Feb 2024 01:27:30 -0600 Subject: [PATCH 0399/1813] Update taxonomy to 0.10.0 (#45674) * Update taxonomy to 0.10.0 * remove python pinning * move rust and maturin to build dependencies and fix PATH * move maturin back to host section --- build-fail-blacklist | 3 --- recipes/taxonomy/LICENSE | 21 --------------------- recipes/taxonomy/build.sh | 21 +++++++++++---------- recipes/taxonomy/meta.yaml | 19 +++++++++++-------- recipes/taxonomy/pyproject.patch | 9 +++++++++ 5 files changed, 31 insertions(+), 42 deletions(-) delete mode 100644 recipes/taxonomy/LICENSE create mode 100644 recipes/taxonomy/pyproject.patch diff --git a/build-fail-blacklist b/build-fail-blacklist index e6c6649ef9f6f..f3f7e72ee6305 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1057,9 +1057,6 @@ recipes/fmlrc2 # tries to download zlib itself, which fails recipes/d4binding -# maturin build fails -recipes/taxonomy - # no matching package named `quickersort` found recipes/mudskipper diff --git a/recipes/taxonomy/LICENSE b/recipes/taxonomy/LICENSE deleted file mode 100644 index 2cdd581feedab..0000000000000 --- a/recipes/taxonomy/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2019 One Codex - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/recipes/taxonomy/build.sh b/recipes/taxonomy/build.sh index 9a5673054d7ff..e7403810f522a 100644 --- a/recipes/taxonomy/build.sh +++ b/recipes/taxonomy/build.sh @@ -1,17 +1,18 @@ #!/bin/bash -set -ex +set -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" if [ `uname` == Darwin ]; then - export HOME=`mktemp -d` + export HOME=`mktemp -d` + export PATH="$CARGO_HOME/bin:$PATH" fi -curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y - -export PATH="$HOME/.cargo/bin:$PATH" - -export CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER="$CC" - -maturin build --interpreter python --release #--cargo-extra-args="--features=python" +# build statically linked binary with Rust +RUST_BACKTRACE=1 +maturin build -b cffi --interpreter "${PYTHON}" --release --strip #--cargo-extra-args="--features=python" -$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv +${PYTHON} -m pip install . --no-deps --no-build-isolation -vvv diff --git a/recipes/taxonomy/meta.yaml b/recipes/taxonomy/meta.yaml index 793be03563091..10c7fb6a093ab 100644 --- a/recipes/taxonomy/meta.yaml +++ b/recipes/taxonomy/meta.yaml @@ -1,26 +1,30 @@ {% set name = "taxonomy" %} -{% set version = "0.9.0" %} +{% set version = "0.10.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/onecodex/taxonomy/archive/v{{ version }}.tar.gz - sha256: 3d9fb6604ce119bd46635eb1ab43212f9da591f0b6fc53cfcd8c97598025d159 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxonomy-{{ version }}.tar.gz + sha256: 3ff7e2299c9554b8b8be2f00bb4cd9722d0ae820e8a271aaf1390a7e790c3f51 + patches: + - pyproject.patch build: - number: 1 - skip: True # [py < 37] + number: 0 + run_exports: + - {{ pin_subpackage('taxonomy', max_pin="x.x") }} requirements: build: - {{ compiler('c') }} + - {{ compiler('rust') }} host: + - python - pip - cffi - maturin - - python run: - python - cffi @@ -31,8 +35,7 @@ test: about: home: https://github.com/onecodex/taxonomy/ - license: MIT License + license: MIT license_family: MIT license_file: LICENSE summary: "Python and Rust library for loading, saving, and manipulating taxonomic trees" - diff --git a/recipes/taxonomy/pyproject.patch b/recipes/taxonomy/pyproject.patch new file mode 100644 index 0000000000000..7d6fc2b1b3235 --- /dev/null +++ b/recipes/taxonomy/pyproject.patch @@ -0,0 +1,9 @@ +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -1,5 +1,5 @@ + [build-system] +-requires = ["maturin>=0.14,<0.15"] ++requires = ["maturin>=1.0,<2.0"] + build-backend = "maturin" + + [project] From 0f639873d577ec2f713c20b966cf8b54dd0a03cd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 9 Feb 2024 02:27:46 -0500 Subject: [PATCH 0400/1813] Update hecatomb to 1.3.2 (#45729) --- recipes/hecatomb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hecatomb/meta.yaml b/recipes/hecatomb/meta.yaml index 6793fb605bf02..3aa74512cf22e 100644 --- a/recipes/hecatomb/meta.yaml +++ b/recipes/hecatomb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "Hecatomb" %} -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/shandley/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: ce078b0d8327e07ba2a814d054b3f7b8c09ec76ad8dd421549676c792ff35ab1 + sha256: d1699d80bef234c6815333d468721a6c57c24697a26d6e26ab9e0a3167373ff8 build: number: 0 From 7ed3d08a5164a36895f779c7d4c4d965beec64b7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 9 Feb 2024 12:07:00 -0500 Subject: [PATCH 0401/1813] Update primer3-py to 2.0.2 (#45738) --- recipes/primer3-py/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/primer3-py/meta.yaml b/recipes/primer3-py/meta.yaml index dd28aab34137d..f9a31011d0db2 100644 --- a/recipes/primer3-py/meta.yaml +++ b/recipes/primer3-py/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primer3-py" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/primer3-py-{{ version }}.tar.gz - sha256: 30b549c568ae5712e3e6cde6c1f5b243f328247ec8d6ec89d4b705873a44e772 + sha256: 1fa140cab651a2841ec71f3e29ef347e6546f644884e3cac1fe536c4feb8eb5c build: - number: 1 + number: 0 skip: True # [py < 38] run_exports: - {{ pin_subpackage('primer3-py', max_pin="x") }} From 25bcd60a2b4ef9dbb3c1d4c13d22a29edd4f8ed1 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 9 Feb 2024 15:10:04 -0800 Subject: [PATCH 0402/1813] Update auspice to 2.52.0 (#45745) --- recipes/auspice/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/auspice/meta.yaml b/recipes/auspice/meta.yaml index 32592ef4fcbe1..2be485192dd3a 100644 --- a/recipes/auspice/meta.yaml +++ b/recipes/auspice/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.50.0" %} +{% set version = "2.52.0" %} package: name: auspice @@ -6,7 +6,7 @@ package: source: url: https://registry.npmjs.org/auspice/-/auspice-{{ version }}.tgz - sha256: 60642de3c9cbbce388a81668f1d116ca8c28520abe5770298dd51aebd94660b0 + sha256: c23a411c10066d173ed2c4b687e3f60429b3ef4cf16cc6e13d79766bafba28df build: number: 0 From e2aedcdaf33b7ca48f570cd5855b793ee2d1cea3 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 9 Feb 2024 15:11:10 -0800 Subject: [PATCH 0403/1813] Update evofr to 0.1.22 (#45744) Includes dependency changes https://github.com/blab/evofr/commit/4b64dfc5cb14620021835aaee41337affcd3a3a4 --- recipes/evofr/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/evofr/meta.yaml b/recipes/evofr/meta.yaml index a5eae9189357a..e874ecf75867f 100644 --- a/recipes/evofr/meta.yaml +++ b/recipes/evofr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.21" %} +{% set version = "0.1.22" %} package: name: evofr @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/e/evofr/evofr-{{ version }}.tar.gz - sha256: 0ec5329a19087992e14e8c5a5b969b6069308f287595125b67574176c73532c0 + sha256: 8643b54c985dd01ce915c1cf4f475d4f29370166ad62cde7619f66c9f50890e6 build: number: 0 @@ -24,9 +24,9 @@ requirements: - python >=3.9,<4 - numpy >=1.22.4 - pandas >=1.4.2 - - jax >=0.4.1,<0.5.0 + - jax >=0.4.14,<0.5.0 - jaxlib >=0.4.1,<0.5.0 - - numpyro >=0.12.0,<0.13.0 + - numpyro >=0.13.2,<0.14.0 - blackjax >=0.9.6,<0.10.0 test: From a5385f0ecfbfbab2b488dfee36b0e44253e91031 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 9 Feb 2024 18:23:55 -0500 Subject: [PATCH 0404/1813] Update aletsch to 1.1.1 (#45736) --- recipes/aletsch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/aletsch/meta.yaml b/recipes/aletsch/meta.yaml index f97373d1f61d4..1abc848d3520a 100644 --- a/recipes/aletsch/meta.yaml +++ b/recipes/aletsch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "aletsch" %} -{% set version = "1.1.0" %} +{% set version = "1.1.1" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/Shao-Group/aletsch/releases/download/v{{ version }}/aletsch-{{ version }}.tar.gz" - sha256: "075e514da0b8e264fb7822d065061f406d5f73bea95c60ab31f08d2c498010a2" + sha256: "3537e90213baa7ea132b1648f4687780537999f3796711cf7398f9168d72f027" build: number: 0 From 0c80d26832b5fc3861c8cb32da7ac298b5e5f87a Mon Sep 17 00:00:00 2001 From: Sergey Koren Date: Sat, 10 Feb 2024 03:19:07 -0500 Subject: [PATCH 0405/1813] update verkko to v2.0 (#45708) * update verkko to v2.0 * try fix osx build * fix --- recipes/verkko/meta.yaml | 15 ++++---- recipes/verkko/osx_availability.patch | 52 +++++++++++++++++++++++++++ recipes/verkko/run_test.sh | 29 +++++++++------ recipes/verkko/version.patch | 2 +- 4 files changed, 80 insertions(+), 18 deletions(-) create mode 100644 recipes/verkko/osx_availability.patch diff --git a/recipes/verkko/meta.yaml b/recipes/verkko/meta.yaml index 5f622352244e0..247baef98498b 100644 --- a/recipes/verkko/meta.yaml +++ b/recipes/verkko/meta.yaml @@ -1,5 +1,5 @@ {% set name = "verkko" %} -{% set version = "1.4.1" %} +{% set version = "2.0" %} package: name: {{ name|lower }} @@ -7,14 +7,16 @@ package: source: url: https://github.com/marbl/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - md5: 37299a7938c9806763586c2d386f38e8 + md5: be5b322b2fcfcee07c0d64fa49c6a9b4 patches: - version.patch - - tips.patch + - osx_availability.patch # [osx] build: number: 0 + run_exports: + - {{ pin_subpackage('verkko', max_pin="x.x") }} requirements: build: @@ -25,15 +27,16 @@ requirements: - rust >=1.66 host: - gsl + - zlib run: - python >=3.7 - perl >=5.6 + - seqtk - parasail-python >=1.3.3 - networkx >=2.6.3 - biopython - - snakemake-minimal >=7.8.0 - - graphaligner >=1.0.17b - - mbg >=1.0.15 + - snakemake-minimal >=7.8.0,<8.0 + - graphaligner >=1.0.19 - findutils >=4.6.0 - mashmap >=3.0.6 - winnowmap >=2.0 diff --git a/recipes/verkko/osx_availability.patch b/recipes/verkko/osx_availability.patch new file mode 100644 index 0000000000000..69344ea5b476f --- /dev/null +++ b/recipes/verkko/osx_availability.patch @@ -0,0 +1,52 @@ +diff --git a/src/MBG/makefile b/src/MBG/makefile +index 0c0113b..c6fd847 100644 +--- a/src/MBG/makefile ++++ b/src/MBG/makefile +@@ -1,7 +1,7 @@ + PLATFORM=$(shell uname -s) + + GPP=$(CXX) +-CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Wno-unused-parameter -Icxxopts/include -Iconcurrentqueue `pkg-config --cflags zlib` ++CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Wno-unused-parameter -Icxxopts/include -Iconcurrentqueue `pkg-config --cflags zlib` -D_LIBCPP_DISABLE_AVAILABILITY + + ODIR=obj + BINDIR=bin +diff --git a/src/hifioverlapper/MBG/makefile b/src/hifioverlapper/MBG/makefile +index 0c0113b..c6fd847 100644 +--- a/src/hifioverlapper/MBG/makefile ++++ b/src/hifioverlapper/MBG/makefile +@@ -1,7 +1,7 @@ + PLATFORM=$(shell uname -s) + + GPP=$(CXX) +-CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Wno-unused-parameter -Icxxopts/include -Iconcurrentqueue `pkg-config --cflags zlib` ++CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Wno-unused-parameter -Icxxopts/include -Iconcurrentqueue `pkg-config --cflags zlib` -D_LIBCPP_DISABLE_AVAILABILITY + + ODIR=obj + BINDIR=bin +diff --git a/src/hifioverlapper/makefile b/src/hifioverlapper/makefile +index 0bc9ee7..0f53de7 100644 +--- a/src/hifioverlapper/makefile ++++ b/src/hifioverlapper/makefile +@@ -1,5 +1,7 @@ ++PLATFORM=$(shell uname -s) ++ + GPP=$(CXX) +-CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Icxxopts/include -Wno-unused-parameter `pkg-config --cflags zlib` -IMBG/src -Iconcurrentqueue ++CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Icxxopts/include -Wno-unused-parameter `pkg-config --cflags zlib` -IMBG/src -Iconcurrentqueue -D_LIBCPP_DISABLE_AVAILABILITY + + ODIR=obj + BINDIR=bin +@@ -14,7 +16,11 @@ DEPS = $(patsubst %, $(SRCDIR)/%, $(_DEPS)) + _OBJ = MatchIndex.o MinimizerIterator.o TwobitString.o ReadStorage.o UnitigKmerCorrector.o UnitigStorage.o ReadMatchposStorage.o + OBJ = $(patsubst %, $(ODIR)/%, $(_OBJ)) + +-LINKFLAGS = $(CPPFLAGS) -Wl,-Bstatic $(LIBS) -Wl,-Bdynamic -Wl,--as-needed -lpthread -pthread -static-libstdc++ ++ifeq ($(PLATFORM),Linux) ++ LINKFLAGS = $(CPPFLAGS) -Wl,-Bstatic $(LIBS) -Wl,-Bdynamic -Wl,--as-needed -lpthread -pthread -static-libstdc++ ++else ++ LINKFLAGS = $(CPPFLAGS) $(LIBS) -lpthread -pthread -static-libstdc++ ++endif + + VERSION := Branch $(shell git rev-parse --abbrev-ref HEAD) commit $(shell git rev-parse HEAD) $(shell git show -s --format=%ci) + diff --git a/recipes/verkko/run_test.sh b/recipes/verkko/run_test.sh index 69595121dea11..05ab448c0a670 100644 --- a/recipes/verkko/run_test.sh +++ b/recipes/verkko/run_test.sh @@ -6,6 +6,8 @@ if [ ! -n "${PREFIX-}" -a "${PREFIX+defined}" != defined ]; then echo "Prefix undefined, setting it to be path to script" PREFIX=$(dirname "$0") PREFIX=$(dirname "$PREFIX") + + export PATH=$PREFIX/bin:$PATH fi # taken from yacrd recipe, see: https://github.com/bioconda/bioconda-recipes/blob/2b02c3db6400499d910bc5f297d23cb20c9db4f8/recipes/yacrd/build.sh @@ -18,20 +20,25 @@ if [ "$(uname)" == "Darwin" ]; then fi # download and run a small assembly, skip alignment of ONT on OSX to save time -rm -f ./hifi.fastq.gz ./ont.fastq.gz +rm -f ./subset.ids ./hifi.fastq.gz ./ont.fastq.gz curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_hifi_subset24x.fastq.gz -o hifi.fastq.gz curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_ont_subset50x.fastq.gz -o ont.fastq.gz +curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_hifi_subset.ids -o subset.ids + +seqtk sample hifi.fastq.gz 0.5 |seqtk subseq - subset.ids > hifi_lowcov.fastq +seqtk sample ont.fastq.gz 0.10 > ont_lowcov.fastq +touch empty.fasta # now start tests -ONT="--nano ./ont.fastq.gz" -if [ "$(uname)" == "Darwin" ]; then - ONT="" -fi +ONT="--nano ./ont_lowcov.fastq" +#if [ "$(uname)" == "Darwin" ]; then +# ONT="" +#fi -verkko -d asm --no-correction --hifi ./hifi.fastq.gz $ONT +verkko -d asm --hifi ./hifi_lowcov.fastq $ONT > run.out 2>&1 if [ -s asm/assembly.fasta ]; then - python $PREFIX/lib/verkko/scripts/circularize_ctgs.py -p 10 -f 0.01 -o asm/assembly_circular.fasta --min-ovl 1000 asm/assembly.fasta + python $PREFIX/lib/verkko/scripts/circularize_ctgs.py -p 5 -f 0.01 -o asm/assembly_circular.fasta --min-ovl 1 asm/assembly.fasta fi if [ ! -s asm/assembly_circular.fasta ]; then @@ -46,9 +53,9 @@ if [ "$(uname)" == "Darwin" ]; then exit 0 fi -verkko -d asm --hifi hifi.fastq.gz $ONT --hic1 hifi.fastq.gz --hic2 hifi.fastq.gz +verkko -d asm --hifi hifi_lowcov.fastq $ONT --hic1 empty.fasta --hic2 empty.fasta > run.out 2>&1 -if [ ! -e asm/assembly.haplotype1.fasta ]; then +if [[ ! -s asm/assembly.unassigned.fasta || -s asm/assembly.haplotype1.fasta || -s asm/assembly.haplotype2.fasta ]]; then echo "Error: verkko hic assembly test failed!" tail -n +1 `find asm -name *.err` exit 1 @@ -56,9 +63,9 @@ fi #now test trio rm -rf asm/8-* asm/6-layoutContigs/ asm/7-consensus/ asm/assembly.* asm/6-rukki/ -$PREFIX/lib/verkko/bin/meryl count compress k=21 memory=4 threads=8 output empty1.meryl hifi.fastq.gz +$PREFIX/lib/verkko/bin/meryl count compress k=21 memory=4 threads=8 output empty1.meryl hifi_lowcov.fastq $PREFIX/lib/verkko/bin/meryl greater-than 100 empty1.meryl/ output empty2.meryl -verkko -d asm --hifi hifi.fastq.gz $ONT --hap-kmers empty1.meryl empty2.meryl trio +verkko -d asm --hifi hifi_lowcov.fastq $ONT --hap-kmers empty1.meryl empty2.meryl trio > run.out 2>&1 if [ ! -s asm/assembly.haplotype1.fasta ]; then echo "Error: verkko trio assembly test failed!" diff --git a/recipes/verkko/version.patch b/recipes/verkko/version.patch index 9566555502810..9a05bb37485c1 100644 --- a/recipes/verkko/version.patch +++ b/recipes/verkko/version.patch @@ -25,7 +25,7 @@ index 5f33ff4..25c2285 100644 # Perform post-processing on global variables as needed. DEFS := $(addprefix -D,${DEFS}) -INCDIRS := $(addprefix -I,$(call CANONICAL_PATH,${INCDIRS})) --VERSION := verkko release v1.4.1 +-VERSION := verkko release v2.0 +INCDIRS := $(addprefix -isystem,$(call CANONICAL_PATH,${INCDIRS})) +VERSION := bioconda $(PKG_NAME) bioconda $(PKG_VERSION) From d00d3bbc7e865a65253db36118da86ec539576ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 05:11:46 -0500 Subject: [PATCH 0406/1813] Update snakemake to 8.4.8 (#45739) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index c1aeb3dbbadc4..9fc08ce4c7cbd 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.7" %} +{% set version = "8.4.8" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 030f299937a09d328254a0705b87b91ecaf7d3bce51f3c4cee16df2a3718158f + sha256: ab64a4f402f78ec252f211d9cc900344fdc2a000dadcec91833efb5fd0f275e7 build: number: 0 From 4849951321ce3a6bd9bca62b1dda07d192b45051 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 05:12:46 -0500 Subject: [PATCH 0407/1813] Update trgt to 0.8.0 (#45740) --- recipes/trgt/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/trgt/meta.yaml b/recipes/trgt/meta.yaml index e56dd01517b57..686a008743d0f 100644 --- a/recipes/trgt/meta.yaml +++ b/recipes/trgt/meta.yaml @@ -1,7 +1,7 @@ {% set name = "trgt" %} -{% set version = "0.7.0" %} -{% set trgt_sha256 = "09ea997ffd90e1c9aba0a25a38eaa70a95d0d4c365518003b6f340b6f6b9e186" %} -{% set trvz_sha256 = "4b7a642dc69093d68eb8d68a10c49749c382f0db8f71131ce703687438b69b13" %} +{% set version = "0.8.0" %} +{% set trgt_sha256 = "1e927aa3befb6e4973798c742747a88e804ff39f34c6d1c9184b2fecf0f23757" %} +{% set trvz_sha256 = "fce346185d15809a5d1b72ca0c01521d5cdefd3fc924ad4682d0398129eb99e1" %} package: name: {{ name }} From b4aba19f5c0c65d5571424050fffa62c6127574a Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Sat, 10 Feb 2024 21:13:26 +1100 Subject: [PATCH 0408/1813] Add hmftools-mark-dups 1.1 (#45728) --- recipes/hmftools-mark-dups/build.sh | 12 +++++ recipes/hmftools-mark-dups/markdups.sh | 69 ++++++++++++++++++++++++++ recipes/hmftools-mark-dups/meta.yaml | 32 ++++++++++++ 3 files changed, 113 insertions(+) create mode 100644 recipes/hmftools-mark-dups/build.sh create mode 100755 recipes/hmftools-mark-dups/markdups.sh create mode 100644 recipes/hmftools-mark-dups/meta.yaml diff --git a/recipes/hmftools-mark-dups/build.sh b/recipes/hmftools-mark-dups/build.sh new file mode 100644 index 0000000000000..55784e8b35b79 --- /dev/null +++ b/recipes/hmftools-mark-dups/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p "$TGT" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +mv mark-dups*.jar $TGT/markdups.jar + +cp $RECIPE_DIR/markdups.sh $TGT/markdups +ln -s $TGT/markdups $PREFIX/bin +chmod 0755 "${PREFIX}/bin/markdups" diff --git a/recipes/hmftools-mark-dups/markdups.sh b/recipes/hmftools-mark-dups/markdups.sh new file mode 100755 index 0000000000000..c69115b6bee1d --- /dev/null +++ b/recipes/hmftools-mark-dups/markdups.sh @@ -0,0 +1,69 @@ +#!/bin/bash +# hmftools MarkDups executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/mark-dups +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' + then + pass_args="$arg" + else + pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg + fi + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == com.hartwig.* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/markdups.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/markdups.jar" $pass_args +fi +exit diff --git a/recipes/hmftools-mark-dups/meta.yaml b/recipes/hmftools-mark-dups/meta.yaml new file mode 100644 index 0000000000000..c1fc3b06c02b4 --- /dev/null +++ b/recipes/hmftools-mark-dups/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.1" %} +{% set sha256 = "f2939d64ef5d96c638264074cf28eaf140d85ff5a21b537dbb156b54ab142047" %} + +package: + name: hmftools-mark-dups + version: '{{ version }}' + +source: + url: https://github.com/hartwigmedical/hmftools/releases/download/mark-dups-v{{ version }}/mark-dups_v{{ version }}.jar + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('hmftools-mark-dups', max_pin="x.x") }} + +requirements: + run: + - openjdk >=8 + - sambamba >=1.0 + - samtools >=1.17 + +test: + commands: + - 'markdups -version | grep MarkDups' + +about: + home: https://github.com/hartwigmedical/hmftools/tree/master/mark-dups + license: GPL-3.0-only + license_family: GPL + summary: Mark read duplicates and form consenus sequences From 62dfb9350b6b2e2baa90339e1c27b60e0f066c4e Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Sat, 10 Feb 2024 21:16:13 +1100 Subject: [PATCH 0409/1813] Add r-linxreport 1.0.0 (#45727) --- recipes/r-linxreport/build.sh | 6 ++++ recipes/r-linxreport/meta.yaml | 56 ++++++++++++++++++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 recipes/r-linxreport/build.sh create mode 100644 recipes/r-linxreport/meta.yaml diff --git a/recipes/r-linxreport/build.sh b/recipes/r-linxreport/build.sh new file mode 100644 index 0000000000000..6fd1541af9a34 --- /dev/null +++ b/recipes/r-linxreport/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash +$R CMD INSTALL --build . + +mkdir -p ${PREFIX}/bin +cp ${SRC_DIR}/inst/cli/linxreport.R ${PREFIX}/bin +chmod +x ${PREFIX}/bin/linxreport.R diff --git a/recipes/r-linxreport/meta.yaml b/recipes/r-linxreport/meta.yaml new file mode 100644 index 0000000000000..a7ac9a43641e4 --- /dev/null +++ b/recipes/r-linxreport/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.0.0" %} +{% set sha256 = "447658b9ac5974f696c6b2c0fce59fc846d7419da8fc79aa81109630701cef55" %} + +package: + name: r-linxreport + version: '{{ version }}' + +source: + url: https://github.com/umccr/linxreport/archive/refs/tags/v{{ version }}.tar.gz + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("r-linxreport", max_pin="x.x") }} + +requirements: + host: + - r-base >=4 + - r-assertthat + - r-details + - r-dplyr + - r-dt + - r-fs + - r-gtools + - r-optparse + - r-readr + - r-rlang + - r-rmarkdown + - r-sessioninfo + - r-stringr + run: + - r-base >=4 + - r-assertthat + - r-details + - r-dplyr + - r-dt + - r-fs + - r-gtools + - r-optparse + - r-readr + - r-rlang + - r-rmarkdown + - r-sessioninfo + - r-stringr + +test: + commands: + - $R -e "library('linxreport')" + +about: + home: https://github.com/umccr/linxreport + license: MIT + file LICENSE + license_family: MIT + summary: LINX Result Reporter From 91f38d4882b9ac44ace35a3fcd532faa0f187ded Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 05:20:55 -0500 Subject: [PATCH 0410/1813] Update freyja to 1.4.9 (#45742) --- recipes/freyja/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/freyja/meta.yaml b/recipes/freyja/meta.yaml index 41ae8a92a8758..6c3686a0eef7c 100644 --- a/recipes/freyja/meta.yaml +++ b/recipes/freyja/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.8" %} +{% set version = "1.4.9" %} {% set name = "Freyja" %} package: @@ -16,7 +16,7 @@ build: source: url: https://github.com/andersen-lab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 4534bf227fc58317c535c2c5d0d031816c8a5b1ae0968175a97cd02cb3530672 + sha256: aeaa1697d7e12386e50c96880ab976e2cc68989bd7fdf4bfe802cb02bb3982ba requirements: host: From 4a232f18b6d402bee5e6e90bf343ce88c513d864 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Sat, 10 Feb 2024 15:26:16 +0100 Subject: [PATCH 0411/1813] require python >=3.9 for varfish-cli (#45731) --- recipes/varfish-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml index 909078b89013b..6baa90f445ec8 100644 --- a/recipes/varfish-cli/meta.yaml +++ b/recipes/varfish-cli/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - varfish-cli = varfish_cli.__main__:main @@ -23,7 +23,7 @@ requirements: - python >=3 - pip run: - - python >=3 + - python >=3.9 - attrs - cattrs - jsonschema From 8b11f2ac11be64b14b120b31c9eaf245d6bebdcd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:01:11 -0500 Subject: [PATCH 0412/1813] Update pymzml to 2.5.4 (#45735) --- recipes/pymzml/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pymzml/meta.yaml b/recipes/pymzml/meta.yaml index a0256bea1be73..626e6ccb8c945 100644 --- a/recipes/pymzml/meta.yaml +++ b/recipes/pymzml/meta.yaml @@ -1,10 +1,10 @@ package: name: pymzml - version: "2.5.3" + version: "2.5.4" source: - url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.3.tar.gz - sha256: 3578da1962670ef90027cb2944ad64dc39a4457cd93a637bbd2655a7f074a2ee + url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.4.tar.gz + sha256: f3da945e09f4b7b091feaf5b168c3543b3489bc8adf0bac48029f8d70b22de7f build: number: 0 From 5d3bb76e667ed706f65bdf5569d3200d6c589006 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:01:27 -0500 Subject: [PATCH 0413/1813] Update nanomotif to 0.1.18 (#45734) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index 8bf32fe611950..afe275f534641 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.17" %} +{% set version = "0.1.18" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: 48bd357472e36ed6336ff555fc55a81779d05ea3cf0e1b25f6a5d1cadf0763f5 + sha256: a8a4e7bfe21617c51003ae9d0ed056b1a5380d7df83b3d115cd079d06e8cd116 build: entry_points: From d8ca160156ddab81d2dbb7b7628b9658bd090c5e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:01:39 -0500 Subject: [PATCH 0414/1813] Update tissuumaps to 3.2.0.4 (#45733) --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index 8555dcfae9eba..5f81144cf6ced 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.0.3" %} +{% set version = "3.2.0.4" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 372a92e7aa8fb5f6149bac1133aae6d04653c87ba3048af9ed95da84a64f2592 + sha256: 02ce7e575075fd5b401c322ade25ed9f52cc4b7af944a9c29441c1784506a1ed build: number: 0 From b5b655c4a33d7c4ab1eeda37caaa39242e3158e4 Mon Sep 17 00:00:00 2001 From: Brandon Seah Date: Sat, 10 Feb 2024 19:01:53 +0100 Subject: [PATCH 0415/1813] Add recipe pytransaln v0.2.1 (#45732) * Add recipe pytransaln from PyPI package Generated by grayskull * Add homepage URL * Add run_exports statement --- recipes/pytransaln/meta.yaml | 50 ++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 recipes/pytransaln/meta.yaml diff --git a/recipes/pytransaln/meta.yaml b/recipes/pytransaln/meta.yaml new file mode 100644 index 0000000000000..d3c02cd1a111b --- /dev/null +++ b/recipes/pytransaln/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "pytransaln" %} +{% set version = "0.2.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pytransaln-{{ version }}.tar.gz + sha256: 280a035573dc2e709d226b628fbee41d1ee6afcff5f7a7185aac05135314a2e2 + +build: + entry_points: + - pytransaln = pytransaln.pytransaln:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('pytransaln', max_pin="x.x") }} + +requirements: + host: + - python + - setuptools >=61.0.0 + - pip + run: + - python + - biopython >=1.80,<2 + - pandas >=1.3,<3 + - matplotlib-base >=3.6,<4 + - pyhmmer ==0.10 + +test: + imports: + - pytransaln + commands: + - pip check + - pytransaln --help + requires: + - pip + +about: + home: https://github.com/monagrland/pytransaln + summary: Translation-guided nucleotide alignment for coding sequences + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - kbseah From 8a7dac75f8a6044b4eace2eadf734b315cdffdc7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:02:03 -0500 Subject: [PATCH 0416/1813] Update mehari to 0.22.0 (#45730) * Update mehari to 0.22.0 * Update homepage URL --------- Co-authored-by: Brandon Seah --- recipes/mehari/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 91cc370330ddc..e410ddacac824 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.21.2" %} -{% set sha256 = "37fc1ef33d8d7f49886312283ac1e4009fba92db40e254cb03356e0e6f643774" %} +{% set version = "0.22.0" %} +{% set sha256 = "1240ac7d026eebfa6a4396548f748848501fd0128e3ca81cc890ee70faf33fac" %} package: name: mehari @@ -38,6 +38,6 @@ test: - mehari -h about: - home: https://github.com/bihealth/varfish-org + home: https://github.com/varfish-org/mehari license: MIT summary: VEP-like tool for sequence ontology and HGVS annotation of VCF files written in Rust. From 7d046117022e58e4d85d62bcd083bd0be3893ac5 Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:02:44 -0500 Subject: [PATCH 0417/1813] Add new graph embedding software for large-scale biological network (#45725) * Update annembed v0.1.4 * Update gsearch v0.1.9 * Add graphembed v0.1.0 --- recipes/graphembed/build.sh | 8 ++++++++ recipes/graphembed/meta.yaml | 35 +++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 recipes/graphembed/build.sh create mode 100644 recipes/graphembed/meta.yaml diff --git a/recipes/graphembed/build.sh b/recipes/graphembed/build.sh new file mode 100644 index 0000000000000..f4634f476014f --- /dev/null +++ b/recipes/graphembed/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --features intel-mkl-static --verbose --path . --root $PREFIX diff --git a/recipes/graphembed/meta.yaml b/recipes/graphembed/meta.yaml new file mode 100644 index 0000000000000..99a1ca4a5f0bc --- /dev/null +++ b/recipes/graphembed/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.1.0" %} + +package: + name: graphembed + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('graphembed', max_pin="x.x") }} + skip: True # [osx] +source: + url: https://github.com/jianshu93/graphembed/archive/v{{ version }}.tar.gz + sha256: 5c38244781574c2dd1aa1c20e1b2b5ea181f3ffab42ea47a014be0de28810210 + +requirements: + build: + - {{ compiler("cxx") }} + - {{ compiler('c') }} + - rust >=1.39 + - make + - cmake + +test: + commands: + - graphembed -h + +about: + home: https://github.com/jean-pierreBoth/graphembed + license: MIT + summary: Efficient Graph Embedding via Recursive Sketching or High-order Transitivity Preserving +extra: + maintainers: + - Jean Pierre-Both + - Jianshu Zhao From 8fd62a5b3021960fff128c6128d43e33af2b99f9 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Sun, 11 Feb 2024 05:09:38 +1100 Subject: [PATCH 0418/1813] Add hmftools-cuppa 1.8.1 (#45643) * Add hmftools-cuppa 1.8.1 * Replace matplotlib with matplotlib-base * Create target subdirectory for cuppa-chart * Remove quotes preventing BASH brace expansion * Pin r-base to minor version only * Fix empty comment line * Set correct path for passthrough BASH script * Further relax r-base version dependency --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/hmftools-cuppa/build.sh | 14 ++++++ recipes/hmftools-cuppa/cuppa-chart.sh | 23 +++++++++ recipes/hmftools-cuppa/cuppa.sh | 69 +++++++++++++++++++++++++++ recipes/hmftools-cuppa/meta.yaml | 46 ++++++++++++++++++ 4 files changed, 152 insertions(+) create mode 100644 recipes/hmftools-cuppa/build.sh create mode 100755 recipes/hmftools-cuppa/cuppa-chart.sh create mode 100755 recipes/hmftools-cuppa/cuppa.sh create mode 100644 recipes/hmftools-cuppa/meta.yaml diff --git a/recipes/hmftools-cuppa/build.sh b/recipes/hmftools-cuppa/build.sh new file mode 100644 index 0000000000000..a11f515c544f5 --- /dev/null +++ b/recipes/hmftools-cuppa/build.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p $TGT/{,chart/} +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +mv jar/cuppa*.jar $TGT/cuppa.jar +mv src/cuppa/src/main/resources/cuppa-chart/* $TGT/chart/ + +cp $RECIPE_DIR/cuppa.sh $TGT/cuppa +cp $RECIPE_DIR/cuppa-chart.sh $TGT/cuppa-chart +ln -s $TGT/cuppa{,-chart} ${PREFIX}/bin/ +chmod 0755 ${PREFIX}/bin/cuppa{,-chart} diff --git a/recipes/hmftools-cuppa/cuppa-chart.sh b/recipes/hmftools-cuppa/cuppa-chart.sh new file mode 100755 index 0000000000000..98ffa9f9ad790 --- /dev/null +++ b/recipes/hmftools-cuppa/cuppa-chart.sh @@ -0,0 +1,23 @@ +#!/bin/bash +# hmftools CUPPA chart executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/cuppa +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Python installed with Anaconda to ensure correct version +python="$ENV_PREFIX/bin/python" + +# Run with argument passthrough +eval ${python} ${DIR}/chart/cuppa-chart.py ${@} diff --git a/recipes/hmftools-cuppa/cuppa.sh b/recipes/hmftools-cuppa/cuppa.sh new file mode 100755 index 0000000000000..33e257cb82296 --- /dev/null +++ b/recipes/hmftools-cuppa/cuppa.sh @@ -0,0 +1,69 @@ +#!/bin/bash +# hmftools CUPPA executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/cuppa +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' + then + pass_args="$arg" + else + pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg + fi + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/cuppa.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/cuppa.jar" $pass_args +fi +exit diff --git a/recipes/hmftools-cuppa/meta.yaml b/recipes/hmftools-cuppa/meta.yaml new file mode 100644 index 0000000000000..4c09d7747c28f --- /dev/null +++ b/recipes/hmftools-cuppa/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.8.1" %} +{% set sha256_jar = "595cf6ba5a60a23cf18005cdc2aed18b3f48470f5479aa4e5ee6f386d23e00bb" %} +{% set sha256_src = "39bb318f590ba905c18c0ed42411c97ba482ed98059e456a0f5ec42ad915c8e1" %} + +package: + name: hmftools-cuppa + version: '{{ version }}' + +source: + - folder: jar + url: https://github.com/hartwigmedical/hmftools/releases/download/cuppa-v{{ version }}/cuppa_v{{ version }}.jar + sha256: '{{ sha256_jar }}' + - folder: src + url: https://github.com/hartwigmedical/hmftools/archive/refs/tags/cuppa-v{{ version }}.tar.gz + sha256: '{{ sha256_src }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("hmftools-cuppa", max_pin="x.x") }} + +requirements: + run: + - openjdk >=8 + - r-base >=4 + - r-cowplot + - r-ggplot2 + - r-gridextra + - r-stringi + - r-tidyr + - matplotlib-base >=3.3,<4 + - numpy >=1.19,<2 + - pandas >=1.1,<2 + - scipy >=1,<2 + - seaborn >=0.11,<1 + +test: + commands: + - 'cuppa | grep Cuppa' + +about: + home: https://github.com/hartwigmedical/hmftools/blob/master/cuppa/README.md + license: GPL-3.0-only + license_family: GPL3 + summary: Predict tissue of origin for tumor samples from WGTS data. From cf7f2de9f609aff32f2e945bfa270f7902ecbe4b Mon Sep 17 00:00:00 2001 From: Jack Huey <31162821+jackh726@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:10:25 -0500 Subject: [PATCH 0419/1813] Add recipes for `bigtools` and `pybigtools` (#45634) * Add bigtools and pybigtools recipes bigtools: Fix urls and sha bigtools: specify pybigtools cargo.toml bigtools: Fix typo bigtools: Add bigtools build bigtools: Point cargo to bigtools dir * MIT License -> MIT --- recipes/bigtools/build.sh | 10 +++++++++ recipes/bigtools/meta.yaml | 35 +++++++++++++++++++++++++++++++ recipes/pybigtools/build.sh | 17 +++++++++++++++ recipes/pybigtools/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++ 4 files changed, 102 insertions(+) create mode 100644 recipes/bigtools/build.sh create mode 100644 recipes/bigtools/meta.yaml create mode 100644 recipes/pybigtools/build.sh create mode 100644 recipes/pybigtools/meta.yaml diff --git a/recipes/bigtools/build.sh b/recipes/bigtools/build.sh new file mode 100644 index 0000000000000..cd115956df52e --- /dev/null +++ b/recipes/bigtools/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash +set -ex + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" +export RUST_BACKTRACE=full + +cargo install --verbose --path ./bigtools --root $PREFIX --locked + diff --git a/recipes/bigtools/meta.yaml b/recipes/bigtools/meta.yaml new file mode 100644 index 0000000000000..72e92841c1718 --- /dev/null +++ b/recipes/bigtools/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.4.1" %} + +package: + name: bigtools + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('bigtools', max_pin="x.x") }} + +source: + url: https://github.com/jackh726/bigtools/archive/refs/tags/v{{ version }}.tar.gz + sha256: "92b9ea165adb1f9b13222d6c78e12148d9ba04a0d6ae96001820d43d9af7b39e" + +requirements: + build: + - {{ compiler('c') }} + - rust >=1.70 + +test: + commands: + - bigtools --help | grep Usage + +about: + home: https://github.com/jackh726/bigtools/ + license: MIT + doc_url: https://docs.rs/bigtools/latest/bigtools/ + summary: 'Bigtools provides a high-level, performant API for reading and writing bigWig and bigBed files.' + license_family: MIT + license_file: LICENSE + +extra: + identifiers: + - doi:10.5281/zenodo.10606493 diff --git a/recipes/pybigtools/build.sh b/recipes/pybigtools/build.sh new file mode 100644 index 0000000000000..d9c921719d1d8 --- /dev/null +++ b/recipes/pybigtools/build.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +# -e = exit on first error +# -x = print every executed command +set -ex + +# Use a custom temporary directory as home on macOS. +# (not sure why this is useful, but people use it in bioconda recipes) +if [ `uname` == Darwin ]; then + export HOME=`mktemp -d` +fi + +# Build the package using maturin - should produce *.whl files. +maturin build -m pybigtools/Cargo.toml --interpreter $PYTHON --release + +# Install *.whl files using pip +$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv diff --git a/recipes/pybigtools/meta.yaml b/recipes/pybigtools/meta.yaml new file mode 100644 index 0000000000000..fb3f24390e236 --- /dev/null +++ b/recipes/pybigtools/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "0.1.0" %} + +package: + name: pybigtools + version: {{ version }} + +source: + url: https://github.com/jackh726/bigtools/archive/refs/tags/pybigtools@v{{ version }}.tar.gz + sha256: "bb1a1f1d1f39ce0b73eafb40e291b1ded26fbb283898371ade3414c008b80cdf" + +build: + number: 0 + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('rust') }} + - maturin + host: + - pip + - python + run: + - python + - numpy + +test: + imports: + - pybigtools + +about: + home: https://github.com/jackh726/bigtools/ + license: MIT + summary: 'pybigtools: Python bindings to the Bigtools Rust library for high-performance BigWig and BigBed I/O' + license_family: MIT + license_file: LICENSE + doc_url: https://bigtools.readthedocs.io + +extra: + identifiers: + - doi:10.5281/zenodo.10606493 From 4c0c5970f8b526c6b817ea76e0b80fea028f60be Mon Sep 17 00:00:00 2001 From: Marco Matthies <71844+marcom@users.noreply.github.com> Date: Sat, 10 Feb 2024 19:11:54 +0100 Subject: [PATCH 0420/1813] Update linearpartition to 1.0.1.dev20240123 (#45593) * Update linearpartition to 1.0.1.dev20240123 This updates linearpartition to git-sha1 fa953f6323274eeadd92cc1f4e5535417f3fb821 from 2024-01-23. The main reason for the update to an unreleased version is that all releases by the upstream repo require python2. Changes to 1.0 (my summary): - driver script uses python3 - support for SHAPE chemical probing data - FASTA file input - dangles -d0 mode support * Retry build --- ...IX-command-broken-with-symbolic-link.patch | 22 +++++-------------- recipes/linearpartition/meta.yaml | 14 +++++++----- 2 files changed, 14 insertions(+), 22 deletions(-) diff --git a/recipes/linearpartition/0001-FIX-command-broken-with-symbolic-link.patch b/recipes/linearpartition/0001-FIX-command-broken-with-symbolic-link.patch index 95a8be08c0583..53c9c754a9810 100644 --- a/recipes/linearpartition/0001-FIX-command-broken-with-symbolic-link.patch +++ b/recipes/linearpartition/0001-FIX-command-broken-with-symbolic-link.patch @@ -1,25 +1,13 @@ -From 7413bfa18dddf47924be0839df0147045db0d045 Mon Sep 17 00:00:00 2001 -From: Fabien Pertuy -Date: Fri, 21 May 2021 10:39:10 +0000 -Subject: [PATCH] FIX command broken with symbolic link - ---- - linearpartition | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - diff --git a/linearpartition b/linearpartition -index 6c9d877..9d8a5b6 100755 +index f6c2a4e..7b0fe1d 100755 --- a/linearpartition +++ b/linearpartition -@@ -87,7 +87,7 @@ def main(): - # if os.path.exists(ThreshKnot_output): os.remove(ThreshKnot_output) - +@@ -80,7 +80,7 @@ def main(): + print("Exit!\n"); + exit(); - path = os.path.dirname(os.path.abspath(__file__)) + path = os.path.dirname(os.path.realpath(__file__)) - cmd = ["%s/%s" % (path, ('bin/linearpartition_v' if use_vienna else 'bin/linearpartition_c')), beamsize, is_sharpturn, is_verbose, bpp_file, bpp_prefix, pf_only, bpp_cutoff, forest_file, mea, gamma, TK, threshold, ThreshKnot_prefix, MEA_prefix, MEA_bpseq] + cmd = ["%s/%s" % (path, ('bin/linearpartition_v' if use_vienna else 'bin/linearpartition_c')), beamsize, is_sharpturn, is_verbose, bpp_file, bpp_prefix, pf_only, bpp_cutoff, forest_file, mea, gamma, TK, threshold, ThreshKnot_prefix, MEA_prefix, MEA_bpseq, shape_file_path, is_fasta, dangles] subprocess.call(cmd, stdin=sys.stdin) --- -2.30.2 - diff --git a/recipes/linearpartition/meta.yaml b/recipes/linearpartition/meta.yaml index eaa4d137d8ee7..7a42168cc778e 100644 --- a/recipes/linearpartition/meta.yaml +++ b/recipes/linearpartition/meta.yaml @@ -1,17 +1,20 @@ {% set name = "LinearPartition" %} -{% set version = "1.0" %} -{% set sha256 = "4fdea96f7ffbd4804d9308ddb46db5f96d1abc4b7bd737725f9bedcae3c88178" %} +{% set version = "1.0.1.dev20240123" %} +{% set git_sha1 = "fa953f6323274eeadd92cc1f4e5535417f3fb821" %} +{% set sha256 = "e93c6a26c246c2e0927592052516d6fb15e7e1e8a378f74474136ba85746be58" %} package: name: {{ name | lower }} version: {{ version }} build: - number: 3 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name | lower, max_pin="x.x.x") }} source: - url: https://github.com/LinearFold/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/LinearFold/{{ name }}/archive/{{ git_sha1 }}.tar.gz sha256: {{ sha256 }} patches: - 0001-FIX-command-broken-with-symbolic-link.patch @@ -25,7 +28,7 @@ requirements: - matplotlib-base - numpy - pandas - - python=2.7 + - python >=3,<4 - python-gflags - seaborn @@ -41,3 +44,4 @@ about: license: custom license_file: LICENSE summary: 'Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities' + From 72c856fa2bfece9dc9dd22423335d785b57987db Mon Sep 17 00:00:00 2001 From: Marco Matthies <71844+marcom@users.noreply.github.com> Date: Sat, 10 Feb 2024 19:12:49 +0100 Subject: [PATCH 0421/1813] Add recipe for MultiRNAFold v2.1 (#45623) * Add recipe for MultiRNAFold v2.1 http://www.rnasoft.ca/download/README.html http://www.rnasoft.ca/download.html The MultiRNAFold package contains software for secondary structure prediction of one, two, or many interacting RNA or DNA molecules. It is composed of three pieces of software: SimFold, PairFold and MultiFold. The programs are also known in the literature as the RNAsoft suite. * Improve description * Fix summary, add run_exports * Shorter summary line * Fix run_exports * Skip osx build * Use SPDX license identifier, add comment on osx build fail * Try and fix OSX build --- recipes/multirnafold/0001-FIX-Makefile.patch | 925 ++++++++++++++++++ .../0002-FIX-printf-missing-arg.patch | 26 + .../0003-FIX-remove-unneeded-include.patch | 126 +++ recipes/multirnafold/build.sh | 13 + recipes/multirnafold/meta.yaml | 43 + 5 files changed, 1133 insertions(+) create mode 100644 recipes/multirnafold/0001-FIX-Makefile.patch create mode 100644 recipes/multirnafold/0002-FIX-printf-missing-arg.patch create mode 100644 recipes/multirnafold/0003-FIX-remove-unneeded-include.patch create mode 100644 recipes/multirnafold/build.sh create mode 100644 recipes/multirnafold/meta.yaml diff --git a/recipes/multirnafold/0001-FIX-Makefile.patch b/recipes/multirnafold/0001-FIX-Makefile.patch new file mode 100644 index 0000000000000..ff8e6c124469c --- /dev/null +++ b/recipes/multirnafold/0001-FIX-Makefile.patch @@ -0,0 +1,925 @@ +diff --git a/Makefile b/Makefile +index 6e3f2fe..28bb7e7 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,7 @@ + # makefile for the MultiRNAFold package + +-CC = g++ +-CFLAGS = -g -I./include -I./src/common -I./src/simfold -I./src/pairfold -I./src/multifold -w -Wno-deprecated ++CXX = g++ ++CXXFLAGS = -O2 -ggdb -I./include -I./src/common -I./src/simfold -I./src/pairfold -I./src/multifold -Wno-deprecated + # -pg for profiling + #-O3 + # -p is for profiler +@@ -101,7 +101,7 @@ L_C_OBJS = $(L_C_SRCS:.cpp=.o) + L_S_OBJS = $(L_S_SRCS:.cpp=.o) + L_P_OBJS = $(L_P_SRCS:.cpp=.o) + L_M_OBJS = $(L_M_SRCS:.cpp=.o) +- ++ + AR = ar + ARFLAGS = rv + RANLIB = ranlib +@@ -114,78 +114,64 @@ default: $(LIB) $(SIMFOLD) $(SIMFOLD_PF) $(PAIRFOLD) $(PAIRFOLD_WEB) $(MULTIFOL + $(LIB): $(L_C_OBJS) $(L_S_OBJS) $(L_P_OBJS) $(L_M_OBJS) + $(RM) $@ + $(AR) $(ARFLAGS) $@ $(L_C_OBJS) $(L_S_OBJS) $(L_P_OBJS) $(L_M_OBJS) +- $(RANLIB) $@ +- ++ $(RANLIB) $@ ++ + $(SIMFOLD): $(S_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) +- ++ $(CXX) -o $@ $@.o $(LFLAGS) ++ + $(SIMFOLD_PF): $(S2_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) +- ++ $(CXX) -o $@ $@.o $(LFLAGS) ++ + $(PAIRFOLD): $(P_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) +- ++ $(CXX) -o $@ $@.o $(LFLAGS) ++ + $(PAIRFOLD_WEB): $(P2_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) +- ++ $(CXX) -o $@ $@.o $(LFLAGS) ++ + $(MULTIFOLD): $(M_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) +- ++ $(CXX) -o $@ $@.o $(LFLAGS) ++ + $(DRIVER): $(D_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) ++ $(CXX) -o $@ $@.o $(LFLAGS) + + $(PARTITION): $(PARTITION).o $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) ++ $(CXX) -o $@ $@.o $(LFLAGS) + + $(DRIVER1): $(DRIVER1).o $(LIB) + mpiCC -o $(DRIVER1) $(DRIVER1).o $(LFLAGS) -L$(LAMDIR)/lib + + $(DRIVER1).o: $(DRIVER1).cpp +- mpiCC -c $(DRIVER1).cpp $(CFLAGS) -I$(LAMDIR)/include -o $(DRIVER1).o ++ mpiCC -c $(DRIVER1).cpp $(CXXFLAGS) -I$(LAMDIR)/include -o $(DRIVER1).o + + $(DRIVER2): $(DRIVER2).o $(LIB) +- mpiCC -o $(DRIVER2) $(DRIVER2).o $(LFLAGS) -L$(LAMDIR)/lib ++ mpiCC -o $(DRIVER2) $(DRIVER2).o $(LFLAGS) -L$(LAMDIR)/lib + + $(DRIVER2).o: $(DRIVER2).cpp +- mpiCC -c $(DRIVER2).cpp $(CFLAGS) -I$(LAMDIR)/include -o $(DRIVER2).o ++ mpiCC -c $(DRIVER2).cpp $(CXXFLAGS) -I$(LAMDIR)/include -o $(DRIVER2).o + +- + $(RUNTIMEV): $(RUNTIMEV).o +- $(CC) -o $@ $@.o -L$(VIENNADIR)/lib -lviennapp $(LFLAGS) ++ $(CXX) -o $@ $@.o -L$(VIENNADIR)/lib -lviennapp $(LFLAGS) + + $(RUNTIMEV).o: $(RUNTIMEV).cpp +- $(CC) -c $(RUNTIMEV).cpp -I$(VIENNADIR)/include $(CFLAGS) +- +- ++ $(CXX) -c $(RUNTIMEV).cpp -I$(VIENNADIR)/include $(CXXFLAGS) ++ + .SUFFIXES: .cpp + .cpp.o: +- $(CC) -c $*.cpp $(CFLAGS) -o $*.o ++ $(CXX) -c $*.cpp $(CXXFLAGS) -o $*.o + + clean: + rm -f $(L_C_OBJS) $(L_S_OBJS) $(L_P_OBJS) $(L_M_OBJS) +- rm -f $(S_OBJS) $(S2_OBJS) $(P_OBJS) $(P2_OBJS) $(M_OBJS) $(D_OBJS) ++ rm -f $(S_OBJS) $(S2_OBJS) $(P_OBJS) $(P2_OBJS) $(M_OBJS) $(D_OBJS) + # $(SIMFOLD) $(SIMFOLD_PF) $(PAIRFOLD) $(MULTIFOLD) $(DRIVER) *~ core + rm -f $(SRC_C)/*~ $(SRC_S)/*~ $(SRC_P)/*~ $(SRC_M)/*~ include/*~ *.a *.bak + + depend: +- makedepend -- $(CFLAGS) -- $(L_C_SRCS) $(L_S_SRCS) $(L_P_SRCS) $(L_M_SRCS) $(S_SRCS) $(S2_SRCS) $(P_SRCS) $(M_SRCS) $(D_SRCS) +- +- ++ makedepend -Y $(CXXFLAGS) -- $(L_C_SRCS) $(L_S_SRCS) $(L_P_SRCS) $(L_M_SRCS) $(S_SRCS) $(S2_SRCS) $(P_SRCS) $(M_SRCS) $(D_SRCS) ++ + # end of makefile + + # DO NOT DELETE + +-src/common/common.o: /usr/include/stdio.h /usr/include/features.h +-src/common/common.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-src/common/common.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-src/common/common.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-src/common/common.o: /usr/include/libio.h /usr/include/_G_config.h +-src/common/common.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/common/common.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-src/common/common.o: /usr/include/bits/sys_errlist.h /usr/include/stdlib.h +-src/common/common.o: /usr/include/math.h /usr/include/bits/huge_val.h +-src/common/common.o: /usr/include/bits/mathdef.h +-src/common/common.o: /usr/include/bits/mathcalls.h /usr/include/string.h + src/common/common.o: ./include/constants.h ./include/structs.h + src/common/common.o: ./include/externs.h src/common/common.h + src/common/common.o: ./src/simfold/s_partition_function.h +@@ -195,16 +181,6 @@ src/common/common.o: ./src/simfold/s_energy_matrix.h + src/common/common.o: ./src/simfold/s_stacked_pair.h + src/common/common.o: ./src/simfold/s_multi_loop.h + src/common/common.o: ./src/simfold/s_multi_loop_sub.h +-src/common/params.o: /usr/include/stdio.h /usr/include/features.h +-src/common/params.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-src/common/params.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-src/common/params.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-src/common/params.o: /usr/include/libio.h /usr/include/_G_config.h +-src/common/params.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/common/params.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-src/common/params.o: /usr/include/bits/sys_errlist.h /usr/include/math.h +-src/common/params.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h +-src/common/params.o: /usr/include/bits/mathcalls.h /usr/include/stdlib.h + src/common/params.o: src/common/params.h ./include/constants.h + src/common/params.o: src/common/common.h ./include/structs.h + src/common/params.o: ./src/simfold/s_partition_function.h +@@ -214,60 +190,20 @@ src/common/params.o: ./src/simfold/s_energy_matrix.h + src/common/params.o: ./src/simfold/s_stacked_pair.h + src/common/params.o: ./src/simfold/s_multi_loop.h + src/common/params.o: ./src/simfold/s_multi_loop_sub.h ./include/externs.h +-src/common/params.o: /usr/include/string.h + src/common/params.o: ./src/simfold/s_specific_functions.h + src/common/params.o: ./src/simfold/s_min_folding.h + src/common/params.o: ./src/simfold/s_sub_folding.h ./include/simfold.h + src/common/params.o: ./include/init.h +-src/common/init.o: /usr/include/stdio.h /usr/include/features.h +-src/common/init.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-src/common/init.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-src/common/init.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-src/common/init.o: /usr/include/libio.h /usr/include/_G_config.h +-src/common/init.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/common/init.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-src/common/init.o: /usr/include/bits/sys_errlist.h /usr/include/stdlib.h +-src/common/init.o: /usr/include/string.h /usr/include/math.h +-src/common/init.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h +-src/common/init.o: /usr/include/bits/mathcalls.h ./include/constants.h +-src/common/init.o: ./include/structs.h ./include/globals.h +-src/common/init.o: src/common/common.h ./src/simfold/s_partition_function.h ++src/common/init.o: ./include/constants.h ./include/structs.h ++src/common/init.o: ./include/globals.h src/common/common.h ++src/common/init.o: ./src/simfold/s_partition_function.h + src/common/init.o: ./src/simfold/s_hairpin_loop.h + src/common/init.o: ./src/simfold/s_internal_loop.h + src/common/init.o: ./src/simfold/s_energy_matrix.h + src/common/init.o: ./src/simfold/s_stacked_pair.h + src/common/init.o: ./src/simfold/s_multi_loop.h +-src/common/init.o: ./src/simfold/s_multi_loop_sub.h +-src/common/timer.o: /usr/include/math.h /usr/include/features.h +-src/common/timer.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-src/common/timer.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-src/common/timer.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h +-src/common/timer.o: /usr/include/bits/mathcalls.h /usr/include/ctype.h +-src/common/timer.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-src/common/timer.o: /usr/include/endian.h /usr/include/bits/endian.h +-src/common/timer.o: /usr/include/time.h /usr/include/bits/time.h +-src/common/timer.o: /usr/include/string.h /usr/include/sys/times.h +-src/common/timer.o: /usr/include/limits.h src/common/timer.h +-src/simfold/s_specific_functions.o: /usr/include/stdio.h +-src/simfold/s_specific_functions.o: /usr/include/features.h +-src/simfold/s_specific_functions.o: /usr/include/sys/cdefs.h +-src/simfold/s_specific_functions.o: /usr/include/bits/wordsize.h +-src/simfold/s_specific_functions.o: /usr/include/gnu/stubs.h +-src/simfold/s_specific_functions.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_specific_functions.o: /usr/include/bits/types.h +-src/simfold/s_specific_functions.o: /usr/include/bits/typesizes.h +-src/simfold/s_specific_functions.o: /usr/include/libio.h +-src/simfold/s_specific_functions.o: /usr/include/_G_config.h +-src/simfold/s_specific_functions.o: /usr/include/wchar.h +-src/simfold/s_specific_functions.o: /usr/include/bits/wchar.h +-src/simfold/s_specific_functions.o: /usr/include/gconv.h +-src/simfold/s_specific_functions.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_specific_functions.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_specific_functions.o: /usr/include/stdlib.h /usr/include/math.h +-src/simfold/s_specific_functions.o: /usr/include/bits/huge_val.h +-src/simfold/s_specific_functions.o: /usr/include/bits/mathdef.h +-src/simfold/s_specific_functions.o: /usr/include/bits/mathcalls.h +-src/simfold/s_specific_functions.o: /usr/include/string.h ++src/common/init.o: ./src/simfold/s_multi_loop_sub.h src/common/params.h ++src/common/timer.o: src/common/timer.h + src/simfold/s_specific_functions.o: ./include/constants.h ./include/structs.h + src/simfold/s_specific_functions.o: ./include/externs.h src/common/common.h + src/simfold/s_specific_functions.o: ./src/simfold/s_partition_function.h +@@ -281,22 +217,6 @@ src/simfold/s_specific_functions.o: ./include/simfold.h ./include/init.h + src/simfold/s_specific_functions.o: ./src/simfold/s_specific_functions.h + src/simfold/s_specific_functions.o: ./src/simfold/s_min_folding.h + src/simfold/s_specific_functions.o: ./src/simfold/s_sub_folding.h +-src/simfold/s_specific_functions.o: src/simfold/s_partition_function_complex.h +-src/simfold/s_specific_functions.o: /usr/include/complex.h +-src/simfold/s_specific_functions.o: /usr/include/bits/cmathcalls.h +-src/simfold/s_min_folding.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_min_folding.o: /usr/include/sys/cdefs.h +-src/simfold/s_min_folding.o: /usr/include/bits/wordsize.h +-src/simfold/s_min_folding.o: /usr/include/gnu/stubs.h +-src/simfold/s_min_folding.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_min_folding.o: /usr/include/bits/types.h +-src/simfold/s_min_folding.o: /usr/include/bits/typesizes.h +-src/simfold/s_min_folding.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_min_folding.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_min_folding.o: /usr/include/gconv.h +-src/simfold/s_min_folding.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_min_folding.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_min_folding.o: /usr/include/string.h /usr/include/stdlib.h + src/simfold/s_min_folding.o: ./include/constants.h ./include/structs.h + src/simfold/s_min_folding.o: ./include/externs.h src/common/common.h + src/simfold/s_min_folding.o: ./src/simfold/s_partition_function.h +@@ -309,22 +229,8 @@ src/simfold/s_min_folding.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_min_folding.o: ./include/simfold.h ./include/init.h + src/simfold/s_min_folding.o: ./src/simfold/s_specific_functions.h + src/simfold/s_min_folding.o: ./src/simfold/s_min_folding.h +-src/simfold/s_hairpin_loop.o: /usr/include/string.h /usr/include/features.h +-src/simfold/s_hairpin_loop.o: /usr/include/sys/cdefs.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/wordsize.h +-src/simfold/s_hairpin_loop.o: /usr/include/gnu/stubs.h +-src/simfold/s_hairpin_loop.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_hairpin_loop.o: /usr/include/ctype.h /usr/include/bits/types.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/typesizes.h +-src/simfold/s_hairpin_loop.o: /usr/include/endian.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/endian.h + src/simfold/s_hairpin_loop.o: ./include/constants.h ./include/structs.h + src/simfold/s_hairpin_loop.o: ./include/externs.h src/common/common.h +-src/simfold/s_hairpin_loop.o: /usr/include/stdio.h /usr/include/libio.h +-src/simfold/s_hairpin_loop.o: /usr/include/_G_config.h /usr/include/wchar.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/wchar.h /usr/include/gconv.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/sys_errlist.h + src/simfold/s_hairpin_loop.o: ./src/simfold/s_partition_function.h + src/simfold/s_hairpin_loop.o: ./src/simfold/s_hairpin_loop.h + src/simfold/s_hairpin_loop.o: ./src/simfold/s_internal_loop.h +@@ -334,20 +240,8 @@ src/simfold/s_hairpin_loop.o: ./src/simfold/s_multi_loop.h + src/simfold/s_hairpin_loop.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_hairpin_loop.o: ./include/simfold.h ./include/init.h + src/simfold/s_hairpin_loop.o: src/common/params.h +-src/simfold/s_stacked_pair.o: /usr/include/string.h /usr/include/features.h +-src/simfold/s_stacked_pair.o: /usr/include/sys/cdefs.h +-src/simfold/s_stacked_pair.o: /usr/include/bits/wordsize.h +-src/simfold/s_stacked_pair.o: /usr/include/gnu/stubs.h +-src/simfold/s_stacked_pair.o: /usr/include/gnu/stubs-32.h + src/simfold/s_stacked_pair.o: ./include/constants.h ./include/structs.h + src/simfold/s_stacked_pair.o: ./include/externs.h src/common/common.h +-src/simfold/s_stacked_pair.o: /usr/include/stdio.h /usr/include/bits/types.h +-src/simfold/s_stacked_pair.o: /usr/include/bits/typesizes.h +-src/simfold/s_stacked_pair.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_stacked_pair.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_stacked_pair.o: /usr/include/gconv.h +-src/simfold/s_stacked_pair.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_stacked_pair.o: /usr/include/bits/sys_errlist.h + src/simfold/s_stacked_pair.o: ./src/simfold/s_partition_function.h + src/simfold/s_stacked_pair.o: ./src/simfold/s_hairpin_loop.h + src/simfold/s_stacked_pair.o: ./src/simfold/s_internal_loop.h +@@ -357,22 +251,8 @@ src/simfold/s_stacked_pair.o: ./src/simfold/s_multi_loop.h + src/simfold/s_stacked_pair.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_stacked_pair.o: ./include/simfold.h ./include/init.h + src/simfold/s_stacked_pair.o: src/common/params.h +-src/simfold/s_energy_matrix.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_energy_matrix.o: /usr/include/sys/cdefs.h +-src/simfold/s_energy_matrix.o: /usr/include/bits/wordsize.h +-src/simfold/s_energy_matrix.o: /usr/include/gnu/stubs.h +-src/simfold/s_energy_matrix.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_energy_matrix.o: /usr/include/bits/types.h +-src/simfold/s_energy_matrix.o: /usr/include/bits/typesizes.h +-src/simfold/s_energy_matrix.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_energy_matrix.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_energy_matrix.o: /usr/include/gconv.h +-src/simfold/s_energy_matrix.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_energy_matrix.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_energy_matrix.o: /usr/include/string.h /usr/include/stdlib.h +-src/simfold/s_energy_matrix.o: /usr/include/malloc.h ./include/constants.h +-src/simfold/s_energy_matrix.o: ./include/structs.h ./include/externs.h +-src/simfold/s_energy_matrix.o: src/common/common.h ++src/simfold/s_energy_matrix.o: ./include/constants.h ./include/structs.h ++src/simfold/s_energy_matrix.o: ./include/externs.h src/common/common.h + src/simfold/s_energy_matrix.o: ./src/simfold/s_partition_function.h + src/simfold/s_energy_matrix.o: ./src/simfold/s_hairpin_loop.h + src/simfold/s_energy_matrix.o: ./src/simfold/s_internal_loop.h +@@ -381,19 +261,6 @@ src/simfold/s_energy_matrix.o: ./src/simfold/s_stacked_pair.h + src/simfold/s_energy_matrix.o: ./src/simfold/s_multi_loop.h + src/simfold/s_energy_matrix.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_energy_matrix.o: ./include/simfold.h ./include/init.h +-src/simfold/s_internal_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_internal_loop.o: /usr/include/sys/cdefs.h +-src/simfold/s_internal_loop.o: /usr/include/bits/wordsize.h +-src/simfold/s_internal_loop.o: /usr/include/gnu/stubs.h +-src/simfold/s_internal_loop.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_internal_loop.o: /usr/include/bits/types.h +-src/simfold/s_internal_loop.o: /usr/include/bits/typesizes.h +-src/simfold/s_internal_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_internal_loop.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_internal_loop.o: /usr/include/gconv.h +-src/simfold/s_internal_loop.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_internal_loop.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_internal_loop.o: /usr/include/string.h /usr/include/stdlib.h + src/simfold/s_internal_loop.o: ./src/simfold/s_internal_loop.h + src/simfold/s_internal_loop.o: ./include/constants.h ./include/structs.h + src/simfold/s_internal_loop.o: ./src/simfold/s_energy_matrix.h +@@ -405,21 +272,8 @@ src/simfold/s_internal_loop.o: ./include/externs.h src/common/common.h + src/simfold/s_internal_loop.o: ./src/simfold/s_partition_function.h + src/simfold/s_internal_loop.o: ./include/simfold.h ./include/init.h + src/simfold/s_internal_loop.o: src/common/params.h +-src/simfold/s_multi_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_multi_loop.o: /usr/include/sys/cdefs.h +-src/simfold/s_multi_loop.o: /usr/include/bits/wordsize.h +-src/simfold/s_multi_loop.o: /usr/include/gnu/stubs.h +-src/simfold/s_multi_loop.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_multi_loop.o: /usr/include/bits/types.h +-src/simfold/s_multi_loop.o: /usr/include/bits/typesizes.h +-src/simfold/s_multi_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_multi_loop.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_multi_loop.o: /usr/include/gconv.h +-src/simfold/s_multi_loop.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_multi_loop.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_multi_loop.o: /usr/include/malloc.h ./include/externs.h +-src/simfold/s_multi_loop.o: ./include/structs.h ./include/constants.h +-src/simfold/s_multi_loop.o: src/common/common.h ++src/simfold/s_multi_loop.o: ./include/externs.h ./include/structs.h ++src/simfold/s_multi_loop.o: ./include/constants.h src/common/common.h + src/simfold/s_multi_loop.o: ./src/simfold/s_partition_function.h + src/simfold/s_multi_loop.o: ./src/simfold/s_hairpin_loop.h + src/simfold/s_multi_loop.o: ./src/simfold/s_internal_loop.h +@@ -428,22 +282,8 @@ src/simfold/s_multi_loop.o: ./src/simfold/s_stacked_pair.h + src/simfold/s_multi_loop.o: ./src/simfold/s_multi_loop.h + src/simfold/s_multi_loop.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_multi_loop.o: ./include/simfold.h ./include/init.h +-src/simfold/s_multi_loop_sub.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_multi_loop_sub.o: /usr/include/sys/cdefs.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/wordsize.h +-src/simfold/s_multi_loop_sub.o: /usr/include/gnu/stubs.h +-src/simfold/s_multi_loop_sub.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/types.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/typesizes.h +-src/simfold/s_multi_loop_sub.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_multi_loop_sub.o: /usr/include/wchar.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/wchar.h +-src/simfold/s_multi_loop_sub.o: /usr/include/gconv.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_multi_loop_sub.o: /usr/include/malloc.h ./include/externs.h +-src/simfold/s_multi_loop_sub.o: ./include/structs.h ./include/constants.h +-src/simfold/s_multi_loop_sub.o: src/common/common.h ++src/simfold/s_multi_loop_sub.o: ./include/externs.h ./include/structs.h ++src/simfold/s_multi_loop_sub.o: ./include/constants.h src/common/common.h + src/simfold/s_multi_loop_sub.o: ./src/simfold/s_partition_function.h + src/simfold/s_multi_loop_sub.o: ./src/simfold/s_hairpin_loop.h + src/simfold/s_multi_loop_sub.o: ./src/simfold/s_internal_loop.h +@@ -452,20 +292,7 @@ src/simfold/s_multi_loop_sub.o: ./src/simfold/s_stacked_pair.h + src/simfold/s_multi_loop_sub.o: ./src/simfold/s_multi_loop.h + src/simfold/s_multi_loop_sub.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_sub_folding.o: ./src/simfold/s_sub_folding.h +-src/simfold/s_sub_folding.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_sub_folding.o: /usr/include/sys/cdefs.h +-src/simfold/s_sub_folding.o: /usr/include/bits/wordsize.h +-src/simfold/s_sub_folding.o: /usr/include/gnu/stubs.h +-src/simfold/s_sub_folding.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_sub_folding.o: /usr/include/bits/types.h +-src/simfold/s_sub_folding.o: /usr/include/bits/typesizes.h +-src/simfold/s_sub_folding.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_sub_folding.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_sub_folding.o: /usr/include/gconv.h +-src/simfold/s_sub_folding.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_sub_folding.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_sub_folding.o: /usr/include/string.h ./include/structs.h +-src/simfold/s_sub_folding.o: ./include/constants.h ++src/simfold/s_sub_folding.o: ./include/structs.h ./include/constants.h + src/simfold/s_sub_folding.o: ./src/simfold/s_energy_matrix.h + src/simfold/s_sub_folding.o: ./src/simfold/s_stacked_pair.h + src/simfold/s_sub_folding.o: ./src/simfold/s_hairpin_loop.h +@@ -475,30 +302,6 @@ src/simfold/s_sub_folding.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_sub_folding.o: ./include/externs.h src/common/common.h + src/simfold/s_sub_folding.o: ./src/simfold/s_partition_function.h + src/simfold/s_sub_folding.o: ./include/simfold.h ./include/init.h +-src/simfold/s_partition_function.o: /usr/include/stdio.h +-src/simfold/s_partition_function.o: /usr/include/features.h +-src/simfold/s_partition_function.o: /usr/include/sys/cdefs.h +-src/simfold/s_partition_function.o: /usr/include/bits/wordsize.h +-src/simfold/s_partition_function.o: /usr/include/gnu/stubs.h +-src/simfold/s_partition_function.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_partition_function.o: /usr/include/bits/types.h +-src/simfold/s_partition_function.o: /usr/include/bits/typesizes.h +-src/simfold/s_partition_function.o: /usr/include/libio.h +-src/simfold/s_partition_function.o: /usr/include/_G_config.h +-src/simfold/s_partition_function.o: /usr/include/wchar.h +-src/simfold/s_partition_function.o: /usr/include/bits/wchar.h +-src/simfold/s_partition_function.o: /usr/include/gconv.h +-src/simfold/s_partition_function.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_partition_function.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_partition_function.o: /usr/include/string.h +-src/simfold/s_partition_function.o: /usr/include/stdlib.h +-src/simfold/s_partition_function.o: /usr/include/malloc.h /usr/include/math.h +-src/simfold/s_partition_function.o: /usr/include/bits/huge_val.h +-src/simfold/s_partition_function.o: /usr/include/bits/mathdef.h +-src/simfold/s_partition_function.o: /usr/include/bits/mathcalls.h +-src/simfold/s_partition_function.o: /usr/include/ctype.h +-src/simfold/s_partition_function.o: /usr/include/endian.h +-src/simfold/s_partition_function.o: /usr/include/bits/endian.h + src/simfold/s_partition_function.o: ./include/constants.h ./include/structs.h + src/simfold/s_partition_function.o: ./include/externs.h src/common/common.h + src/simfold/s_partition_function.o: ./src/simfold/s_partition_function.h +@@ -512,31 +315,6 @@ src/simfold/s_partition_function.o: ./include/simfold.h ./include/init.h + src/simfold/s_partition_function.o: ./src/simfold/s_min_folding.h + src/simfold/s_partition_function.o: ./src/simfold/s_sub_folding.h + src/simfold/s_partition_function.o: src/common/params.h +-src/simfold/s_partition_function_complex.o: /usr/include/stdio.h +-src/simfold/s_partition_function_complex.o: /usr/include/features.h +-src/simfold/s_partition_function_complex.o: /usr/include/sys/cdefs.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/wordsize.h +-src/simfold/s_partition_function_complex.o: /usr/include/gnu/stubs.h +-src/simfold/s_partition_function_complex.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/types.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/typesizes.h +-src/simfold/s_partition_function_complex.o: /usr/include/libio.h +-src/simfold/s_partition_function_complex.o: /usr/include/_G_config.h +-src/simfold/s_partition_function_complex.o: /usr/include/wchar.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/wchar.h +-src/simfold/s_partition_function_complex.o: /usr/include/gconv.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_partition_function_complex.o: /usr/include/string.h +-src/simfold/s_partition_function_complex.o: /usr/include/stdlib.h +-src/simfold/s_partition_function_complex.o: /usr/include/malloc.h +-src/simfold/s_partition_function_complex.o: /usr/include/math.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/huge_val.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/mathdef.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/mathcalls.h +-src/simfold/s_partition_function_complex.o: /usr/include/ctype.h +-src/simfold/s_partition_function_complex.o: /usr/include/endian.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/endian.h + src/simfold/s_partition_function_complex.o: ./include/constants.h + src/simfold/s_partition_function_complex.o: ./include/structs.h + src/simfold/s_partition_function_complex.o: ./include/externs.h +@@ -551,32 +329,9 @@ src/simfold/s_partition_function_complex.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_partition_function_complex.o: ./include/simfold.h + src/simfold/s_partition_function_complex.o: ./include/init.h + src/simfold/s_partition_function_complex.o: src/simfold/s_partition_function_complex.h +-src/simfold/s_partition_function_complex.o: /usr/include/complex.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/cmathcalls.h + src/simfold/s_partition_function_complex.o: ./src/simfold/s_min_folding.h + src/simfold/s_partition_function_complex.o: ./src/simfold/s_sub_folding.h + src/simfold/s_partition_function_complex.o: src/common/params.h +-src/pairfold/p_specific_functions.o: /usr/include/stdio.h +-src/pairfold/p_specific_functions.o: /usr/include/features.h +-src/pairfold/p_specific_functions.o: /usr/include/sys/cdefs.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/wordsize.h +-src/pairfold/p_specific_functions.o: /usr/include/gnu/stubs.h +-src/pairfold/p_specific_functions.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/types.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/typesizes.h +-src/pairfold/p_specific_functions.o: /usr/include/libio.h +-src/pairfold/p_specific_functions.o: /usr/include/_G_config.h +-src/pairfold/p_specific_functions.o: /usr/include/wchar.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/wchar.h +-src/pairfold/p_specific_functions.o: /usr/include/gconv.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_specific_functions.o: /usr/include/stdlib.h +-src/pairfold/p_specific_functions.o: /usr/include/math.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/huge_val.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/mathdef.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/mathcalls.h +-src/pairfold/p_specific_functions.o: /usr/include/string.h + src/pairfold/p_specific_functions.o: ./include/constants.h + src/pairfold/p_specific_functions.o: ./include/structs.h ./include/externs.h + src/pairfold/p_specific_functions.o: src/common/common.h +@@ -597,19 +352,6 @@ src/pairfold/p_specific_functions.o: src/pairfold/p_multi_loop.h + src/pairfold/p_specific_functions.o: src/pairfold/p_multi_loop_sub.h + src/pairfold/p_specific_functions.o: src/pairfold/p_sub_folding.h + src/pairfold/p_specific_functions.o: src/pairfold/p_specific_functions.h +-src/pairfold/p_min_folding.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_min_folding.o: /usr/include/sys/cdefs.h +-src/pairfold/p_min_folding.o: /usr/include/bits/wordsize.h +-src/pairfold/p_min_folding.o: /usr/include/gnu/stubs.h +-src/pairfold/p_min_folding.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_min_folding.o: /usr/include/bits/types.h +-src/pairfold/p_min_folding.o: /usr/include/bits/typesizes.h +-src/pairfold/p_min_folding.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_min_folding.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/pairfold/p_min_folding.o: /usr/include/gconv.h +-src/pairfold/p_min_folding.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_min_folding.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_min_folding.o: /usr/include/string.h + src/pairfold/p_min_folding.o: src/pairfold/p_min_folding.h + src/pairfold/p_min_folding.o: ./include/structs.h ./include/constants.h + src/pairfold/p_min_folding.o: src/pairfold/p_energy_matrix.h +@@ -627,20 +369,8 @@ src/pairfold/p_min_folding.o: ./src/simfold/s_stacked_pair.h + src/pairfold/p_min_folding.o: ./src/simfold/s_multi_loop.h + src/pairfold/p_min_folding.o: ./src/simfold/s_multi_loop_sub.h + src/pairfold/p_min_folding.o: ./include/pairfold.h ./include/init.h +-src/pairfold/p_hairpin_loop.o: /usr/include/string.h /usr/include/features.h +-src/pairfold/p_hairpin_loop.o: /usr/include/sys/cdefs.h +-src/pairfold/p_hairpin_loop.o: /usr/include/bits/wordsize.h +-src/pairfold/p_hairpin_loop.o: /usr/include/gnu/stubs.h +-src/pairfold/p_hairpin_loop.o: /usr/include/gnu/stubs-32.h + src/pairfold/p_hairpin_loop.o: ./include/constants.h ./include/structs.h + src/pairfold/p_hairpin_loop.o: ./include/externs.h src/common/common.h +-src/pairfold/p_hairpin_loop.o: /usr/include/stdio.h /usr/include/bits/types.h +-src/pairfold/p_hairpin_loop.o: /usr/include/bits/typesizes.h +-src/pairfold/p_hairpin_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_hairpin_loop.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/pairfold/p_hairpin_loop.o: /usr/include/gconv.h +-src/pairfold/p_hairpin_loop.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_hairpin_loop.o: /usr/include/bits/sys_errlist.h + src/pairfold/p_hairpin_loop.o: ./src/simfold/s_partition_function.h + src/pairfold/p_hairpin_loop.o: ./src/simfold/s_hairpin_loop.h + src/pairfold/p_hairpin_loop.o: ./src/simfold/s_internal_loop.h +@@ -650,20 +380,8 @@ src/pairfold/p_hairpin_loop.o: ./src/simfold/s_multi_loop.h + src/pairfold/p_hairpin_loop.o: ./src/simfold/s_multi_loop_sub.h + src/pairfold/p_hairpin_loop.o: ./include/pairfold.h ./include/init.h + src/pairfold/p_hairpin_loop.o: src/pairfold/p_hairpin_loop.h +-src/pairfold/p_stacked_pair.o: /usr/include/string.h /usr/include/features.h +-src/pairfold/p_stacked_pair.o: /usr/include/sys/cdefs.h +-src/pairfold/p_stacked_pair.o: /usr/include/bits/wordsize.h +-src/pairfold/p_stacked_pair.o: /usr/include/gnu/stubs.h +-src/pairfold/p_stacked_pair.o: /usr/include/gnu/stubs-32.h + src/pairfold/p_stacked_pair.o: ./include/constants.h ./include/structs.h + src/pairfold/p_stacked_pair.o: ./include/externs.h src/common/common.h +-src/pairfold/p_stacked_pair.o: /usr/include/stdio.h /usr/include/bits/types.h +-src/pairfold/p_stacked_pair.o: /usr/include/bits/typesizes.h +-src/pairfold/p_stacked_pair.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_stacked_pair.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/pairfold/p_stacked_pair.o: /usr/include/gconv.h +-src/pairfold/p_stacked_pair.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_stacked_pair.o: /usr/include/bits/sys_errlist.h + src/pairfold/p_stacked_pair.o: ./src/simfold/s_partition_function.h + src/pairfold/p_stacked_pair.o: ./src/simfold/s_hairpin_loop.h + src/pairfold/p_stacked_pair.o: ./src/simfold/s_internal_loop.h +@@ -678,23 +396,8 @@ src/pairfold/p_stacked_pair.o: src/pairfold/p_hairpin_loop.h + src/pairfold/p_stacked_pair.o: src/pairfold/p_internal_loop.h + src/pairfold/p_stacked_pair.o: src/pairfold/p_multi_loop.h + src/pairfold/p_stacked_pair.o: src/pairfold/p_multi_loop_sub.h +-src/pairfold/p_energy_matrix.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_energy_matrix.o: /usr/include/sys/cdefs.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/wordsize.h +-src/pairfold/p_energy_matrix.o: /usr/include/gnu/stubs.h +-src/pairfold/p_energy_matrix.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/types.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/typesizes.h +-src/pairfold/p_energy_matrix.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_energy_matrix.o: /usr/include/wchar.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/wchar.h +-src/pairfold/p_energy_matrix.o: /usr/include/gconv.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_energy_matrix.o: /usr/include/string.h /usr/include/stdlib.h +-src/pairfold/p_energy_matrix.o: /usr/include/malloc.h ./include/constants.h +-src/pairfold/p_energy_matrix.o: ./include/structs.h ./include/externs.h +-src/pairfold/p_energy_matrix.o: src/common/common.h ++src/pairfold/p_energy_matrix.o: ./include/constants.h ./include/structs.h ++src/pairfold/p_energy_matrix.o: ./include/externs.h src/common/common.h + src/pairfold/p_energy_matrix.o: ./src/simfold/s_partition_function.h + src/pairfold/p_energy_matrix.o: ./src/simfold/s_hairpin_loop.h + src/pairfold/p_energy_matrix.o: ./src/simfold/s_internal_loop.h +@@ -709,20 +412,6 @@ src/pairfold/p_energy_matrix.o: src/pairfold/p_hairpin_loop.h + src/pairfold/p_energy_matrix.o: src/pairfold/p_internal_loop.h + src/pairfold/p_energy_matrix.o: src/pairfold/p_multi_loop.h + src/pairfold/p_energy_matrix.o: src/pairfold/p_multi_loop_sub.h +-src/pairfold/p_internal_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_internal_loop.o: /usr/include/sys/cdefs.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/wordsize.h +-src/pairfold/p_internal_loop.o: /usr/include/gnu/stubs.h +-src/pairfold/p_internal_loop.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/types.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/typesizes.h +-src/pairfold/p_internal_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_internal_loop.o: /usr/include/wchar.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/wchar.h +-src/pairfold/p_internal_loop.o: /usr/include/gconv.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_internal_loop.o: /usr/include/string.h /usr/include/stdlib.h + src/pairfold/p_internal_loop.o: src/pairfold/p_internal_loop.h + src/pairfold/p_internal_loop.o: ./include/constants.h ./include/structs.h + src/pairfold/p_internal_loop.o: src/pairfold/p_energy_matrix.h +@@ -740,21 +429,8 @@ src/pairfold/p_internal_loop.o: ./src/simfold/s_multi_loop.h + src/pairfold/p_internal_loop.o: ./src/simfold/s_multi_loop_sub.h + src/pairfold/p_internal_loop.o: ./include/pairfold.h ./include/init.h + src/pairfold/p_internal_loop.o: src/pairfold/p_specific_functions.h +-src/pairfold/p_multi_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_multi_loop.o: /usr/include/sys/cdefs.h +-src/pairfold/p_multi_loop.o: /usr/include/bits/wordsize.h +-src/pairfold/p_multi_loop.o: /usr/include/gnu/stubs.h +-src/pairfold/p_multi_loop.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_multi_loop.o: /usr/include/bits/types.h +-src/pairfold/p_multi_loop.o: /usr/include/bits/typesizes.h +-src/pairfold/p_multi_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_multi_loop.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/pairfold/p_multi_loop.o: /usr/include/gconv.h +-src/pairfold/p_multi_loop.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_multi_loop.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_multi_loop.o: /usr/include/malloc.h ./include/externs.h +-src/pairfold/p_multi_loop.o: ./include/structs.h ./include/constants.h +-src/pairfold/p_multi_loop.o: src/common/common.h ++src/pairfold/p_multi_loop.o: ./include/externs.h ./include/structs.h ++src/pairfold/p_multi_loop.o: ./include/constants.h src/common/common.h + src/pairfold/p_multi_loop.o: ./src/simfold/s_partition_function.h + src/pairfold/p_multi_loop.o: ./src/simfold/s_hairpin_loop.h + src/pairfold/p_multi_loop.o: ./src/simfold/s_internal_loop.h +@@ -769,23 +445,8 @@ src/pairfold/p_multi_loop.o: src/pairfold/p_hairpin_loop.h + src/pairfold/p_multi_loop.o: src/pairfold/p_internal_loop.h + src/pairfold/p_multi_loop.o: src/pairfold/p_multi_loop_sub.h + src/pairfold/p_multi_loop.o: ./include/pairfold.h ./include/init.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/sys/cdefs.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/wordsize.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/gnu/stubs.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/types.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/typesizes.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/libio.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/_G_config.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/wchar.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/wchar.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/gconv.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/malloc.h ./include/externs.h +-src/pairfold/p_multi_loop_sub.o: ./include/structs.h ./include/constants.h +-src/pairfold/p_multi_loop_sub.o: src/common/common.h ++src/pairfold/p_multi_loop_sub.o: ./include/externs.h ./include/structs.h ++src/pairfold/p_multi_loop_sub.o: ./include/constants.h src/common/common.h + src/pairfold/p_multi_loop_sub.o: ./src/simfold/s_partition_function.h + src/pairfold/p_multi_loop_sub.o: ./src/simfold/s_hairpin_loop.h + src/pairfold/p_multi_loop_sub.o: ./src/simfold/s_internal_loop.h +@@ -801,20 +462,7 @@ src/pairfold/p_multi_loop_sub.o: src/pairfold/p_internal_loop.h + src/pairfold/p_multi_loop_sub.o: src/pairfold/p_multi_loop.h + src/pairfold/p_multi_loop_sub.o: ./include/pairfold.h ./include/init.h + src/pairfold/p_sub_folding.o: src/pairfold/p_sub_folding.h +-src/pairfold/p_sub_folding.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_sub_folding.o: /usr/include/sys/cdefs.h +-src/pairfold/p_sub_folding.o: /usr/include/bits/wordsize.h +-src/pairfold/p_sub_folding.o: /usr/include/gnu/stubs.h +-src/pairfold/p_sub_folding.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_sub_folding.o: /usr/include/bits/types.h +-src/pairfold/p_sub_folding.o: /usr/include/bits/typesizes.h +-src/pairfold/p_sub_folding.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_sub_folding.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/pairfold/p_sub_folding.o: /usr/include/gconv.h +-src/pairfold/p_sub_folding.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_sub_folding.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_sub_folding.o: /usr/include/string.h ./include/structs.h +-src/pairfold/p_sub_folding.o: ./include/constants.h ++src/pairfold/p_sub_folding.o: ./include/structs.h ./include/constants.h + src/pairfold/p_sub_folding.o: src/pairfold/p_energy_matrix.h + src/pairfold/p_sub_folding.o: src/pairfold/p_stacked_pair.h + src/pairfold/p_sub_folding.o: src/pairfold/p_hairpin_loop.h +@@ -830,27 +478,6 @@ src/pairfold/p_sub_folding.o: ./src/simfold/s_stacked_pair.h + src/pairfold/p_sub_folding.o: ./src/simfold/s_multi_loop.h + src/pairfold/p_sub_folding.o: ./src/simfold/s_multi_loop_sub.h + src/pairfold/p_sub_folding.o: ./include/pairfold.h ./include/init.h +-src/multifold/m_specific_functions.o: /usr/include/stdio.h +-src/multifold/m_specific_functions.o: /usr/include/features.h +-src/multifold/m_specific_functions.o: /usr/include/sys/cdefs.h +-src/multifold/m_specific_functions.o: /usr/include/bits/wordsize.h +-src/multifold/m_specific_functions.o: /usr/include/gnu/stubs.h +-src/multifold/m_specific_functions.o: /usr/include/gnu/stubs-32.h +-src/multifold/m_specific_functions.o: /usr/include/bits/types.h +-src/multifold/m_specific_functions.o: /usr/include/bits/typesizes.h +-src/multifold/m_specific_functions.o: /usr/include/libio.h +-src/multifold/m_specific_functions.o: /usr/include/_G_config.h +-src/multifold/m_specific_functions.o: /usr/include/wchar.h +-src/multifold/m_specific_functions.o: /usr/include/bits/wchar.h +-src/multifold/m_specific_functions.o: /usr/include/gconv.h +-src/multifold/m_specific_functions.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_specific_functions.o: /usr/include/bits/sys_errlist.h +-src/multifold/m_specific_functions.o: /usr/include/stdlib.h +-src/multifold/m_specific_functions.o: /usr/include/math.h +-src/multifold/m_specific_functions.o: /usr/include/bits/huge_val.h +-src/multifold/m_specific_functions.o: /usr/include/bits/mathdef.h +-src/multifold/m_specific_functions.o: /usr/include/bits/mathcalls.h +-src/multifold/m_specific_functions.o: /usr/include/string.h + src/multifold/m_specific_functions.o: ./include/constants.h + src/multifold/m_specific_functions.o: ./include/structs.h ./include/externs.h + src/multifold/m_specific_functions.o: src/common/common.h +@@ -869,19 +496,6 @@ src/multifold/m_specific_functions.o: src/multifold/m_hairpin_loop.h + src/multifold/m_specific_functions.o: src/multifold/m_internal_loop.h + src/multifold/m_specific_functions.o: src/multifold/m_multi_loop.h + src/multifold/m_specific_functions.o: src/multifold/m_specific_functions.h +-src/multifold/m_min_folding.o: /usr/include/stdio.h /usr/include/features.h +-src/multifold/m_min_folding.o: /usr/include/sys/cdefs.h +-src/multifold/m_min_folding.o: /usr/include/bits/wordsize.h +-src/multifold/m_min_folding.o: /usr/include/gnu/stubs.h +-src/multifold/m_min_folding.o: /usr/include/gnu/stubs-32.h +-src/multifold/m_min_folding.o: /usr/include/bits/types.h +-src/multifold/m_min_folding.o: /usr/include/bits/typesizes.h +-src/multifold/m_min_folding.o: /usr/include/libio.h /usr/include/_G_config.h +-src/multifold/m_min_folding.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/multifold/m_min_folding.o: /usr/include/gconv.h +-src/multifold/m_min_folding.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_min_folding.o: /usr/include/bits/sys_errlist.h +-src/multifold/m_min_folding.o: /usr/include/string.h + src/multifold/m_min_folding.o: src/multifold/m_min_folding.h + src/multifold/m_min_folding.o: ./include/structs.h ./include/constants.h + src/multifold/m_min_folding.o: src/multifold/m_energy_matrix.h +@@ -899,22 +513,8 @@ src/multifold/m_min_folding.o: ./src/simfold/s_multi_loop.h + src/multifold/m_min_folding.o: ./src/simfold/s_multi_loop_sub.h + src/multifold/m_min_folding.o: ./include/multifold.h ./include/init.h + src/multifold/m_min_folding.o: src/multifold/m_specific_functions.h +-src/multifold/m_hairpin_loop.o: /usr/include/string.h /usr/include/features.h +-src/multifold/m_hairpin_loop.o: /usr/include/sys/cdefs.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/wordsize.h +-src/multifold/m_hairpin_loop.o: /usr/include/gnu/stubs.h +-src/multifold/m_hairpin_loop.o: /usr/include/gnu/stubs-32.h + src/multifold/m_hairpin_loop.o: ./include/constants.h ./include/structs.h + src/multifold/m_hairpin_loop.o: ./include/externs.h src/common/common.h +-src/multifold/m_hairpin_loop.o: /usr/include/stdio.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/types.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/typesizes.h +-src/multifold/m_hairpin_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/multifold/m_hairpin_loop.o: /usr/include/wchar.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/wchar.h +-src/multifold/m_hairpin_loop.o: /usr/include/gconv.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/sys_errlist.h + src/multifold/m_hairpin_loop.o: ./src/simfold/s_partition_function.h + src/multifold/m_hairpin_loop.o: ./src/simfold/s_hairpin_loop.h + src/multifold/m_hairpin_loop.o: ./src/simfold/s_internal_loop.h +@@ -925,22 +525,8 @@ src/multifold/m_hairpin_loop.o: ./src/simfold/s_multi_loop_sub.h + src/multifold/m_hairpin_loop.o: ./include/multifold.h ./include/init.h + src/multifold/m_hairpin_loop.o: src/multifold/m_hairpin_loop.h + src/multifold/m_hairpin_loop.o: src/multifold/m_specific_functions.h +-src/multifold/m_stacked_pair.o: /usr/include/string.h /usr/include/features.h +-src/multifold/m_stacked_pair.o: /usr/include/sys/cdefs.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/wordsize.h +-src/multifold/m_stacked_pair.o: /usr/include/gnu/stubs.h +-src/multifold/m_stacked_pair.o: /usr/include/gnu/stubs-32.h + src/multifold/m_stacked_pair.o: ./include/constants.h ./include/structs.h + src/multifold/m_stacked_pair.o: ./include/externs.h src/common/common.h +-src/multifold/m_stacked_pair.o: /usr/include/stdio.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/types.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/typesizes.h +-src/multifold/m_stacked_pair.o: /usr/include/libio.h /usr/include/_G_config.h +-src/multifold/m_stacked_pair.o: /usr/include/wchar.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/wchar.h +-src/multifold/m_stacked_pair.o: /usr/include/gconv.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/sys_errlist.h + src/multifold/m_stacked_pair.o: ./src/simfold/s_partition_function.h + src/multifold/m_stacked_pair.o: ./src/simfold/s_hairpin_loop.h + src/multifold/m_stacked_pair.o: ./src/simfold/s_internal_loop.h +@@ -955,24 +541,8 @@ src/multifold/m_stacked_pair.o: src/multifold/m_hairpin_loop.h + src/multifold/m_stacked_pair.o: src/multifold/m_internal_loop.h + src/multifold/m_stacked_pair.o: src/multifold/m_multi_loop.h + src/multifold/m_stacked_pair.o: src/multifold/m_specific_functions.h +-src/multifold/m_energy_matrix.o: /usr/include/stdio.h /usr/include/features.h +-src/multifold/m_energy_matrix.o: /usr/include/sys/cdefs.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/wordsize.h +-src/multifold/m_energy_matrix.o: /usr/include/gnu/stubs.h +-src/multifold/m_energy_matrix.o: /usr/include/gnu/stubs-32.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/types.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/typesizes.h +-src/multifold/m_energy_matrix.o: /usr/include/libio.h +-src/multifold/m_energy_matrix.o: /usr/include/_G_config.h +-src/multifold/m_energy_matrix.o: /usr/include/wchar.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/wchar.h +-src/multifold/m_energy_matrix.o: /usr/include/gconv.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/sys_errlist.h +-src/multifold/m_energy_matrix.o: /usr/include/string.h /usr/include/stdlib.h +-src/multifold/m_energy_matrix.o: /usr/include/malloc.h ./include/constants.h +-src/multifold/m_energy_matrix.o: ./include/structs.h ./include/externs.h +-src/multifold/m_energy_matrix.o: src/common/common.h ++src/multifold/m_energy_matrix.o: ./include/constants.h ./include/structs.h ++src/multifold/m_energy_matrix.o: ./include/externs.h src/common/common.h + src/multifold/m_energy_matrix.o: ./src/simfold/s_partition_function.h + src/multifold/m_energy_matrix.o: ./src/simfold/s_hairpin_loop.h + src/multifold/m_energy_matrix.o: ./src/simfold/s_internal_loop.h +@@ -986,21 +556,6 @@ src/multifold/m_energy_matrix.o: src/multifold/m_stacked_pair.h + src/multifold/m_energy_matrix.o: src/multifold/m_hairpin_loop.h + src/multifold/m_energy_matrix.o: src/multifold/m_internal_loop.h + src/multifold/m_energy_matrix.o: src/multifold/m_multi_loop.h +-src/multifold/m_internal_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/multifold/m_internal_loop.o: /usr/include/sys/cdefs.h +-src/multifold/m_internal_loop.o: /usr/include/bits/wordsize.h +-src/multifold/m_internal_loop.o: /usr/include/gnu/stubs.h +-src/multifold/m_internal_loop.o: /usr/include/gnu/stubs-32.h +-src/multifold/m_internal_loop.o: /usr/include/bits/types.h +-src/multifold/m_internal_loop.o: /usr/include/bits/typesizes.h +-src/multifold/m_internal_loop.o: /usr/include/libio.h +-src/multifold/m_internal_loop.o: /usr/include/_G_config.h +-src/multifold/m_internal_loop.o: /usr/include/wchar.h +-src/multifold/m_internal_loop.o: /usr/include/bits/wchar.h +-src/multifold/m_internal_loop.o: /usr/include/gconv.h +-src/multifold/m_internal_loop.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_internal_loop.o: /usr/include/bits/sys_errlist.h +-src/multifold/m_internal_loop.o: /usr/include/string.h /usr/include/stdlib.h + src/multifold/m_internal_loop.o: src/multifold/m_internal_loop.h + src/multifold/m_internal_loop.o: ./include/constants.h ./include/structs.h + src/multifold/m_internal_loop.o: src/multifold/m_energy_matrix.h +@@ -1017,21 +572,8 @@ src/multifold/m_internal_loop.o: ./src/simfold/s_multi_loop.h + src/multifold/m_internal_loop.o: ./src/simfold/s_multi_loop_sub.h + src/multifold/m_internal_loop.o: ./include/multifold.h ./include/init.h + src/multifold/m_internal_loop.o: src/multifold/m_specific_functions.h +-src/multifold/m_multi_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/multifold/m_multi_loop.o: /usr/include/sys/cdefs.h +-src/multifold/m_multi_loop.o: /usr/include/bits/wordsize.h +-src/multifold/m_multi_loop.o: /usr/include/gnu/stubs.h +-src/multifold/m_multi_loop.o: /usr/include/gnu/stubs-32.h +-src/multifold/m_multi_loop.o: /usr/include/bits/types.h +-src/multifold/m_multi_loop.o: /usr/include/bits/typesizes.h +-src/multifold/m_multi_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/multifold/m_multi_loop.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/multifold/m_multi_loop.o: /usr/include/gconv.h +-src/multifold/m_multi_loop.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_multi_loop.o: /usr/include/bits/sys_errlist.h +-src/multifold/m_multi_loop.o: /usr/include/malloc.h ./include/externs.h +-src/multifold/m_multi_loop.o: ./include/structs.h ./include/constants.h +-src/multifold/m_multi_loop.o: src/common/common.h ++src/multifold/m_multi_loop.o: ./include/externs.h ./include/structs.h ++src/multifold/m_multi_loop.o: ./include/constants.h src/common/common.h + src/multifold/m_multi_loop.o: ./src/simfold/s_partition_function.h + src/multifold/m_multi_loop.o: ./src/simfold/s_hairpin_loop.h + src/multifold/m_multi_loop.o: ./src/simfold/s_internal_loop.h +@@ -1046,68 +588,31 @@ src/multifold/m_multi_loop.o: src/multifold/m_hairpin_loop.h + src/multifold/m_multi_loop.o: src/multifold/m_internal_loop.h + src/multifold/m_multi_loop.o: ./include/multifold.h ./include/init.h + src/multifold/m_multi_loop.o: src/multifold/m_specific_functions.h +-simfold.o: /usr/include/stdio.h /usr/include/features.h +-simfold.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-simfold.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-simfold.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-simfold.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h +-simfold.o: /usr/include/bits/wchar.h /usr/include/gconv.h +-simfold.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h +-simfold.o: /usr/include/string.h /usr/include/stdlib.h /usr/include/time.h +-simfold.o: /usr/include/bits/time.h /usr/include/unistd.h +-simfold.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h + simfold.o: ./include/simfold.h ./include/constants.h ./include/init.h + simfold.o: ./include/externs.h ./include/structs.h src/common/params.h +-simfold_pf.o: /usr/include/stdio.h /usr/include/features.h +-simfold_pf.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-simfold_pf.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-simfold_pf.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-simfold_pf.o: /usr/include/libio.h /usr/include/_G_config.h +-simfold_pf.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-simfold_pf.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-simfold_pf.o: /usr/include/bits/sys_errlist.h /usr/include/string.h +-simfold_pf.o: /usr/include/stdlib.h /usr/include/time.h +-simfold_pf.o: /usr/include/bits/time.h /usr/include/unistd.h +-simfold_pf.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h ++simfold.o: ./src/simfold/s_partition_function.h ++simfold.o: ./src/simfold/s_hairpin_loop.h ./src/simfold/s_internal_loop.h ++simfold.o: ./src/simfold/s_energy_matrix.h ./src/simfold/s_stacked_pair.h ++simfold.o: ./src/simfold/s_multi_loop.h ./src/simfold/s_multi_loop_sub.h ++simfold.o: src/common/common.h + simfold_pf.o: ./include/simfold.h ./include/constants.h ./include/init.h + simfold_pf.o: ./include/externs.h ./include/structs.h src/common/params.h + simfold_pf.o: ./src/simfold/s_partition_function.h + simfold_pf.o: ./src/simfold/s_hairpin_loop.h ./src/simfold/s_internal_loop.h + simfold_pf.o: ./src/simfold/s_energy_matrix.h ./src/simfold/s_stacked_pair.h + simfold_pf.o: ./src/simfold/s_multi_loop.h ./src/simfold/s_multi_loop_sub.h +-pairfold.o: /usr/include/stdio.h /usr/include/features.h +-pairfold.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-pairfold.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-pairfold.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-pairfold.o: /usr/include/libio.h /usr/include/_G_config.h +-pairfold.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-pairfold.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-pairfold.o: /usr/include/bits/sys_errlist.h /usr/include/string.h +-pairfold.o: /usr/include/stdlib.h /usr/include/time.h +-pairfold.o: /usr/include/bits/time.h ./include/pairfold.h +-pairfold.o: ./include/constants.h ./include/init.h ./include/externs.h +-pairfold.o: ./include/structs.h src/common/timer.h /usr/include/sys/times.h +-pairfold.o: /usr/include/limits.h +-multifold.o: /usr/include/stdio.h /usr/include/features.h +-multifold.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-multifold.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-multifold.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-multifold.o: /usr/include/libio.h /usr/include/_G_config.h +-multifold.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-multifold.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-multifold.o: /usr/include/bits/sys_errlist.h /usr/include/string.h +-multifold.o: /usr/include/stdlib.h ./include/multifold.h +-multifold.o: ./include/constants.h ./include/init.h ./include/externs.h +-multifold.o: ./include/structs.h +-test_get_counts.o: /usr/include/stdio.h /usr/include/features.h +-test_get_counts.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-test_get_counts.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-test_get_counts.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-test_get_counts.o: /usr/include/libio.h /usr/include/_G_config.h +-test_get_counts.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-test_get_counts.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-test_get_counts.o: /usr/include/bits/sys_errlist.h /usr/include/string.h +-test_get_counts.o: /usr/include/stdlib.h /usr/include/time.h +-test_get_counts.o: /usr/include/bits/time.h ./include/simfold.h +-test_get_counts.o: ./include/constants.h ./include/init.h ./include/externs.h +-test_get_counts.o: ./include/structs.h src/common/params.h ++pairfold.o: ./include/pairfold.h ./include/constants.h ./include/init.h ++pairfold.o: ./include/externs.h ./include/structs.h src/common/timer.h ++multifold.o: ./include/multifold.h ./include/constants.h ./include/init.h ++multifold.o: ./include/externs.h ./include/structs.h ++feature_description.o: ./include/simfold.h ./include/constants.h ++feature_description.o: ./include/init.h ./include/externs.h ++feature_description.o: ./include/structs.h src/common/params.h ++feature_description.o: src/common/common.h ++feature_description.o: ./src/simfold/s_partition_function.h ++feature_description.o: ./src/simfold/s_hairpin_loop.h ++feature_description.o: ./src/simfold/s_internal_loop.h ++feature_description.o: ./src/simfold/s_energy_matrix.h ++feature_description.o: ./src/simfold/s_stacked_pair.h ++feature_description.o: ./src/simfold/s_multi_loop.h ++feature_description.o: ./src/simfold/s_multi_loop_sub.h diff --git a/recipes/multirnafold/0002-FIX-printf-missing-arg.patch b/recipes/multirnafold/0002-FIX-printf-missing-arg.patch new file mode 100644 index 0000000000000..471631385a018 --- /dev/null +++ b/recipes/multirnafold/0002-FIX-printf-missing-arg.patch @@ -0,0 +1,26 @@ +diff --git a/simfold.cpp b/simfold.cpp +index 08cffe2..0ca03e3 100644 +--- a/simfold.cpp ++++ b/simfold.cpp +@@ -64,7 +64,7 @@ void usage (const char *prog) + printf ("Examples:\n"); + printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -n 10 \n", prog); + printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -n 10 -r \"(____________________________)\"\n", prog); +- printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -p params/CG_best_parameters_ISMB2007.txt\n"); ++ printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -p params/CG_best_parameters_ISMB2007.txt\n", prog); + exit (0); + } + +diff --git a/simfold_pf.cpp b/simfold_pf.cpp +index e3ba56e..424ee85 100644 +--- a/simfold_pf.cpp ++++ b/simfold_pf.cpp +@@ -35,7 +35,7 @@ void usage (const char *prog) + printf ("Examples:\n"); + printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\"\n", prog); + printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -t 0.5\n", prog); +- printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -p params/CG_best_parameters_ISMB2007.txt\n"); ++ printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -p params/CG_best_parameters_ISMB2007.txt\n", prog); + exit (0); + } + diff --git a/recipes/multirnafold/0003-FIX-remove-unneeded-include.patch b/recipes/multirnafold/0003-FIX-remove-unneeded-include.patch new file mode 100644 index 0000000000000..51509cbcf874a --- /dev/null +++ b/recipes/multirnafold/0003-FIX-remove-unneeded-include.patch @@ -0,0 +1,126 @@ +commit 625122c01dbf740131c2419a5d2bfd65d8d315d8 +Author: Marco Matthies <71844+marcom@users.noreply.github.com> +Date: Thu Feb 8 16:12:41 2024 +0100 + + Remove unneeded include of malloc.h + +diff --git a/src/multifold/m_energy_matrix.cpp b/src/multifold/m_energy_matrix.cpp +index 4d47d90..4030513 100644 +--- a/src/multifold/m_energy_matrix.cpp ++++ b/src/multifold/m_energy_matrix.cpp +@@ -18,7 +18,6 @@ + #include + #include + #include +-#include + + #include "constants.h" + #include "structs.h" +diff --git a/src/multifold/m_multi_loop.cpp b/src/multifold/m_multi_loop.cpp +index a017da8..382d57a 100644 +--- a/src/multifold/m_multi_loop.cpp ++++ b/src/multifold/m_multi_loop.cpp +@@ -16,7 +16,6 @@ + ***************************************************************************/ + + #include +-#include + + #include "externs.h" + #include "common.h" +diff --git a/src/pairfold/p_energy_matrix.cpp b/src/pairfold/p_energy_matrix.cpp +index 42c15c2..dc23e29 100644 +--- a/src/pairfold/p_energy_matrix.cpp ++++ b/src/pairfold/p_energy_matrix.cpp +@@ -18,7 +18,6 @@ + #include + #include + #include +-#include + + #include "constants.h" + #include "structs.h" +diff --git a/src/pairfold/p_multi_loop.cpp b/src/pairfold/p_multi_loop.cpp +index f562ce0..267035a 100644 +--- a/src/pairfold/p_multi_loop.cpp ++++ b/src/pairfold/p_multi_loop.cpp +@@ -16,7 +16,6 @@ + ***************************************************************************/ + + #include +-#include + + #include "externs.h" + #include "common.h" +diff --git a/src/pairfold/p_multi_loop_sub.cpp b/src/pairfold/p_multi_loop_sub.cpp +index 467fb53..a418218 100644 +--- a/src/pairfold/p_multi_loop_sub.cpp ++++ b/src/pairfold/p_multi_loop_sub.cpp +@@ -16,7 +16,6 @@ + ***************************************************************************/ + + #include +-#include + + #include "externs.h" + #include "common.h" +diff --git a/src/simfold/s_energy_matrix.cpp b/src/simfold/s_energy_matrix.cpp +index cafc1d7..ce09162 100644 +--- a/src/simfold/s_energy_matrix.cpp ++++ b/src/simfold/s_energy_matrix.cpp +@@ -20,7 +20,6 @@ + #include + #include + #include +-#include + + #include "constants.h" + #include "structs.h" +diff --git a/src/simfold/s_multi_loop.cpp b/src/simfold/s_multi_loop.cpp +index 6c5998a..de7991e 100644 +--- a/src/simfold/s_multi_loop.cpp ++++ b/src/simfold/s_multi_loop.cpp +@@ -18,7 +18,6 @@ + // The main class for multi-loop related functions, the mfe case + + #include +-#include + + #include "externs.h" + #include "common.h" +diff --git a/src/simfold/s_multi_loop_sub.cpp b/src/simfold/s_multi_loop_sub.cpp +index e8f5219..bbdeb98 100644 +--- a/src/simfold/s_multi_loop_sub.cpp ++++ b/src/simfold/s_multi_loop_sub.cpp +@@ -18,7 +18,6 @@ + // this class represents multi-loops for suboptimal pairfold, it implements the Wuchty complete suboptimal paper + + #include +-#include + + #include "externs.h" + #include "common.h" +diff --git a/src/simfold/s_partition_function.cpp b/src/simfold/s_partition_function.cpp +index c551b6d..c63e8b4 100644 +--- a/src/simfold/s_partition_function.cpp ++++ b/src/simfold/s_partition_function.cpp +@@ -18,7 +18,6 @@ + #include + #include + #include +-#include + #include + #include + +diff --git a/src/simfold/s_partition_function_complex.cpp b/src/simfold/s_partition_function_complex.cpp +index 2654f25..2fb2a00 100644 +--- a/src/simfold/s_partition_function_complex.cpp ++++ b/src/simfold/s_partition_function_complex.cpp +@@ -18,7 +18,6 @@ + #include + #include + #include +-#include + #include + #include + diff --git a/recipes/multirnafold/build.sh b/recipes/multirnafold/build.sh new file mode 100644 index 0000000000000..1a10377f73b68 --- /dev/null +++ b/recipes/multirnafold/build.sh @@ -0,0 +1,13 @@ +# build +make CC="${CC}" CXX="${CXX}" + +# install +mkdir -p "$PREFIX/bin" +mkdir -p "$PREFIX/shared/${PKG_NAME}/params" +mkdir -p "$PREFIX/include" +mkdir -p "$PREFIX/lib" + +cp feature_description multifold pairfold pairfold-web simfold simfold_pf "$PREFIX/bin/" +cp -r params/* "$PREFIX/shared/${PKG_NAME}/params/" +cp -r include/* "$PREFIX/include/" +cp libMultiRNAFold.a "$PREFIX/lib/" diff --git a/recipes/multirnafold/meta.yaml b/recipes/multirnafold/meta.yaml new file mode 100644 index 0000000000000..ad45a1c49cb85 --- /dev/null +++ b/recipes/multirnafold/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "MultiRNAFold" %} +{% set version = "2.1" %} +{% set sha256 = "cb5462e03c70da24caaa9706f493fa329b1e15f697fbffd5bf460cd873243306" %} + +package: + name: {{ name | lower }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name | lower, max_pin="x.x") }} + +source: + url: http://www.rnasoft.ca/download/MultiRNAFold-{{ version }}.tar.gz + sha256: {{ sha256 }} + patches: + - 0001-FIX-Makefile.patch + - 0002-FIX-printf-missing-arg.patch + - 0003-FIX-remove-unneeded-include.patch + +requirements: + build: + - make + - {{ compiler('cxx') }} + +test: + commands: + - "test -x $PREFIX/bin/feature_description" + - "test -x $PREFIX/bin/multifold" + - "test -x $PREFIX/bin/pairfold" + - "test -x $PREFIX/bin/pairfold-web" + - "test -x $PREFIX/bin/simfold" + - "test -x $PREFIX/bin/simfold_pf" + - "pairfold -h" + - "simfold -h" + - "simfold_pf -h" + - "multifold -h" + +about: + home: http://www.rnasoft.ca/download/README.html + license: GPL-2.0-or-later + summary: 'RNA/DNA secondary structure prediction for one, two, or many interacting strands' From a51deec5f491b39a14f6952a20aa12f07c4e4978 Mon Sep 17 00:00:00 2001 From: Reid Wagner <74672860+reid-wagner@users.noreply.github.com> Date: Sat, 10 Feb 2024 14:06:46 -0600 Subject: [PATCH 0422/1813] Add MSFragger recipe. (#45127) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/msfragger/academic_install.py | 74 +++++++++++++++++++++++ recipes/msfragger/build.sh | 33 ++++++++++ recipes/msfragger/meta.yaml | 54 +++++++++++++++++ recipes/msfragger/msfragger.py | 86 +++++++++++++++++++++++++++ 4 files changed, 247 insertions(+) create mode 100755 recipes/msfragger/academic_install.py create mode 100644 recipes/msfragger/build.sh create mode 100644 recipes/msfragger/meta.yaml create mode 100755 recipes/msfragger/msfragger.py diff --git a/recipes/msfragger/academic_install.py b/recipes/msfragger/academic_install.py new file mode 100755 index 0000000000000..2f47dc5e87cfa --- /dev/null +++ b/recipes/msfragger/academic_install.py @@ -0,0 +1,74 @@ +#!/usr/bin/env python3 + +# Automates accepting the academic license agreements in order to download MSFragger. A user of this package is then expected to accept the terms themselves when they download a license key from the MSFragger site, which is enforced by the wrapper script and MSFragger jar file. + +import argparse +import hashlib +import os +import re +import sys +import urllib.request +import urllib.parse + +MSFRAGGER_URL = 'http://msfragger-upgrader.nesvilab.org/upgrader/upgrade_download.php' +DOWNLOAD_READ_SIZE = 1000000 + +def download_url(url, post_dict, dest): + data = urllib.parse.urlencode(post_dict).encode('ascii') + with open(dest, 'wb') as wh: + size = 0 + m = hashlib.sha256() + with urllib.request.urlopen(url, data) as f: + while True: + seg = f.read(DOWNLOAD_READ_SIZE) + m.update(seg) + bytes_read = len(seg) + if bytes_read < 1: + break + size += bytes_read + wh.write(seg) + + return m.hexdigest() + +def parse_version(version_string): + version_pattern = '([\\d.]+)' + m = re.search(version_pattern, version_string.strip()) + if m: + return m.groups()[0] + return None + +parser = argparse.ArgumentParser( + description="Download MSFragger zip file." +) +parser.add_argument( + '-n', '--name', help='user name' +) +parser.add_argument( + '-e', '--email', help='email' +) +parser.add_argument( + '-o', '--organization', help='institutional organization' +) +parser.add_argument( + '-m', '--msfragger_version', help='MSFragger version', required=True +) +parser.add_argument( + '-p', '--path', default='.', help='path in which to install' +) +parser.add_argument( + '--hash', default='.', help='SHA256 hash of downloaded zip' +) + +args = parser.parse_args() +fgr_ver = parse_version(args.msfragger_version) +if fgr_ver is None: + print(f'Could not find version: {args.msfragger_version}', file=sys.stderr) + sys.exit(1) + +fgr_zip = 'Release ' + fgr_ver + '$zip' +dest = os.path.join(args.path, 'MSFragger-' + fgr_ver + '.zip') +data = {'transfer': 'academic', 'agreement1': 'true', 'agreement2': 'true','agreement3': 'true', 'name': args.name, 'email' : args.email, 'organization' : args.organization, 'download': fgr_zip} + +if download_url(MSFRAGGER_URL, data, dest) != args.hash: + print('Invalid hash calculated.', file=sys.stderr) + sys.exit(1) diff --git a/recipes/msfragger/build.sh b/recipes/msfragger/build.sh new file mode 100644 index 0000000000000..f3d467463dbdd --- /dev/null +++ b/recipes/msfragger/build.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +# These values are submitted to the MSFragger site when downloading the application zip. +if [[ -z "$NAME" ]]; then + NAME="${USERNAME:-bioconda}"; +fi +if [[ -z "$EMAIL" ]]; then + EMAIL="${NAME}@${HOSTNAME:-bioconda.org}"; +fi +if [[ -z "$INSTITUTION" ]]; then + INSTITUTION="${HOSTNAME:-bioconda.org}"; +fi + +# Create directories +TARGET="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +mkdir -p "$TARGET" + +# Add wrapper python script and link to unprefixed name. +cp "$RECIPE_DIR/msfragger.py" "$TARGET" +ln -s "$TARGET/msfragger.py" "$PREFIX/bin/msfragger" +chmod 0755 "${PREFIX}/bin/msfragger" + +# This script automates accepting the academic license agreements in order to download MSFragger and build the package. A user of this package is then expected to accept the terms themselves when they download a license key from the MSFragger site, which is enforced by the wrapper script and MSFragger jar file. +"${RECIPE_DIR}/academic_install.py" -n galaxy -e "$EMAIL" -o "$INSTITUTION" -m "$PKG_VERSION" -p "$TARGET" --hash "$SHA256SUM" +if [[ $? -ne 0 ]]; then + echo "Problem downloading jar file." > /dev/stderr + exit 1; +fi + +# Unzip and link jar. +cd "$TARGET" +unzip "MSFragger-$PKG_VERSION.zip" +ln -s "MSFragger-$PKG_VERSION/MSFragger-$PKG_VERSION.jar" "MSFragger.jar" diff --git a/recipes/msfragger/meta.yaml b/recipes/msfragger/meta.yaml new file mode 100644 index 0000000000000..000aa4ee6fe93 --- /dev/null +++ b/recipes/msfragger/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "4.0" %} + +# This key was generated ONLY for the testing of this bioconda package. +# Users must generate their own key by agreeing to the terms at https://msfragger.arsci.com/upgrader/MSFragger-LICENSE.pdf. +{% set academic_use_only_key = "f28c4be2-759b0a11-6c1ea652-1240565a" %} +{% set sha256sum = "25bdab705c4ac97729d1da8d7a075e3920d8a447596fa52eff8e564606d1720e" %} + +package: + name: msfragger + version: {{ version }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('msfragger', max_pin="x.x") }} + script_env: + - SHA256SUM={{ sha256sum }} + +requirements: + host: + - python >3.9 + - unzip + run: + - openjdk >=11 + - python >=3.9 + - mono >=5, <6 + - zlib >=1.2.13 + +test: + commands: + - msfragger --key {{ academic_use_only_key }} -Xms512m -Xmx1g --help 2>&1 | grep 'MSFragger' + +about: + home: https://github.com/Nesvilab/MSFragger + license: Academic License (https://msfragger.arsci.com/upgrader/MSFragger-LICENSE.pdf) + summary: Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics + description: | + MSFragger is an ultrafast database search tool for peptide identification in mass spectrometry-based proteomics. + It has demonstrated excellent performance across a wide range of datasets and applications. + MSFragger is suitable for standard shotgun proteomics analyses as well as large datasets (including timsTOF PASEF data), + enzyme unconstrained searches (e.g., peptidome), + open database searches (e.g., precursor mass tolerance set to hundreds of Daltons) for identification + of modified peptides, and glycopeptide identification (N-linked and O-linked). + + MSFragger is available freely for academic research and educational purposes only, in accordance with the terms at https://msfragger.arsci.com/upgrader/MSFragger-LICENSE.pdf. + +extra: + notes: | + The "msfragger" command runs the MSFragger java program. + identifiers: + - doi:10.1038/nmeth.4256 + - doi:10.1038/s41467-020-17921-y + - doi:10.1038/s41592-020-0967-9 diff --git a/recipes/msfragger/msfragger.py b/recipes/msfragger/msfragger.py new file mode 100755 index 0000000000000..05d98f890af37 --- /dev/null +++ b/recipes/msfragger/msfragger.py @@ -0,0 +1,86 @@ +#!/usr/bin/env python +# +# Wrapper script for Java Conda packages that ensures that the java runtime +# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). +# + +import os +import sys +import subprocess +from os import access, getenv, X_OK + +jar_file = os.path.join(os.path.dirname(__file__), "MSFragger.jar") + +default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] + +license_agreement_text = ''' +Please provide pass a license key with the --key argument. You may obtain a key by agreeing to the terms at msfragger-upgrader.nesvilab.org/upgrader/. +''' + +def real_dirname(path): + """Return the symlink-resolved, canonicalized directory-portion of path.""" + return os.path.dirname(os.path.realpath(path)) + + +def java_executable(): + """Return the executable name of the Java interpreter.""" + java_home = getenv('JAVA_HOME') + java_bin = os.path.join('bin', 'java') + + if java_home and access(os.path.join(java_home, java_bin), X_OK): + return os.path.join(java_home, java_bin) + else: + return 'java' + + +def jvm_opts(argv): + """Construct list of Java arguments based on our argument list. + + The argument list passed in argv must not include the script name. + The return value is a 3-tuple lists of strings of the form: + (memory_options, prop_options, passthrough_options) + """ + mem_opts = [] + prop_opts = [] + pass_args = [] + + for arg in argv: + if arg.startswith('-D'): + prop_opts.append(arg) + elif arg.startswith('-XX'): + prop_opts.append(arg) + elif arg.startswith('-Xm'): + mem_opts.append(arg) + else: + pass_args.append(arg) + + # In the original shell script the test coded below read: + # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] + # To reproduce the behaviour of the above shell code fragment + # it is important to explictly check for equality with None + # in the second condition, so a null envar value counts as True! + + if mem_opts == [] and getenv('_JAVA_OPTIONS') == None: + mem_opts = default_jvm_mem_opts + + return (mem_opts, prop_opts, pass_args) + + +def main(): + java = java_executable() + jar_dir = real_dirname(sys.argv[0]) + jar_path = os.path.join(jar_dir, jar_file) + jar_arg = '-jar' + + (mem_opts, prop_opts, pass_args) = jvm_opts(sys.argv[1:]) + + if '--key' not in sys.argv: + print(license_agreement_text) + sys.exit(1) + + java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args + + sys.exit(subprocess.call(java_args)) + +if __name__ == '__main__': + main() From 64208352e20d25220efa97419a4ab085a2cbabbb Mon Sep 17 00:00:00 2001 From: Alejandro Buendia Date: Sat, 10 Feb 2024 15:31:27 -0500 Subject: [PATCH 0423/1813] Update arcas-hla to 0.6.0 (#45718) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update arcas-hla to 0.6.0 * Linting fix * Fix run_export statement * Add extra deps * Add dep * Unpin conda-forge deps * Remove channels and unpin deps * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/arcas-hla/meta.yaml | 30 ++++++++++++++++++------------ 1 file changed, 18 insertions(+), 12 deletions(-) diff --git a/recipes/arcas-hla/meta.yaml b/recipes/arcas-hla/meta.yaml index fa98f4d095d42..9121cf059a94f 100644 --- a/recipes/arcas-hla/meta.yaml +++ b/recipes/arcas-hla/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.0" %} +{% set version = "0.6.0" %} package: name: arcas-hla @@ -6,26 +6,31 @@ package: source: url: https://github.com/RabadanLab/arcasHLA/archive/v{{ version }}.tar.gz - sha256: fb17b3ba74facf4edb3329099b158910bdc7c4e73074efab9880d4136a0d4e93 + sha256: 75bef1a5596a9dfabccb901420f5d852d6d8a15d9c676e4c94787b8d25dd708b build: - number: 3 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage("arcas-hla", max_pin="x.x") }} requirements: run: + - bedtools + - biopython - coreutils - - bedtools >=2.27.1 - - biopython <=1.77 - git - git-lfs - - kallisto ==0.44.0 + - kallisto ==0.44 - numpy - pandas - pigz - - python >=3.6.1 - - samtools >=1.9 - - scipy ==1.1.0 + - pip + - pyarrow + - pytest + - python + - samtools + - scipy test: commands: @@ -33,10 +38,11 @@ test: about: home: https://github.com/RabadanLab/arcasHLA - license: GPL-3.0 - summary: high resolution HLA typing from RNA seq + license: GPL-3.0-only + license_file: LICENSE + summary: high-resolution HLA typing from RNA seq description: | - arcasHLA performs high resolution genotyping for HLA class I and class II + arcasHLA performs high-resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples. extra: From a2e2a5dc4e64b112d926c089fef769a9c866d693 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 17:04:09 -0500 Subject: [PATCH 0424/1813] Update phykit to 1.13.1 (#45747) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index fdbe8d3ddefe3..5199781fe01be 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.13.0" %} +{% set version = "1.13.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 22d074a5862dc6ee8402eaae9202d49d7c38e1ca15f4b55188ad14a99c292aaa + sha256: bd8076262d7f25f6780deed903af3d16abeb268975420e8f2fd2a3e5379e40cd build: noarch: python From 9944be365b68cf81c8fc76f6b4737779b4dcaec6 Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Sun, 11 Feb 2024 15:10:37 +0000 Subject: [PATCH 0425/1813] Update scanpy-scripts to scanpy 1.9.x (#45750) * Update scanpy-scripts to scanpy 1.9.x * Pin part * Separate package from constraints --- recipes/scanpy-scripts/meta.yaml | 68 ++++++++++++++++++++------------ 1 file changed, 43 insertions(+), 25 deletions(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index 5428c9ec3c8ab..6cad46ec670b5 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -1,23 +1,20 @@ {% set name = "scanpy-scripts" %} -{% set version = "1.1.6" %} +{% set version = "1.9.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 1701e35f93f5370ab451760b3892caf01b46d2898c3dd149e1dcba602e45eea1 + # - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + - url: https://github.com/ebi-gene-expression-group/scanpy-scripts/archive/refs/heads/develop.tar.gz + sha256: 669fb6f12e23a689e2e889d160c3f4f09d05d33068bef36a88bb94f9053c7b9c folder: scanpy-scripts - - url: https://pypi.io/packages/source/s/scanpy/scanpy-1.8.1.tar.gz - sha256: 1b8603a868d783bd6c18c8db763a450153feefc8daed862c440749790d47c654 - folder: scanpy - patches: - - scrublet.patch build: number: 0 noarch: python + run_exports: '{{ pin_compatible("scanpy-scripts", max_pin="x.x") }}' entry_points: - scanpy-cli=scanpy_scripts.cli:cli - scanpy-read-10x=scanpy_scripts.cmds:READ_CMD @@ -36,37 +33,57 @@ build: - scanpy-integrate=scanpy_scripts.cli:integrate - scanpy-multiplet=scanpy_scripts.cli:multiplet script: - - "{{ PYTHON }} -m pip install {{ SRC_DIR }}/scanpy --no-deps --ignore-installed -vv" - "{{ PYTHON }} -m pip install {{ SRC_DIR }}/scanpy-scripts --no-deps --ignore-installed -vv" requirements: host: - - python >=3.7 + - python <3.10 - pip + - scanpy =1.9.3 + - louvain + - igraph + - leidenalg + - loompy + - Click <8 + - harmonypy >=0.0.5 + - bbknn >=1.5.0,<1.6.0 + - mnnpy >=0.1.9.5 + - scipy <1.9.0 + - scikit-learn <1.3.0 + - scrublet + - fa2 + # for testing + - bats + - black + - pytest - flit-core - setuptools_scm - pytoml - packaging run: - - anndata - - bbknn>=1.5.0 - - click<8 - - fa2 - - h5py<3.0.0 - - harmonypy>=0.0.5 + - python <3.10 + - scanpy =1.9.3 - leidenalg - loompy - louvain - - matplotlib-base - - mnnpy>=0.1.9.5 - - packaging - - pandas - - python>=3.6 - - scanpy=1.8.1 - - scikit-misc - - scipy + - igraph + - Click <8 + - harmonypy >=0.0.5 + - bbknn >=1.5.0,<1.6.0 + - mnnpy >=0.1.9.5 + # for mnnpy using n_jobs + - scipy <1.9.0 + - scikit-learn <1.3.0 - scrublet - - umap-learn + - fa2 + # for testing + - bats + - black + - pytest + - flit-core + - setuptools_scm + - pytoml + - packaging test: imports: @@ -104,3 +121,4 @@ extra: recipe-maintainers: - nh3 - pinin4fjords + - pcm32 From 7031a376dba991c1fafc5487a67bc5f01d911025 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 11 Feb 2024 12:32:45 -0500 Subject: [PATCH 0426/1813] Update sourmash to 4.8.6 (#45749) Co-authored-by: C. Titus Brown --- recipes/sourmash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sourmash/meta.yaml b/recipes/sourmash/meta.yaml index 4feaa4aaee077..262fde0161307 100644 --- a/recipes/sourmash/meta.yaml +++ b/recipes/sourmash/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.8.5" %} +{% set version = "4.8.6" %} package: name: sourmash @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/sourmash/sourmash-{{ version }}.tar.gz - sha256: 9016c338d6b01f152d2c7becf5631000b058ff657f4fc50daa6ef15373d8a02a + sha256: 5a09c5d12cb07f8d73eb60db8dbd30e4e74aabf53a718610ddb5e6c91b341dca build: number: 0 From 7957f2156f99eeb825d811b2bf586ca238a44a97 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 11 Feb 2024 16:15:43 -0500 Subject: [PATCH 0427/1813] Update bx-python to 0.11.0 (#45748) * Update bx-python to 0.11.0 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/bx-python/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/bx-python/meta.yaml b/recipes/bx-python/meta.yaml index bbf510cd6ac66..4190c732ecd3c 100644 --- a/recipes/bx-python/meta.yaml +++ b/recipes/bx-python/meta.yaml @@ -1,6 +1,6 @@ {% set name = "bx-python" %} -{% set version = "0.10.0" %} -{% set sha256 = "bfe9541d7b18a98e907b085e31f58d3989fbca4dc667c4ae48c33b753e0e2da8" %} +{% set version = "0.11.0" %} +{% set sha256 = "2cf8872572817e0d36145cc2711889df5729987ffed4e51280da1e3c2ccb9429" %} package: name: {{ name|lower }} @@ -14,6 +14,8 @@ build: number: 0 skip: True # [py < 37] script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv + run_exports: + - {{ pin_subpackage(name|lower, max_pin='x') }} requirements: build: From db59ef1a6107681170c73dadd5d14d0b7ca294f9 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Mon, 12 Feb 2024 18:53:34 +1100 Subject: [PATCH 0428/1813] Update hmftools-bam-tools 1.2 recipe (#45754) * Fix class-path detection in BASH script * Bump build number --- recipes/hmftools-bam-tools/bamtools.sh | 2 +- recipes/hmftools-bam-tools/meta.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-bam-tools/bamtools.sh b/recipes/hmftools-bam-tools/bamtools.sh index bee5781030da9..b62ff17d5670f 100755 --- a/recipes/hmftools-bam-tools/bamtools.sh +++ b/recipes/hmftools-bam-tools/bamtools.sh @@ -60,7 +60,7 @@ if [ "$jvm_mem_opts" == "" ]; then fi pass_arr=($pass_args) -if [[ ${pass_arr[0]:=} == org* ]] +if [[ ${pass_arr[0]:=} == com.hartwig.* ]] then eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/bamtools.jar" $pass_args else diff --git a/recipes/hmftools-bam-tools/meta.yaml b/recipes/hmftools-bam-tools/meta.yaml index 138a0147d66af..58f205663e016 100644 --- a/recipes/hmftools-bam-tools/meta.yaml +++ b/recipes/hmftools-bam-tools/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage("hmftools-bam-tools", max_pin="x.x") }} From bd58ecdb18c0426c957aaebbf9b8aebe22c61cdb Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Mon, 12 Feb 2024 18:53:56 +1100 Subject: [PATCH 0429/1813] Update hmftools-sage 3.4 recipe (#45755) * Fix class-path detection in BASH script * Bump build number --- recipes/hmftools-sage/meta.yaml | 2 +- recipes/hmftools-sage/sage.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-sage/meta.yaml b/recipes/hmftools-sage/meta.yaml index 8f31690dab7d3..36e0eef3e635a 100644 --- a/recipes/hmftools-sage/meta.yaml +++ b/recipes/hmftools-sage/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('hmftools-sage', max_pin="x") }} diff --git a/recipes/hmftools-sage/sage.sh b/recipes/hmftools-sage/sage.sh index d5a456e118ba2..0164c0f1b3c2c 100755 --- a/recipes/hmftools-sage/sage.sh +++ b/recipes/hmftools-sage/sage.sh @@ -60,7 +60,7 @@ if [ "$jvm_mem_opts" == "" ]; then fi pass_arr=($pass_args) -if [[ ${pass_arr[0]:=} == org* ]] +if [[ ${pass_arr[0]:=} == com.hartwig.* ]] then eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/sage.jar" $pass_args else From 78b2433e1a82aa18d40b4d0ba1b67fa89d72d20e Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Mon, 12 Feb 2024 12:43:06 +0100 Subject: [PATCH 0430/1813] Bump GATK4 gcnvkernel (#45759) Bumped underlying gatk version, relaxed some dependencies causing issues --- recipes/gcnvkernel/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/gcnvkernel/meta.yaml b/recipes/gcnvkernel/meta.yaml index da4ef22df24e6..f8c6448ea98bb 100644 --- a/recipes/gcnvkernel/meta.yaml +++ b/recipes/gcnvkernel/meta.yaml @@ -1,7 +1,7 @@ {% set name = "gcnvkernel" %} {% set version = "0.8" %} -{% set gatk_version = "4.3.0.0" %} -{% set gatk_sha256 = "e2c27229b34c3e22445964adf00639a0909887bbfcc040f6910079177bc6e2dd" %} +{% set gatk_version = "4.5.0.0" %} +{% set gatk_sha256 = "dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916" %} package: name: {{ name|lower }} @@ -13,7 +13,9 @@ source: build: noarch: python - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('gcnvkernel', max_pin="x") }} requirements: build: @@ -24,17 +26,17 @@ requirements: # # https://github.com/broadinstitute/gatk/blob/master/scripts/gatkcondaenv.yml.template - conda-forge::python =3.6.10 - - pip =20.0.2 + - pip =21.3.1 - conda-forge::mkl =2019.5 - conda-forge::mkl-service =2.3.0 - conda-forge::numpy =1.17.5 - conda-forge::theano =1.0.4 - - defaults::tensorflow =1.15.0 + - tensorflow <2 - conda-forge::scipy =1.0.0 - conda-forge::pymc3 =3.1 - conda-forge::h5py =2.10.0 - conda-forge::keras =2.2.4 - - defaults::intel-openmp =2019.4 + - conda-forge::intel-openmp - conda-forge::scikit-learn =0.23.1 - conda-forge::matplotlib =3.2.1 - conda-forge::pandas =1.0.3 From 086444d2bfe19a268e41b8f654dc0c4d5651af5f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 08:03:17 -0500 Subject: [PATCH 0431/1813] Update pymzml to 2.5.5 (#45761) --- recipes/pymzml/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pymzml/meta.yaml b/recipes/pymzml/meta.yaml index 626e6ccb8c945..5ac2c87b095ef 100644 --- a/recipes/pymzml/meta.yaml +++ b/recipes/pymzml/meta.yaml @@ -1,10 +1,10 @@ package: name: pymzml - version: "2.5.4" + version: "2.5.5" source: - url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.4.tar.gz - sha256: f3da945e09f4b7b091feaf5b168c3543b3489bc8adf0bac48029f8d70b22de7f + url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.5.tar.gz + sha256: ffe96ccad5bd1eb7214b4afbc8c42c07d3a1a9f8cb41bcc0bad422c71af625c4 build: number: 0 From 4e93822a71f81bc4ea93e9f7ab45225d8b9f29e0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 08:03:57 -0500 Subject: [PATCH 0432/1813] Update bigtools to 0.4.2 (#45756) --- recipes/bigtools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bigtools/meta.yaml b/recipes/bigtools/meta.yaml index 72e92841c1718..ff77a44e62f1c 100644 --- a/recipes/bigtools/meta.yaml +++ b/recipes/bigtools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: bigtools @@ -11,7 +11,7 @@ build: source: url: https://github.com/jackh726/bigtools/archive/refs/tags/v{{ version }}.tar.gz - sha256: "92b9ea165adb1f9b13222d6c78e12148d9ba04a0d6ae96001820d43d9af7b39e" + sha256: "bd26a59e89cd00b1c7c82e038f03528ebf853182ae26213aeae2c936f203633e" requirements: build: From 017040de4a3d9f389d565440375a2870e7a7a1f3 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:58:49 +0100 Subject: [PATCH 0433/1813] Update GATK4 to 4.5.0.0 (#45762) * bump gatk4 version * add run_exports * add run_exports * pin R version to agree with gcnvkernel * pin R to correct version --- recipes/gatk4/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/gatk4/meta.yaml b/recipes/gatk4/meta.yaml index 5e77a8f9a2ef8..f588a9884779c 100644 --- a/recipes/gatk4/meta.yaml +++ b/recipes/gatk4/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GATK4" %} -{% set version = "4.4.0.0" %} -{% set sha256 = "444600f7b38b46ad0b3606b7d40ce921e0ff1910a50165872f1c73c7c4a1a390" %} +{% set version = "4.5.0.0" %} +{% set sha256 = "dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916" %} package: name: {{ name|lower }} @@ -13,24 +13,26 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('gatk4', max_pin="x") }} requirements: host: - - r-base + - r-base =3.6 - r-gplots - r-ggplot2 - r-gsalib - r-reshape - - gcnvkernel + - gcnvkernel =0.8 run: - openjdk >=17,<18 - python - - r-base + - r-base =3.6 - r-gplots - r-ggplot2 - r-gsalib - r-reshape - - gcnvkernel + - gcnvkernel =0.8 test: commands: From 71936332f62a4bfd4dbc3ff317f784f46bfd01b1 Mon Sep 17 00:00:00 2001 From: Yuri Pirola Date: Mon, 12 Feb 2024 16:05:49 +0100 Subject: [PATCH 0434/1813] Add RecGraph (#45680) * Add RecGraph v1.0.0 --- recipes/recgraph/build.sh | 6 ++++++ recipes/recgraph/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 recipes/recgraph/build.sh create mode 100644 recipes/recgraph/meta.yaml diff --git a/recipes/recgraph/build.sh b/recipes/recgraph/build.sh new file mode 100644 index 0000000000000..049babcc91015 --- /dev/null +++ b/recipes/recgraph/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash -euo + +RUST_BACKTRACE=1 CARGO_HOME="${BUILD_PREFIX}/.cargo" cargo build --release + +mkdir -p $PREFIX/bin +cp target/release/recgraph $PREFIX/bin diff --git a/recipes/recgraph/meta.yaml b/recipes/recgraph/meta.yaml new file mode 100644 index 0000000000000..227ff06ebd53e --- /dev/null +++ b/recipes/recgraph/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "RecGraph" %} +{% set version = "1.0.0" %} +{% set sha256 = "a68a49ecc457f4070604244a21abde60c76b12dba03e8d4136c3fe20abae7ffc" %} + + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/AlgoLab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - rust =1.74 + +test: + commands: + - recgraph --help + +about: + home: https://github.com/AlgoLab/{{ name }} + license: MIT + license_file: LICENSE + summary: Optimal sequence-to-graph alignment with recombinations + +extra: + recipe-maintainers: + - yp From c7e641680d387bde75c6b43e47cb09274f07bc38 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Mon, 12 Feb 2024 08:34:59 -0800 Subject: [PATCH 0435/1813] Add pass (#45722) * add pass * Add LICENSE file * Update meta.yaml * Fix LICENSE (SPDX identifier) --- recipes/pass/LICENSE | 674 +++++++++++++++++++++++++++++++++++++++++ recipes/pass/build.sh | 3 + recipes/pass/meta.yaml | 33 ++ 3 files changed, 710 insertions(+) create mode 100644 recipes/pass/LICENSE create mode 100755 recipes/pass/build.sh create mode 100644 recipes/pass/meta.yaml diff --git a/recipes/pass/LICENSE b/recipes/pass/LICENSE new file mode 100644 index 0000000000000..8f286b96aa63f --- /dev/null +++ b/recipes/pass/LICENSE @@ -0,0 +1,674 @@ +GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + ntEdit: scalable genome sequence polishing + Copyright (C) 2018-2019 BC Cancer + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + ntEdit Copyright (C) 2018-2019 Rene Warren @ BC Cancer + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/pass/build.sh b/recipes/pass/build.sh new file mode 100755 index 0000000000000..5bf1eeb9bd3a7 --- /dev/null +++ b/recipes/pass/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash +mkdir -p ${PREFIX}/bin +cp PASS ${PREFIX}/bin \ No newline at end of file diff --git a/recipes/pass/meta.yaml b/recipes/pass/meta.yaml new file mode 100644 index 0000000000000..96d7ce28ab436 --- /dev/null +++ b/recipes/pass/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "0.3.1" %} +{% set version_tar = "0-3-1" %} +{% set name = "pass" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/bcgsc/{{ name | upper }}/releases/download/v{{ version }}/pass_v{{ version_tar}}.tar.gz + sha256: 813fab567b1159c6dc32ed8ad537d19c50e70bde347b4e8b1249a4ece1de4383 + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('pass', max_pin="x") }} + +requirements: + run: + - perl + +test: + commands: + - PASS -h | grep "Usage" + +about: + summary: Proteome Assembler with Short Sequence peptides + home: https://github.com/bcgsc/PASS + license: GPL-3.0-only + license_file: LICENSE + doc_url: https://github.com/bcgsc/PASS + From 75a32ff8c75d24eb4649dc4481e52f59f1256878 Mon Sep 17 00:00:00 2001 From: Vlad Savelyev Date: Mon, 12 Feb 2024 17:35:24 +0100 Subject: [PATCH 0436/1813] MultiQC 1.20 (#45764) * MultiQC 1.20 * kaleido -> python-kaleido * Fix SHA --- recipes/multiqc/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 2d17086c661b8..489e083760ed5 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.19" %} +{% set version = "1.20" %} package: name: multiqc @@ -6,7 +6,7 @@ package: source: url: https://github.com/ewels/MultiQC/archive/v{{ version }}.tar.gz - sha256: 7c1501c8306f69a6f32777fe732fb4a53f71b066512a2252a8b2b4b89f994ca8 + sha256: 46e01394ee4c213eee3c14fde01afcb0da3e87a29b09a119e5aaeabf2817313d build: number: 0 @@ -33,6 +33,9 @@ requirements: - lzstring - markdown - matplotlib-base >=2.1.1 + - plotly + - python-kaleido + - pillow >=10.2.0 - networkx >=2.5.1 - numpy - packaging From aaa927d0464a1d9148b65b6c99547b7b1612bcb3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 12:53:25 -0500 Subject: [PATCH 0437/1813] Update thapbi-pict to 1.0.9 (#45767) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 9ea4719fe92bd..c643e4772b02d 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.8" %} +{% set version = "1.0.9" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: 3e0eac668b35351ea5588b0e1890ccf2e10e7aa847efd7777fd5eca497f4eef0 + sha256: 2b271400901dc7378302c7279416b591f4317d6deb43ae6bb6fa3ae1ee1d1a49 build: noarch: python From 4ce897b6d9d64b6b5ac44eae6c5f68ce631b89c4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:00:07 -0500 Subject: [PATCH 0438/1813] Update ska2 to 0.3.6 (#45768) --- recipes/ska2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ska2/meta.yaml b/recipes/ska2/meta.yaml index bd250923fcb6e..575802314f7b1 100644 --- a/recipes/ska2/meta.yaml +++ b/recipes/ska2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ska2" %} -{% set version = "0.3.5" %} +{% set version = "0.3.6" %} package: name: {{ name|lower}} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/ska.rust/archive/v{{ version }}.tar.gz - sha256: 507290aef6ec268e2b5098b60a208dddfc690f1c029e50b68eb5169ba3b1c9f0 + sha256: b1f7aecec7ff50c982d4dabceeb091b4c00071bfb4385aa5ea931fdbdca32e1e build: number: 0 From ccabcb7eca30389daf287962c6b15ae91a075285 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:00:17 -0500 Subject: [PATCH 0439/1813] Update integron_finder to 2.0.3 (#45766) * Update integron_finder to 2.0.3 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/integron_finder/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/integron_finder/meta.yaml b/recipes/integron_finder/meta.yaml index ddbeab522060d..6aebd892b1ec7 100644 --- a/recipes/integron_finder/meta.yaml +++ b/recipes/integron_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name="integron_finder" %} -{% set version="2.0.2" %} +{% set version="2.0.3" %} package: name: {{ name }} @@ -9,10 +9,12 @@ build: noarch: python number: 0 script: python -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage("integron_finder", max_pin="x.x") }} source: - url: https://files.pythonhosted.org/packages/4a/39/816165ed051a41560c9167590bf974a83de34e5a43509e9501f79cdf4ba4/integron_finder-2.0.2.tar.gz - sha256: 62444c43895c2b68289bc7ceaa2da417766c82852b5ecf1c3280e41ba3beaa6f + url: https://files.pythonhosted.org/packages/e7/b0/00059b74aed8542f276cfd377c51b6cf5695d0b97fcc90dd39da9b68f552/integron_finder-2.0.3.tar.gz + sha256: 2ecc0579490daf5b75a5cedfb22b446e830a0ca547c8acae92ee2ab2a755aa01 requirements: host: From 3adc1bbf8064042051815ec500d8858eff828e5b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:00:24 -0500 Subject: [PATCH 0440/1813] Update assembly_finder to 0.4.2 (#45765) --- recipes/assembly_finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index 0da7d56f0b95d..d54840930f3be 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: - url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: be7b470ad55c5ca304816b7414bf6d8f50db351b92ed9c6be6842ec0ed8cee8b + sha256: 6f035d34e562c0727fa0a43172de61b879714c3a1d964b6a5952afb49301129b build: number: 0 entry_points: From fb56c6d95e6c26249c71801262c6e8b105e4bbdf Mon Sep 17 00:00:00 2001 From: AllenWLynch Date: Mon, 12 Feb 2024 14:05:07 -0500 Subject: [PATCH 0441/1813] Update Lisa2 (#45753) * Update lisa2 to version 2.3.2 * bumped build number for lisa 2.3.2 * Update meta.yaml Added space between packages and version to pass linting --- recipes/lisa2/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/lisa2/meta.yaml b/recipes/lisa2/meta.yaml index 2725f8ee5badf..20859b72ef139 100644 --- a/recipes/lisa2/meta.yaml +++ b/recipes/lisa2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: dc9df3495322c94f93c12372fb8d88d355447f7b8b69ea639394fc6274e9affb build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . -vv run_exports: @@ -22,10 +22,10 @@ requirements: - python >=3.5 run: - h5py >=2 - - numpy <2,>=1.17 + - numpy >=1.17,<2 - python >=3.5 - - scikit-learn <2,>=0.22 - - scipy <2,>=1.4 + - scikit-learn >=0.22,<2 + - scipy >=1.4,<2 test: imports: From 4c2291ed2544fd1e72e932fff7b7f2ce6f42ac13 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:50:17 -0500 Subject: [PATCH 0442/1813] Update mira-multiome to 2.1.1 (#45763) * Update mira-multiome to 2.1.1 * run_exports * clean up recipe and pin python to <3.12 --------- Co-authored-by: Thanh Lee Co-authored-by: mencian --- recipes/mira-multiome/meta.yaml | 33 +++++++++++++++------------------ 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/recipes/mira-multiome/meta.yaml b/recipes/mira-multiome/meta.yaml index d897c3b0eddf6..98ec59647c8a5 100644 --- a/recipes/mira-multiome/meta.yaml +++ b/recipes/mira-multiome/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mira-multiome" %} -{% set version = "2.1.0" %} +{% set version = "2.1.1" %} package: name: {{ name|lower }} @@ -7,42 +7,39 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mira-multiome-{{ version }}.tar.gz - sha256: c28a8fe8388f35c020815e27ad4d046a796680c4e43400decd53952e0502159d + sha256: f981bc40542097c3892cb02efca0c25766dfa0bbafcbd4e94ea18b3e5e27157b build: noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - - python >=3.7 + - python >=3.7,<3.12 - wheel - pip - - setuptools >=35.0 - setuptools_scm run: - - python >=3.7 - - pytorch <2,>=1.8.0 - - pyro-ppl <2,>=1.5.2 - - networkx <3,>=2.3 - - optuna <3,>=2.8 - - anndata <1,>=0.7.6 + - python >=3.7,<3.12 + - pytorch >=1.8.0,<2 + - pyro-ppl >=1.5.2,<2 + - networkx >=2.3,<3 + - optuna >=2.8,<3 + - anndata >=0.7.6,<1 - moods >=1.9.4.1 - - pyfaidx <1,>=0.5 - - matplotlib-base <4,>=3.4 + - pyfaidx >=0.5,<1 + - matplotlib-base >=3.4,<4 - lisa2 >=2.3.0 - - requests <3,>=2 + - requests >=2,<3 - tqdm - tensorboard test: imports: - mira - commands: - - pip check - requires: - - pip about: home: https://mira-multiome.readthedocs.io/en/latest/ From df9609260fb2d9e2770e84d996937a07fe62415c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:50:32 -0500 Subject: [PATCH 0443/1813] Update samestr to 1.2024.2.post1 (#45737) * Update samestr to 1.2024.2.post1 * add run_exports --------- Co-authored-by: mencian --- recipes/samestr/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/samestr/meta.yaml b/recipes/samestr/meta.yaml index 36690b13adb95..54f65bf516a7c 100644 --- a/recipes/samestr/meta.yaml +++ b/recipes/samestr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "samestr" %} -{% set version = "1.2023.4" %} +{% set version = "1.2024.2.post1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 268b26ea7e7225373ea35ff75f30e4f0f8840946a92469b6bf51a7433d0b7d2c + sha256: d03c5f1fd89fd018409bcf332c3a95e752aca9fb47b88c617fad702581630bdd build: number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('samestr', max_pin=None) }} requirements: host: @@ -47,7 +49,7 @@ test: about: home: "https://github.com/danielpodlesny/samestr/" - license: "GNU Affero General Public License v3" + license: "AGPL-3.0-or-later" license_family: AGPL license_file: LICENSE summary: "SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles." From 1fbda083e18b6d488db0b508a5223f628ebd56af Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 17:38:45 -0500 Subject: [PATCH 0444/1813] Update augur to 24.2.0 (#45771) --- recipes/augur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index 9d585bfd5ce39..7eb5aee525913 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.1.0" %} +{% set version = "24.2.0" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: 22d349581fbbdfdcca0df02ce5d093965c9963931ef42c946a63b87d79a7ab08 + sha256: 965ab4808e937f5772022aa45444a42d89d293e9ed72272c639a570bc54540e2 build: number: 0 From bfbf553c18ff0b0482357c0232b77db93321696b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 21:44:01 -0500 Subject: [PATCH 0445/1813] Update ontime to 0.3.1 (#45773) --- recipes/ontime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ontime/meta.yaml b/recipes/ontime/meta.yaml index 1528ba3889c8a..b0764d525b178 100644 --- a/recipes/ontime/meta.yaml +++ b/recipes/ontime/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} {% set name = "ontime" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: 808833ade04fa7fb318e37b2f0aad2f19a46ba678decdd34e208bf3042050ee1 + sha256: 1caee3197d1032da38c55a47c3b626fe00b07831362e734fb2174747fca17fc4 build: number: 0 From 8ccecf12f762406fe643925f5fef0b704aa7c03f Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Tue, 13 Feb 2024 01:09:24 -0800 Subject: [PATCH 0446/1813] Update nextclade to 3.2.0 (#45777) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index fa81294b44098..b53743caebf7f 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.1.0" %} +{% set version = "3.2.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 949ec8ea1eb9705529425543292347ce7fbf9c799ec9f82fb3a9dab5f9e39450 # [linux64] + sha256: 392f5b980f291f1580cfc09abc51779955c83811aa0537f6dba7d755e03c8fa9 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: 878523f7c278c16bb19c47ab6421c63ccb876bbd2820cc997bcda62dcf3eb4d4 # [osx and x86_64] + sha256: deabdd06b1e6b6052c0ae50985b36db9839dfd8393de3a8d44b812b4b8b52cf6 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: 967ed5de693aa162ba010521d397462c7a73ff9430b2d70af42bc05b52782881 # [arm64] + sha256: 3b6185ff3741da4f15bd382f2f3c9cefb342e8add90a29be6050e20e4b3e66d2 # [arm64] build: number: 0 From 0406d34104abfb30638c0e388aa4861382822cfa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 04:48:44 -0500 Subject: [PATCH 0447/1813] Update clipkit to 2.2.0 (#45774) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index f2d9cc734178e..63fb201258cb4 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.1.3" %} +{% set version = "2.2.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e56e6c2c3a0c938f5026151ea191ff8fc2df7822d4aaf6487a65e9357c292487 + sha256: 7f973cec1842a3066c1478752b8692012174f5a58df870c1518a56cd37264605 build: number: 0 From 3ecea45d15b7f76d544678de01cadde2cf873cf5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 04:49:22 -0500 Subject: [PATCH 0448/1813] Update dajin2 to 0.4.1 (#45776) --- recipes/dajin2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index 9c3310af914d4..2c1bd818cfbc1 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.4.0" %} +{% set version = "0.4.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: 0b0abcc8f40679bec605c85643b069b55914ac1ac9031f6ad73c319899abd002 + sha256: 5a0c360cf52d506c1c60ba94a13f408a2789c66443ba92f3d2a6f1a7acd0aa3e build: entry_points: From 2094e1c611eedfe500a145bd442640f0440f68a5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 08:58:55 -0500 Subject: [PATCH 0449/1813] Update earlgrey to 4.0.8 (#45781) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index c9c4b8f190d19..e53bf3657fabd 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.7" %} -{% set sha256 = "d986ede4ffd3f06c5ea6ac3578c656942214031786b7e7e462b4b0ed4dbec6bd" %} +{% set version = "4.0.8" %} +{% set sha256 = "ae68c9bc464320d07ee026079c7fc2819d5768f29b7742224fc481fd03c46615" %} package: name: {{ name|lower }} From e05aadb23e2426fb3762e65a3df3002d627b91da Mon Sep 17 00:00:00 2001 From: richard-burhans Date: Tue, 13 Feb 2024 15:44:54 -0500 Subject: [PATCH 0450/1813] recipe for segalign-full (#45783) * recipe for segalign-full * adding "noarch: generic" to the build section * removed skip from build section * changed license_file to license_url * change lastz command * user lastz --version instead of --help * changing twobit commands * changing twobit commands again --------- Co-authored-by: Richard C. Burhans --- recipes/segalign-full/meta.yaml | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/segalign-full/meta.yaml diff --git a/recipes/segalign-full/meta.yaml b/recipes/segalign-full/meta.yaml new file mode 100644 index 0000000000000..ef44b90632061 --- /dev/null +++ b/recipes/segalign-full/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "0.1.2" %} + +package: + name: segalign-full + version: {{ version }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_compatible('segalign-full', max_pin='x.x') }} + +requirements: + run: + - segalign + - lastz + - ucsc-fatotwobit + - ucsc-twobittofa + +test: + commands: + - segalign --help + - segalign_repeat_masker --help + - lastz --version 2>&1 | grep released + - which faToTwoBit + - which twoBitToFa + +about: + home: https://github.com/gsneha26/SegAlign + summary: 'SegAlign: A Scalable GPU-Based Whole Genome Aligner' + description: | + SegAlign is a Scalable GPU System for Pairwise Whole Genome + Alignments based on LASTZ's seed-filter-extend paradigm. + license: MIT + license_family: MIT + license_url: https://github.com/gsneha26/SegAlign/blob/main/LICENSE + doc_url: https://github.com/gsneha26/SegAlign/blob/main/README.md + dev_url: https://github.com/gsneha26/SegAlign + +extra: + identifiers: + - doi:10.1109/SC41405.2020.00043 + - doi:10.5281/zenodo.3880947 From 6a80caee8f50d93231c130d1cd7ce04cfdf37a6c Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 13 Feb 2024 23:52:03 +0100 Subject: [PATCH 0451/1813] Update: sepp subrecipe 4.3.10 (#44540) * using latest release of upstream * use recent gapc update with hopes to compile on OSX * add subrecipe for older version 4.3.10 (pinned in qiime2) which shall additionally expose upp.config * adding run_exports * pin dendropy * pin pymongo, a dependency of pasta * link to identically main recipe, instead of actual file copies * relax dendropy version & remove explicit pymongo dependency * looks like symlinks don't work * attempt to apply condas mechanism for PREFIX replacement for upp.config file * more explicit mechanism to copy files * use $SP_DIR to avoid issues with py >=3.1x * Update meta.yaml pin python to <=3.9 * adding info why python is pinned --- recipes/sepp/4.3.10/build.sh | 42 +++++++++++++ recipes/sepp/4.3.10/meta.yaml | 63 +++++++++++++++++++ recipes/sepp/4.3.10/nodeps.setup.py.patch | 11 ++++ .../sepp/4.3.10/relocate.run-sepp.sh.patch | 36 +++++++++++ .../sepp/4.3.10/relocate.sepp.config.patch | 28 +++++++++ 5 files changed, 180 insertions(+) create mode 100644 recipes/sepp/4.3.10/build.sh create mode 100644 recipes/sepp/4.3.10/meta.yaml create mode 100644 recipes/sepp/4.3.10/nodeps.setup.py.patch create mode 100644 recipes/sepp/4.3.10/relocate.run-sepp.sh.patch create mode 100644 recipes/sepp/4.3.10/relocate.sepp.config.patch diff --git a/recipes/sepp/4.3.10/build.sh b/recipes/sepp/4.3.10/build.sh new file mode 100644 index 0000000000000..a21681feb1e3a --- /dev/null +++ b/recipes/sepp/4.3.10/build.sh @@ -0,0 +1,42 @@ +#!/bin/bash +set -ex +python setup.py config -c +python setup.py upp -c + +# ensure SEPP's configuration file is at the correct location ... +echo "${PREFIX}/share/sepp/sepp" > home.path +# ensure directory is created ... ($SP_DIR = Python's site-packages location, see https://docs.conda.io/projects/conda-build/en/stable/user-guide/environment-variables.html#environment-variables-set-during-the-build-process) +mkdir -p $SP_DIR/ +# ... before we copy content into it +cp -rv home.path $SP_DIR/ +mkdir -p $PREFIX/share/sepp/sepp +# ... and holds correct path names +mv -v sepp-package/sepp/default.main.config $PREFIX/share/sepp/sepp/main.config +# copy upp config, as it's still needed +cp ./.sepp/upp.config $PREFIX/share/sepp/sepp/upp.config +# replace $PREFIX with /opt/anaconda1anaconda2anaconda3 for later replacement of concrete build PREFIX +# note: can't apply a patch here, as upp.config is not part of upstream but gets generated during python setup +if [ $unamestr == 'Linux' ]; +then + sed -i 's@'"$PREFIX"'@/opt/anaconda1anaconda2anaconda3@g' $PREFIX/share/sepp/sepp/upp.config +elif [ $unamestr == 'Darwin' ]; +then + gsed -i 's@'"$PREFIX"'@/opt/anaconda1anaconda2anaconda3@g' $PREFIX/share/sepp/sepp/upp.config +fi + +$PYTHON -m pip install . --ignore-installed --no-deps -vv + +# copy bundled binaries, but hmmer which should be provided by conda, into $PREFIX/bin/ +mkdir -p $PREFIX/bin/ +cp `cat $SRC_DIR/.sepp/main.config | grep "^path" -m 1 | grep -v "hmm" | cut -d "=" -f 2 | xargs dirname`/* $PREFIX/bin/ +cp `cat $SRC_DIR/.sepp/upp.config | grep "^path" -m 1 | grep -v "hmm" | cut -d "=" -f 2 | xargs dirname`/* $PREFIX/bin/ + +# configure run-sepp.sh for qiime2 fragment-insertion +mv -v sepp-package/run-sepp.sh $PREFIX/bin/run-sepp.sh + +# copy files for tests to shared conda directory +mkdir -p $PREFIX/share/sepp/ref/ +cp -v test/unittest/data/q2-fragment-insertion/input_fragments.fasta $PREFIX/share/sepp/ref/ +cp -v test/unittest/data/q2-fragment-insertion/reference_alignment_tiny.fasta $PREFIX/share/sepp/ref/ +cp -v test/unittest/data/q2-fragment-insertion/reference_phylogeny_tiny.nwk $PREFIX/share/sepp/ref/ +cp -v test/unittest/data/q2-fragment-insertion/RAxML_info-reference-gg-raxml-bl.info $PREFIX/share/sepp/ref/ diff --git a/recipes/sepp/4.3.10/meta.yaml b/recipes/sepp/4.3.10/meta.yaml new file mode 100644 index 0000000000000..74c5177ff7068 --- /dev/null +++ b/recipes/sepp/4.3.10/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "4.3.10" %} +{% set sha256 = "24d8d410138563017e6f2f1263d5e34427f5bbddb875b72a036f7c879cef203b" %} +package: + name: sepp + version: '{{version}}' + +source: + - url: https://github.com/smirarab/sepp/archive/{{version}}.tar.gz + sha256: '{{sha256}}' + patches: + - relocate.run-sepp.sh.patch + - relocate.sepp.config.patch + # prevent python's setup to search for dendropy dependency via pip. + # Instead use dendropy provided by conda: + - nodeps.setup.py.patch + +build: + number: 3 + run_exports: + - {{ pin_subpackage('sepp', max_pin="x") }} + +# upstream is not (yet) compatible with python >=3.10 +requirements: + host: + - python <=3.9 + - setuptools + - pip + - dendropy 4.4.0 + - openjdk + - hmmer ==3.1b2 + + run: + - python <=3.9 + - dendropy 4.4.0 + - openjdk + - hmmer ==3.1b2 + - pasta + # TODO: source bundled binaries as conda packages. + # But pplacer / guppy are not available for OSX. + # - pplacer + +test: + commands: + - run_sepp.py --help + - run-sepp.sh $PREFIX/share/sepp/ref/input_fragments.fasta testrun_tiny -a $PREFIX/share/sepp/ref/reference_alignment_tiny.fasta -t $PREFIX/share/sepp/ref/reference_phylogeny_tiny.nwk -r $PREFIX/share/sepp/ref/RAxML_info-reference-gg-raxml-bl.info -x 1 -b 1 + - grep "f__Halomonadaceae" testrun_tiny_placement.tog.relabelled.tre + - grep "testseqd" testrun_tiny_placement.tog.relabelled.tre + - run_upp.py --help + +about: + home: https://github.com/smirarab/sepp + license: GPLv3 + license_family: GPL3 + license_file: LICENSE + summary: SATe-enabled phylogenetic placement + +extra: + identifiers: + - biotools:sepp + skip-lints: + # necessary, because sepp is NOT platform independent: + # during build time, platform specific binaries for pplacer / guppy are copied into the PREFIX/bin dir + - should_be_noarch_generic diff --git a/recipes/sepp/4.3.10/nodeps.setup.py.patch b/recipes/sepp/4.3.10/nodeps.setup.py.patch new file mode 100644 index 0000000000000..f93b859cf421e --- /dev/null +++ b/recipes/sepp/4.3.10/nodeps.setup.py.patch @@ -0,0 +1,11 @@ +--- setup.py 2019-03-31 07:43:25.000000000 +0200 ++++ setup.py 2019-04-03 12:12:30.701516881 +0200 +@@ -219,7 +219,7 @@ + author_email="smirarab@gmail.com, namphuon@cs.utah.edu", + + license="General Public License (GPL)", +- install_requires=["dendropy >= 4.0.0"], ++ install_requires=[], + provides=["sepp"], + scripts=["run_sepp.py", 'run_tipp.py', 'run_upp.py', 'run_abundance.py', + "split_sequences.py", "run_tipp_tool.py"], diff --git a/recipes/sepp/4.3.10/relocate.run-sepp.sh.patch b/recipes/sepp/4.3.10/relocate.run-sepp.sh.patch new file mode 100644 index 0000000000000..89839cb66476f --- /dev/null +++ b/recipes/sepp/4.3.10/relocate.run-sepp.sh.patch @@ -0,0 +1,36 @@ +--- sepp/sepp-package/run-sepp.sh 2019-03-19 16:33:17.267182143 +0100 ++++ sepp-package/run-sepp.sh 2019-03-19 20:23:08.591954892 +0100 +@@ -111,7 +111,7 @@ + done + + +-DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) ++DIR=/opt/anaconda1anaconda2anaconda3/share/sepp/ + + # Reference tree + if [ -z $t ]; then +@@ -134,7 +134,7 @@ + if [ ! -z "$printDebug" ]; then + export SEPP_DEBUG=True + fi; +-python $DIR/sepp/run_sepp.py -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log ++run_sepp.py -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log + + tail sepp-$name-* + +@@ -146,13 +146,11 @@ + # we might want to split computation in two parts: a) obtaining placements and b) creation of an insertion tree. + # If -n set to something, we stop after a) and leave it to the user to compute b) afterwards. + if [ -z ${noTree+x} ]; then +- gbin=$( dirname `grep -A1 "pplacer" $DIR/sepp/.sepp/main.config |grep path|sed -e "s/^path=//g"` ) +- +- $gbin/guppy tog ${name}_placement.json ++ guppy tog ${name}_placement.json + + cat ${name}_placement.tog.tre | python ${name}_rename-json.py > ${name}_placement.tog.relabelled.tre + +- $gbin/guppy tog --xml ${name}_placement.json ++ guppy tog --xml ${name}_placement.json + + cat ${name}_placement.tog.xml | python ${name}_rename-json.py > ${name}_placement.tog.relabelled.xml + else diff --git a/recipes/sepp/4.3.10/relocate.sepp.config.patch b/recipes/sepp/4.3.10/relocate.sepp.config.patch new file mode 100644 index 0000000000000..cb5f917265157 --- /dev/null +++ b/recipes/sepp/4.3.10/relocate.sepp.config.patch @@ -0,0 +1,28 @@ +--- sepp-package/sepp/default.main.config 2019-03-18 10:14:42.363446570 +0100 ++++ sepp-package/sepp/default.main.config 2019-04-04 10:10:22.171485197 +0200 +@@ -1,20 +1,20 @@ + [pplacer] +-path=~/pplacer ++path=/opt/anaconda1anaconda2anaconda3/bin/pplacer + + [hmmalign] +-path=~/hmmalign ++path=/opt/anaconda1anaconda2anaconda3/bin/hmmalign + + [hmmsearch] +-path=~/hmmsearch ++path=/opt/anaconda1anaconda2anaconda3/bin/hmmsearch + piped=False + elim=10000 + filters=True + + [hmmbuild] +-path=~/hmmbuild ++path=/opt/anaconda1anaconda2anaconda3/bin/hmmbuild + + [jsonmerger] +-path=~/seppJsonMerger.jar ++path=/opt/anaconda1anaconda2anaconda3/bin/seppJsonMerger.jar + + [exhaustive] + strategy = centroid From 875f82260bc8bc5873682ed0323c16a787c11536 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 17:52:40 -0500 Subject: [PATCH 0452/1813] Update ncbi-datasets-pylib to 16.4.7 (#45782) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 1659ccf273071..adb9708118530 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.5" %} -{% set sha256 = "c7b0aaeda5327e1fccd41774c43bfa936bb176e7790b63bd9ef7d8e14bbd0e27" %} +{% set version = "16.4.7" %} +{% set sha256 = "6d637d0b730426a35fa89f8107ada4573abe374214a1c93f9bafdb265986c9f4" %} package: name: {{ name|lower }} From 0aa47b07464256caa9902598524fad5cfaa1e72f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 17:53:31 -0500 Subject: [PATCH 0453/1813] Update dxpy to 0.369.1 (#45785) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 5dd102f8d5615..e2bc358122061 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.369.0" %} +{% set version = "0.369.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: dc2f58723d70c6d02155c08d4ac65f41f63aeb05000e4782940d2196b05a962b + sha256: 6e83d6c0756ff2b6691c9b789298ef5fdbe3f3df67b8fd90beb8420782219d41 build: number: 0 From 823a0c13a36c4d82273d529b836ae8ef74c69634 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 17:54:12 -0500 Subject: [PATCH 0454/1813] Update panaroo to 1.4.0 (#45786) --- recipes/panaroo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/panaroo/meta.yaml b/recipes/panaroo/meta.yaml index 4a3566f47f25b..8d83ad1beb7c2 100644 --- a/recipes/panaroo/meta.yaml +++ b/recipes/panaroo/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.4" %} +{% set version = "1.4.0" %} {% set name = "panaroo" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/gtonkinhill/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 95d9b166b0f554ca9b6b9326d3a85a065edee468e7d469f77d8b5242d7f82b9b + sha256: 651a11c9326bf885709ad555722ffefc5f67a365dce8a6475c09cd8d3537a89c build: number: 0 From 010a0451cde31c35879896f6c1656a26606dc7a0 Mon Sep 17 00:00:00 2001 From: Mike Tisza Date: Tue, 13 Feb 2024 17:10:13 -0600 Subject: [PATCH 0455/1813] Update meta.yaml (#45769) --- recipes/cenote-taker3/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/cenote-taker3/meta.yaml b/recipes/cenote-taker3/meta.yaml index 6717368a52f63..8a3b8e9aadc5e 100644 --- a/recipes/cenote-taker3/meta.yaml +++ b/recipes/cenote-taker3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cenote-taker3" %} -{% set version = "3.2.0" %} +{% set version = "3.2.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/mtisza1/{{ name }}/archive/v{{ version }}.tar.gz" - sha256: fe28c66009a4b1ee6755fbabcfbe5a8d0cba985977818155d6aefd0324ea9f95 + sha256: ffda0fcc8bee4c9200e46833008664bbe9155b6aae2b62d741943f27f6532a16 build: number: 0 @@ -43,6 +43,8 @@ requirements: - sed - grep - samtools + - pandas + - pyarrow test: From 59fd6d156a9274ea277f2fc07f59e60d86e873f9 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 14 Feb 2024 12:11:45 +1300 Subject: [PATCH 0456/1813] Add LTR_FINDER_parallel (#45772) * Added recipe for ltr_finder_parallel * Fixed typo * Locked version of ltr_finder to 1.07 * Replacing ltr_finder problematic line * Added a explanatory comment for the patch --- recipes/ltr_finder_parallel/build.sh | 24 +++++++++++++++++ recipes/ltr_finder_parallel/meta.yaml | 39 +++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 recipes/ltr_finder_parallel/build.sh create mode 100644 recipes/ltr_finder_parallel/meta.yaml diff --git a/recipes/ltr_finder_parallel/build.sh b/recipes/ltr_finder_parallel/build.sh new file mode 100644 index 0000000000000..5967719b8716f --- /dev/null +++ b/recipes/ltr_finder_parallel/build.sh @@ -0,0 +1,24 @@ +#!/bin/sh +set -x -e + +LTR_FINDER_PARALLEL_DIR=${PREFIX}/share/LTR_FINDER_parallel + +mkdir -p ${PREFIX}/bin +mkdir -p ${LTR_FINDER_PARALLEL_DIR} +cp -r * ${LTR_FINDER_PARALLEL_DIR} + +# LTR_FINDER_parallel creates the path to ltr_finder by using `which ltr_finder` +# `which ltr_finder` returns the path along with a newline character '\n'. +# To replace the newline character, LTR_FINDER_parallel matches regex 'ltr_finder\\n?' +# This regex logic fails in the case of this CONDA recipe because the path to +# ltr_finder includes ltr_finder_parallel which is replaced as _parallel, resulting in +# an invalid path. I have changed the regex so that ltr_finder_parallel is not replaced. +sed -i.bak 's|\$ltr_finder=~s/ltr_finder\\n?//;|\$ltr_finder=~s/\\bltr_finder\\n?\$//m;|' \ + ${LTR_FINDER_PARALLEL_DIR}/LTR_FINDER_parallel + +cat <>${PREFIX}/bin/LTR_FINDER_parallel +#!/bin/bash +perl ${LTR_FINDER_PARALLEL_DIR}/LTR_FINDER_parallel \$@ +END + +chmod a+x ${PREFIX}/bin/LTR_FINDER_parallel diff --git a/recipes/ltr_finder_parallel/meta.yaml b/recipes/ltr_finder_parallel/meta.yaml new file mode 100644 index 0000000000000..70c9f77428cf8 --- /dev/null +++ b/recipes/ltr_finder_parallel/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "LTR_FINDER_parallel" %} +{% set version = "1.1" %} +{% set sha256 = "5d1fed2a3a38c0927ccd7fc6cc38ba13ce293c5b1805299c999c5d52d085a1b9" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/oushujun/LTR_FINDER_parallel/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('ltr_finder_parallel', max_pin='x') }} + +requirements: + run: + - ltr_finder ==1.07 + +test: + commands: + - ltr_finder 2>&1 | grep -i usage + - LTR_FINDER_parallel -check_dependencies > /dev/null + +about: + home: https://github.com/oushujun/LTR_FINDER_parallel + license: MIT + license_family: MIT + license_file: LICENSE + summary: Perl wrapper to parallelize ltr_finder + dev_url: https://github.com/oushujun/LTR_FINDER_parallel + doc_url: https://github.com/oushujun/LTR_FINDER_parallel + +extra: + identifiers: + - doi:10.1186/s13100-019-0193-0 From c3021e9b8a5ee31214cbf3a864e61bba32ac3c2a Mon Sep 17 00:00:00 2001 From: Ryan James Kennedy <67742838+ryanjameskennedy@users.noreply.github.com> Date: Wed, 14 Feb 2024 00:21:40 +0100 Subject: [PATCH 0457/1813] Update serotypefinder to v2.0.2 (#45770) * Update serotypefinder to v2.0.2 * Add run_exports to fix linting error * Update build script commit id re serotypefinder_db * Add python3.8 to host requirements, update build script, add download-db script * Fix mamba solver errors --- recipes/serotypefinder/build.sh | 25 ++++++++----------------- recipes/serotypefinder/download-db.sh | 21 +++++++++++++++++++++ recipes/serotypefinder/meta.yaml | 16 ++++++++++------ 3 files changed, 39 insertions(+), 23 deletions(-) create mode 100644 recipes/serotypefinder/download-db.sh diff --git a/recipes/serotypefinder/build.sh b/recipes/serotypefinder/build.sh index f86371d384563..448adcd673160 100644 --- a/recipes/serotypefinder/build.sh +++ b/recipes/serotypefinder/build.sh @@ -9,28 +9,19 @@ cp serotypefinder.py ${PREFIX}/bin/serotypefinder chmod +x ${RECIPE_DIR}/update-serotypefinder-db.sh cp ${RECIPE_DIR}/update-serotypefinder-db.sh ${PREFIX}/bin/update-serotypefinder-db -# Grab latest database -# The SerotypeFinder database is not tagged and versioned, but it's also not updated -# very often (~7 commits in 5 years). 25ddd141d245db6382ca5876f7c7ddd0288aeb30 is the -# latest commit as of 2021/07/22. A script is provided to allow users to update in the -# event an update is made. -mkdir database/ -git clone https://bitbucket.org/genomicepidemiology/serotypefinder_db.git database/ -cd database/ -git checkout 25ddd141d245db6382ca5876f7c7ddd0288aeb30 -python3 INSTALL.py -echo "25ddd141d245db6382ca5876f7c7ddd0288aeb30" > serotypefinder-db-commit.txt -cd .. +# create folder for database download +target=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION} +mkdir -p ${target}/db/ +touch ${target}/db/.empty -# Path for database -outdir=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM} -mkdir -p ${outdir}/ -mv ./database/ ${outdir}/ +# copy script to download database +cp ${RECIPE_DIR}/download-db.sh ${PREFIX}/bin +chmod +x ${PREFIX}/bin/download-db.sh # set SEROTYPEFINDER_DB variable on env activation mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d cat <> ${PREFIX}/etc/conda/activate.d/serotypefinder.sh -export SEROTYPEFINDER_DB=${outdir}/database/ +export SEROTYPEFINDER_DB=${target}/db/ EOF cat <> ${PREFIX}/etc/conda/deactivate.d/serotypefinder.sh diff --git a/recipes/serotypefinder/download-db.sh b/recipes/serotypefinder/download-db.sh new file mode 100644 index 0000000000000..74296aca0dcd7 --- /dev/null +++ b/recipes/serotypefinder/download-db.sh @@ -0,0 +1,21 @@ +#!/usr/bin/env bash + +echo "Downloading SerotypeFinder database to ${SEROTYPEFINDER_DB}..." + +# Grab latest database +# The SerotypeFinder database is not tagged and versioned, but it's also not updated +# very often (~7 commits in 5 years). ada62c62a7fa74032448bb2273d1f7045c59fdda is the +# latest commit as of 2022/05/16. A script is provided to allow users to update in the +# event an update is made. + +cd ${SEROTYPEFINDER_DB} +# download SerotypeFinder database +git clone https://bitbucket.org/genomicepidemiology/serotypefinder_db.git db_serotypefinder +cd db_serotypefinder +python3 INSTALL.py +git rev-parse HEAD > serotypefinder-db-commit.txt +cd .. + +echo "SerotypeFinder database is downloaded." + +exit 0 diff --git a/recipes/serotypefinder/meta.yaml b/recipes/serotypefinder/meta.yaml index ae555ddfebb03..6fb2ab6ca1434 100644 --- a/recipes/serotypefinder/meta.yaml +++ b/recipes/serotypefinder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SerotypeFinder" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: "{{ name|lower }}" @@ -7,22 +7,26 @@ package: source: url: https://bitbucket.org/genomicepidemiology/{{ name|lower }}/get/{{ version }}.tar.gz - sha256: b937c0d85085f77f750665f28181656e5fb689e0d19a920ff7064f2ab4463783 + sha256: c6e13a3ef91c2f137bad99925a6b64e31330b768a4d8214bb767a51b3ea11446 patches: - - database_path.patch + - database_path.patch build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('serotypefinder', max_pin="x") }} requirements: + host: + - python >=3.8 run: - - biopython =1.73 + - biopython >=1.79 - blast >=2.8.1 - cgecore >=1.5.5 - kma - - python >=3 - - tabulate >=0.7.7 + - python >=3.8 + - tabulate >=0.8.9 test: From f1480ab89fbcea7b1aeaa480e87be293f47f8b2e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Wed, 14 Feb 2024 00:56:56 +0100 Subject: [PATCH 0458/1813] Update Integron finder to new release 2.0.3 (#45778) * add recipe to build squizz * update version * fixtypo in test section * update integron_finder recipe for new release 2.0.3 * clean up recipe --------- Co-authored-by: mencian --- recipes/integron_finder/meta.yaml | 59 ++++++++++++++++++------------- 1 file changed, 35 insertions(+), 24 deletions(-) diff --git a/recipes/integron_finder/meta.yaml b/recipes/integron_finder/meta.yaml index 6aebd892b1ec7..7e8566ea79450 100644 --- a/recipes/integron_finder/meta.yaml +++ b/recipes/integron_finder/meta.yaml @@ -1,48 +1,59 @@ -{% set name="integron_finder" %} -{% set version="2.0.3" %} +{% set name = "integron_finder" %} +{% set version = "2.0.3" %} package: - name: {{ name }} + name: {{ name|lower }} version: {{ version }} +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/integron_finder-{{ version }}.tar.gz + sha256: 2ecc0579490daf5b75a5cedfb22b446e830a0ca547c8acae92ee2ab2a755aa01 + build: + entry_points: + - integron_finder=integron_finder.scripts.finder:main + - integron_split=integron_finder.scripts.split:main + - integron_merge=integron_finder.scripts.merge:main noarch: python - number: 0 - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + number: 1 run_exports: - - {{ pin_subpackage("integron_finder", max_pin="x.x") }} - -source: - url: https://files.pythonhosted.org/packages/e7/b0/00059b74aed8542f276cfd377c51b6cf5695d0b97fcc90dd39da9b68f552/integron_finder-2.0.3.tar.gz - sha256: 2ecc0579490daf5b75a5cedfb22b446e830a0ca547c8acae92ee2ab2a755aa01 + - {{ pin_subpackage('integron_finder', max_pin="x") }} requirements: host: - - python >=3.7,<=3.10 + - python >=3.10 - pip run: - - python >=3.7,<=3.10 - - biopython ==1.78 - - numpy ==1.19.4 - - matplotlib-base ==3.3.3 - - colorlog <=6.6.0 - - pandas ==1.1.5 + - python >=3.10 + - numpy >=1.26 + - matplotlib-base >=3.8 + - pandas >=2 + - biopython >=1.82 + - colorlog - hmmer >=3.1b2,<=3.3.2 - infernal >=1.1.2,<=1.1.4 - prodigal >=2.6.3 test: + imports: + - integron_finder commands: - - integron_finder --version + - integron_finder --help + - integron_split --help + - integron_merge --help about: - home: https://github.com/gem-pasteur/Integron_Finder - license: 'GPLv3' + home: https://github.com/gem-pasteur/Integron_Finder/ + summary: Integron Finder aims at detecting integrons in DNA sequences + license: GPL-3.0-or-later + license_family: GPL3 license_file: COPYING - summary: 'Finds integrons in DNA sequences' + doc_url: https://integronfinder.readthedocs.io/en/latest/ + dev_url: https://github.com/gem-pasteur/Integron_Finder/ extra: recipe-maintainers: - - thanhleviet - doi: - - 10.1093/nar/gkw319 + - bneron + identifiers: + - doi:10.3390/microorganisms10040700 From 4129452ab1c7c47a42ab1681390f3455650a64ab Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 13 Feb 2024 18:42:06 -0600 Subject: [PATCH 0459/1813] Update infernal to 1.1.5 (#45787) --- recipes/infernal/build.sh | 5 ++--- recipes/infernal/meta.yaml | 29 +++++++++++++++++++++-------- 2 files changed, 23 insertions(+), 11 deletions(-) diff --git a/recipes/infernal/build.sh b/recipes/infernal/build.sh index e81bb592239ce..cf8e77142882d 100644 --- a/recipes/infernal/build.sh +++ b/recipes/infernal/build.sh @@ -4,8 +4,7 @@ set -ex grep -l -r "/usr/bin/perl" . | xargs sed -i.bak -e 's/usr\/bin\/perl/usr\/bin\/env perl/g' - -./configure --prefix=$PREFIX +autoreconf -i +./configure --prefix="${PREFIX}" --enable-sse make -j 2 -make check make install diff --git a/recipes/infernal/meta.yaml b/recipes/infernal/meta.yaml index 67b3bcad6bc71..33fd6e2aa733d 100644 --- a/recipes/infernal/meta.yaml +++ b/recipes/infernal/meta.yaml @@ -1,29 +1,34 @@ -{% set version = "1.1.4" %} +{% set name = "infernal" %} +{% set version = "1.1.5" %} package: - name: infernal + name: {{ name }} version: {{ version }} source: - url: http://eddylab.org/infernal/infernal-{{ version }}.tar.gz - sha256: f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc + url: http://eddylab.org/infernal/{{ name }}-{{ version }}.tar.gz + sha256: ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage('infernal', max_pin="x") }} requirements: build: - - make - {{ compiler('c') }} + - make + - autoconf + - automake + - libtool host: - perl - run: test: commands: - cmalign -h - cmbuild -h - - cmcalibrate -h + - cmcalibrate -h - cmconvert -h - cmemit -h - cmfetch -h @@ -35,6 +40,14 @@ test: about: home: http://eddylab.org/infernal license: BSD-3-Clause + license_family: BSD license_file: LICENSE summary: Infernal is for searching DNA sequence databases for RNA structure and sequence similarities. description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. + doc_url: http://eddylab.org/infernal/Userguide.pdf + dev_url: https://github.com/EddyRivasLab/infernal + +extra: + identifiers: + - doi:10.1093/bioinformatics/btt509 + - biotools:infernal From a4a82199b160b5ee608205bc9175d03304d19e29 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 23:00:59 -0500 Subject: [PATCH 0460/1813] Update augur to 24.2.1 (#45788) --- recipes/augur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index 7eb5aee525913..acab680fa5d8b 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.2.0" %} +{% set version = "24.2.1" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: 965ab4808e937f5772022aa45444a42d89d293e9ed72272c639a570bc54540e2 + sha256: c1fe7c357357d9b73dd614db7641695bbd780d884bebe2fb6082f19a28bb0f3b build: number: 0 From fb7b2b274637351929e990a6329a62f56c5aea37 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 23:01:14 -0500 Subject: [PATCH 0461/1813] Update submission-excel2xml to 2.6 (#45789) --- recipes/submission-excel2xml/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/submission-excel2xml/meta.yaml b/recipes/submission-excel2xml/meta.yaml index aaa47188eaa55..8a1c9a794ed3f 100644 --- a/recipes/submission-excel2xml/meta.yaml +++ b/recipes/submission-excel2xml/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5" %} +{% set version = "2.6" %} package: name: submission-excel2xml @@ -12,7 +12,7 @@ build: source: url: https://github.com/ddbj/submission-excel2xml/archive/refs/tags/v{{ version }}.tar.gz - md5: 14369dca823b18bc4c345913d689ae64 + sha256: 50d903242184967be8a39a88bb0e0bd0cf6d0d185c89b89fe3ed9525875fe01d requirements: host: From cc889a725b504292430940839ca818cf3245279e Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 13 Feb 2024 22:31:53 -0600 Subject: [PATCH 0462/1813] Update antismash to 7.1.0 (#45331) * Update antismash to 7.1.0 * add post-link.sh back * remove post-link.sh again * add post-link.sh message --- recipes/antismash/build.sh | 4 ++-- recipes/antismash/meta.yaml | 36 +++++++++++++++++++++------------- recipes/antismash/post-link.sh | 9 ++++++++- 3 files changed, 32 insertions(+), 17 deletions(-) diff --git a/recipes/antismash/build.sh b/recipes/antismash/build.sh index e60c5bc782d58..336e0d884c8bf 100644 --- a/recipes/antismash/build.sh +++ b/recipes/antismash/build.sh @@ -1,5 +1,5 @@ #!/bin/bash echo "include antismash/detection/genefinding/data/train_crypto" >> MANIFEST.in -df -h -$PYTHON -m pip install . --ignore-installed --no-deps -vv +df -h +${PYTHON} -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv diff --git a/recipes/antismash/meta.yaml b/recipes/antismash/meta.yaml index 6d4818140a158..c6ae23bcad79e 100644 --- a/recipes/antismash/meta.yaml +++ b/recipes/antismash/meta.yaml @@ -1,6 +1,6 @@ {% set name = "antiSMASH" %} -{% set version = "6.1.1" %} -{% set sha256 = "38c9fa8d34dea2552d3b21e3cb2ca293864f2f53d381764de9dd3d5f0b40139e" %} +{% set version = "7.1.0" %} +{% set sha256 = "5c01cce48ef5cc2bc60bfd2e185a5937e731e86a711c4c822a336640984e9b48" %} package: name: {{ name|lower }} @@ -9,6 +9,11 @@ package: build: number: 0 noarch: python + entry_points: + - download-antismash-databases=antismash.download_databases:_main + - antismash=antismash.__main__:entrypoint + run_exports: + - {{ pin_subpackage('antismash', max_pin="x") }} source: url: https://dl.secondarymetabolites.org/releases/{{ version }}/antismash-{{ version }}.tar.gz @@ -16,31 +21,33 @@ source: requirements: host: - - python >=3.7 + - python >=3.9 - pip + - pytest run: - - python >=3.7 + - python >=3.9 + - brawn >=1.0.1 - numpy - - biopython 1.78 - - helperlibs >=0.2.0 + - biopython 1.78.* + - helperlibs >=0.2.1 - jinja2 - joblib - jsonschema - markupsafe >=2.0 + - nrpys >=0.1.1 - pysvg-py3 - bcbio-gff - - pyscss + - libsass - matplotlib-base - scipy - - openjdk - - scikit-learn >=0.19 - - diamond 0.9.* + - scikit-learn >=1.3.2 + - moods >=1.9.4.2 + - diamond - fasttree 2.1.* - glimmerhmm ==3.0.* - hmmer2 - - hmmer ==3.1b2 - - meme <=4.11.2 - - muscle 3.8.* + - hmmer >=3.1b2 + - meme 4.11.2 - blast - prodigal @@ -53,7 +60,7 @@ test: about: home: https://docs.antismash.secondarymetabolites.org/intro/ - license: AGPL-3.0 + license: AGPL-3.0-or-later license_family: AGPL license_file: LICENSE.txt summary: antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell @@ -72,4 +79,5 @@ extra: - doi:10.1093/nar/gkx319 - doi:10.1093/nar/gkz310 - doi:10.1093/nar/gkab335 + - doi:10.1093/nar/gkad344 - usegalaxy-eu:antismash diff --git a/recipes/antismash/post-link.sh b/recipes/antismash/post-link.sh index 26fdad9e1d1cd..0df651f1df344 100644 --- a/recipes/antismash/post-link.sh +++ b/recipes/antismash/post-link.sh @@ -1,4 +1,11 @@ #!/bin/bash -# download the databases required by several options +cat <> ${PREFIX}/.messages.txt + + +antiSMASH databases are no longer included in the antismash conda package due to a "no space left on device" error. +Before using antiSMASH, please download the databases required by several options: download-antismash-databases + + +EOF From eadb3533f6a074938147f2ffd7b4d1751a117012 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 03:42:07 -0500 Subject: [PATCH 0463/1813] Update pangolin-data to 1.25 (#45791) --- recipes/pangolin-data/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangolin-data/meta.yaml b/recipes/pangolin-data/meta.yaml index d8b1f3721fb4d..6cbc9961cc1f7 100644 --- a/recipes/pangolin-data/meta.yaml +++ b/recipes/pangolin-data/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.24" %} +{% set version = "1.25" %} package: name: pangolin-data @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pangolin-data/archive/refs/tags/v{{ version }}.tar.gz - sha256: 63e3eb2598b90d0b0c3ab6b9be34cd520c7b060751f5511e653616146407f839 + sha256: abb7a1cdd2ac9f00f33bc1158262548e9219c631d363bc83d8ba4b3d914ca910 build: number: 0 From a3e12f472e1c96ad347151ad5dd8bb4aa9c91915 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 03:42:17 -0500 Subject: [PATCH 0464/1813] Update metacerberus to 1.2.1 (#45790) --- recipes/metacerberus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metacerberus/meta.yaml b/recipes/metacerberus/meta.yaml index 79300581b533d..670a203a2f29b 100644 --- a/recipes/metacerberus/meta.yaml +++ b/recipes/metacerberus/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MetaCerberus" %} -{% set version = "1.2" %} +{% set version = "1.2.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 6103002803d448df349f770a38e0da9a261a688993b5d33afbf1a9024ecbba07 + sha256: 1140732198b95c0d670fccb213c84464eb80bbe27127e4a85560de30c4873ac6 build: number: 0 From b50c73748031d8a5e0fa2f7e870645c3af7eafdd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 04:14:49 -0500 Subject: [PATCH 0465/1813] Update riassigner to 0.4.0 (#45779) * Update riassigner to 0.4.0 * add run_exports and use pypi source --------- Co-authored-by: Helge Hecht Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/riassigner/meta.yaml | 34 +++++++++++++++++++--------------- 1 file changed, 19 insertions(+), 15 deletions(-) diff --git a/recipes/riassigner/meta.yaml b/recipes/riassigner/meta.yaml index ee61afd653b1c..25837214f09ca 100644 --- a/recipes/riassigner/meta.yaml +++ b/recipes/riassigner/meta.yaml @@ -1,32 +1,35 @@ -{% set version = "0.3.4" %} +{% set name = "riassigner" %} +{% set version = "0.4.0" %} package: - name: riassigner - version: "{{ version }}" + name: {{ name }} + version: {{ version }} source: - url: "https://github.com/RECETOX/RIAssigner/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 7a8977603e659b76e87a558add2ae7960eb7e352365c289a7a193d4d8f68da3a + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/riassigner-{{ version }}.tar.gz + sha256: 32d0306ba76feb7d470eb504b2bd382f0d78c85f7795bc275abad0c874ee7d61 build: noarch: python - preserve_egg_dir: True - number: 4 - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv + number: 0 + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + run_exports: + - {{ pin_subpackage('riassigner', max_pin="x.x") }} requirements: host: - - python >=3.7,<3.9 + - python >=3.10,<3.13 - pip - - pytest-runner - - setuptools + - poetry-core run: - - numpy <=1.23 - - matchms >=0.14.0,<0.18.0 - - pint >=0.17,<0.20 + - numpy + - matchms >=0.24.1,<0.25.0 + - pint >=0.23.0,<0.24.0 - pandas - - python >=3.7,<3.9 + - python >=3.10,<3.13 - scipy + - urllib3 1.26.15 + - fastparquet >=2023.10.1,<2024.0.0 test: imports: @@ -35,6 +38,7 @@ test: about: home: https://github.com/RECETOX/RIAssigner license: MIT + license_family: MIT license_file: LICENSE summary: 'GC-MS retention index calculation' description: | From f9a378d7a8f6ec0161d4b7d4840c586346c0c993 Mon Sep 17 00:00:00 2001 From: Vlad Savelyev Date: Wed, 14 Feb 2024 11:17:10 +0100 Subject: [PATCH 0466/1813] MultiQC: pin plotly version (#45780) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/multiqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 489e083760ed5..cb8edecf3f5a4 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 46e01394ee4c213eee3c14fde01afcb0da3e87a29b09a119e5aaeabf2817313d build: - number: 0 + number: 1 entry_points: - multiqc=multiqc.__main__:run_multiqc noarch: python @@ -33,7 +33,7 @@ requirements: - lzstring - markdown - matplotlib-base >=2.1.1 - - plotly + - plotly >=5.18 - python-kaleido - pillow >=10.2.0 - networkx >=2.5.1 From 64d836ed20f75a23271ac4bf4f32e480b1e7e406 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 13:30:59 -0500 Subject: [PATCH 0467/1813] Update pybiolib to 1.1.1747 (#45800) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 102a78061d184..4d20a5881de64 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1745" %} +{% set version = "1.1.1747" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 3215bc496f4ddaf85d3cb327ccc19bf6a6b5f4c0edc339e0967804239dfb44e5 + sha256: b6e014d302e0551db14697ec438ec07fecbf7bdd3634ccd22a47c4410a7a7839 build: noarch: python From da6e73d4547017f6df1c2f71dee0873219459685 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 14:53:21 -0500 Subject: [PATCH 0468/1813] Update hiphase to 1.4.0 (#45804) --- recipes/hiphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index 59ee793e0ae92..92a902546ec07 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "1.3.0" %} -{% set hiphase_sha256 = "dd2708f5dd057009be555bf548aecfe30b189c4da086d026bdbb226bd4fb576e" %} +{% set version = "1.4.0" %} +{% set hiphase_sha256 = "ca38d56df8c644c3f60db26107d21dcaf58bdf53ee166c316fb51de7b8d21768" %} package: name: {{ name }} From 45de3acad953b47bfa951bcb8eb117282c445acc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:06:32 -0500 Subject: [PATCH 0469/1813] Update biocommons.seqrepo to 0.6.7 (#45803) --- recipes/biocommons.seqrepo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biocommons.seqrepo/meta.yaml b/recipes/biocommons.seqrepo/meta.yaml index f70cee72ac83a..190a81d3545ba 100644 --- a/recipes/biocommons.seqrepo/meta.yaml +++ b/recipes/biocommons.seqrepo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biocommons.seqrepo" %} -{% set version = "0.6.6" %} +{% set version = "0.6.7" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/biocommons.seqrepo-{{ version }}.tar.gz - sha256: 655eb8a2b6e3d4564ef2cbfaa2db6415ccb066f9fd786bd4b3303bbba00e752a + sha256: 2c3f982c1ed3adb1971a0dd2e7a554d096a1c5801075e384a62dd3f73d5e8c81 build: number: 0 From 29368ea6861ae934ce0a765873c503f4c6b46590 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:06:52 -0500 Subject: [PATCH 0470/1813] Update ena-webin-cli to 7.0.1 (#45802) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index b76445e0d12fe..2046d32218378 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "7.0.0" %} -{% set sha256 = "8b372aa08fe3e039f6d47d546ca18a20cbfcb1feb64748ea5a00527d81c7a418" %} +{% set version = "7.0.1" %} +{% set sha256 = "7adf27f5d333045a3a960b0cb6342e2facc082239ee815ba446d6c8f51492184" %} package: name: ena-webin-cli From bfe2e1481db03f2e4400625e5e358e55cb4a197a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:07:01 -0500 Subject: [PATCH 0471/1813] Update pyteomics to 4.7.1 (#45801) --- recipes/pyteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyteomics/meta.yaml b/recipes/pyteomics/meta.yaml index 3a7d5dfd42122..feb0274d684e9 100644 --- a/recipes/pyteomics/meta.yaml +++ b/recipes/pyteomics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.7" %} +{% set version = "4.7.1" %} package: name: pyteomics @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz - sha256: 9f3f83da617c9e7576a927f1dd668f0725789384545e3bc1fd53401d829534c2 + sha256: e5e5d3204af3050b9bf95bb64941b6156331335216e125ac253e7c8dfb1cf0ab build: noarch: python From fa506f892a92675dcdb073da8863d2209948aa01 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:07:06 -0500 Subject: [PATCH 0472/1813] Update savana to 1.0.5 (#45796) --- recipes/savana/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/savana/meta.yaml b/recipes/savana/meta.yaml index 1e02c7e699603..346e21295480e 100644 --- a/recipes/savana/meta.yaml +++ b/recipes/savana/meta.yaml @@ -1,5 +1,5 @@ {% set name = "savana" %} -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/cortes-ciriano-lab/{{ name }}/archive/{{ version }}.tar.gz" - sha256: f870ec9d36b20c1caf7849a4bff7af8cc984cd076b2f4d39153661e15776c644 + sha256: 987cf91c355f98e45b29fbca32d7766284eea98d63333ed34f60885d8234510e build: number: 0 From 4f63d0ff645cc217a2ba9d11e49d17e2e712491a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 17:19:54 -0500 Subject: [PATCH 0473/1813] Update hmftools-bam-tools to 1.2.1 (#45805) --- recipes/hmftools-bam-tools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hmftools-bam-tools/meta.yaml b/recipes/hmftools-bam-tools/meta.yaml index 58f205663e016..68e1d104b1102 100644 --- a/recipes/hmftools-bam-tools/meta.yaml +++ b/recipes/hmftools-bam-tools/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2" %} -{% set sha256 = "552f157861c22a0af22ce19400e6771a8034bdbfedbc760f287a30ac794d36c8" %} +{% set version = "1.2.1" %} +{% set sha256 = "3be174019a397a0ff7049be60c9abf8826c59b58b0a3b416fce26cf2a8c12695" %} package: name: hmftools-bam-tools @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage("hmftools-bam-tools", max_pin="x.x") }} From 53c75699db76299096146b02d619c2861e3e5c47 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 05:32:37 -0500 Subject: [PATCH 0474/1813] Update umi_tools to 1.1.5 (#45795) * Update umi_tools to 1.1.5 * Add run_exports --------- Co-authored-by: Jonathan Manning --- recipes/umi_tools/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/umi_tools/meta.yaml b/recipes/umi_tools/meta.yaml index 1dfa3b6caa4b6..8a309583a61c8 100644 --- a/recipes/umi_tools/meta.yaml +++ b/recipes/umi_tools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "umi_tools" %} -{% set version = "1.1.4" %} -{% set sha256hash = "945c4c98e2007369c301a7a009c6f9deb0fda74b0117cd14e14bd134164a4ff6" %} +{% set version = "1.1.5" %} +{% set sha256hash = "2a87b75364ebe3e6ccf467d3b6d0501c458a48f3e6c8ab8b7c4dfb3fd7627fab" %} package: name: {{ name }} @@ -11,11 +11,13 @@ source: sha256: {{ sha256hash }} build: - number: 2 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" skip: True # [py27] entry_points: - umi_tools = umi_tools.umi_tools:main + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: From 2b5150146e3812a52f91d08c179616e8e7d3bb0a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 11:10:37 -0500 Subject: [PATCH 0475/1813] Update pangolin-data to 1.25.1 (#45806) --- recipes/pangolin-data/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangolin-data/meta.yaml b/recipes/pangolin-data/meta.yaml index 6cbc9961cc1f7..172b1dbf9901b 100644 --- a/recipes/pangolin-data/meta.yaml +++ b/recipes/pangolin-data/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.25" %} +{% set version = "1.25.1" %} package: name: pangolin-data @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pangolin-data/archive/refs/tags/v{{ version }}.tar.gz - sha256: abb7a1cdd2ac9f00f33bc1158262548e9219c631d363bc83d8ba4b3d914ca910 + sha256: d92af7f5563cf8b3c0db4fa16748476d0033153865d75711a2dec46039c2473a build: number: 0 From e03216be911afcb087f52a142351cb3a9572c94b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 11:10:45 -0500 Subject: [PATCH 0476/1813] Update hicstuff to 3.2.2 (#45811) --- recipes/hicstuff/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hicstuff/meta.yaml b/recipes/hicstuff/meta.yaml index e0c50b567fcdf..fe9ff01dcad2e 100644 --- a/recipes/hicstuff/meta.yaml +++ b/recipes/hicstuff/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.2.1" %} +{% set version = "3.2.2" %} package: name: hicstuff @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/h/hicstuff/hicstuff-{{ version }}.tar.gz - sha256: cfea38c69d2594168d734f8e292a84b1f4d2135a31dd877fb175fad0aac4bdf4 + sha256: 8d1dc203fa5352e9b0014ec29d03dc796f2dbc0d51fef1a9b0df4c3aedb4065d build: number: 0 From 2f0d9d8b2cd485d78072545c6b72b2493ac96e10 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 12:25:39 -0500 Subject: [PATCH 0477/1813] Update defense-finder to 1.2.1 (#45817) --- recipes/defense-finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/defense-finder/meta.yaml b/recipes/defense-finder/meta.yaml index 91d9f8225e58c..3bb41bf1ac853 100644 --- a/recipes/defense-finder/meta.yaml +++ b/recipes/defense-finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "defense-finder" %} -{% set version = "1.2.0" %} +{% set version = "1.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/mdmparis/defense-finder/archive/v{{ version }}.tar.gz - sha256: 79547704ebe5d758b7692c2a9bdd1c4ccd6084a35ee18201dabb2e494da3ec36 + sha256: bff50fce7442e1bcc7fb7dd9ed202176662e5e02205551eee5ca05e4172cd2cd # patches: 0001-fix-no-results.patch build: From c81ff73f44c1cbe3142ab740f35cbd43e50da3aa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:28:13 -0500 Subject: [PATCH 0478/1813] Update terrace to 1.1.2 (#45818) --- recipes/terrace/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/terrace/meta.yaml b/recipes/terrace/meta.yaml index 136afdf510081..6def5bd34e555 100644 --- a/recipes/terrace/meta.yaml +++ b/recipes/terrace/meta.yaml @@ -1,5 +1,5 @@ {% set name = "terrace" %} -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/Shao-Group/TERRACE/releases/download/v{{ version }}/terrace-{{ version }}.tar.gz" - sha256: "2014bce67e6d05cf7c71ba16033f044c7043dc60217ca390741cff8818538664" + sha256: "cac4e9ae9ec61f49089c898f8c9484057ff16534fa1b12b02a5a06346dc56e8c" build: number: 0 From 24e5ffaf3c07150b25d3a6f53ce82d3555cd0c3b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:29:42 -0500 Subject: [PATCH 0479/1813] Update snakemake-executor-plugin-slurm to 0.3.1 (#45797) --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 3d08d331ed1ed..38c4d83d70a5c 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 0200006e4860d4966ed092e0b2d335068a2b0aef33f8938bca435890b790e5fa + sha256: 3c45605515f73020d437872e6003de661ddd17a09e2e60780b2d19a5668f0eb5 build: noarch: python From 1e6dfb92c66e049fcdf1df0715266cd87bb01d69 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:30:02 -0500 Subject: [PATCH 0480/1813] Update snakemake-interface-common to 1.16.0 (#45798) * Update snakemake-interface-common to 1.15.4 * Update snakemake-interface-common to 1.16.0 --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 525b28533b34c..f7298deb2e3a2 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.15.3" %} +{% set version = "1.16.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 7587c5e553c6ddaf0e2542bad1ffda55c3adf5b8ca651f4bc359a17d3f747ceb + sha256: b0780b9c3525435031815fd1f01079828d55c83fef18b5a0b05caa965408046b build: noarch: python From 3c294645b122a7df75b93bbc2e796ffe84b9fcb9 Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" <19176506+pdimens@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:46:12 -0500 Subject: [PATCH 0481/1813] Update harpy to 0.5.0 (#45714) * update to 0.5.0 * fix and add description * fix typo * clean up recipe * revert to noarch:generic * rm entry point * add pandas * rm no build isolation * fix build? * rm entrypoint * return build to what it was * add missing dso * fix python version and add DSO * add libcc/libz * restore the OSX skip --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/harpy/build.sh | 17 +++++------- recipes/harpy/meta.yaml | 59 ++++++++++++++++------------------------- 2 files changed, 30 insertions(+), 46 deletions(-) diff --git a/recipes/harpy/build.sh b/recipes/harpy/build.sh index 535a622944105..dacb8c084c852 100644 --- a/recipes/harpy/build.sh +++ b/recipes/harpy/build.sh @@ -1,19 +1,16 @@ -#!/bin/bash +#!/usr/bin/env bash mkdir -p ${PREFIX}/bin -# Harpy executable -#cp harpy ${PREFIX}/bin/ - -# build harpy -${PREFIX}/bin/python -m pip install . --ignore-installed --no-deps -vv +# install harpy proper +${PYTHON} -m pip install . --no-deps -vv # rules -cp rules/*.smk ${PREFIX}/bin/ +cp workflow/rules/*.smk ${PREFIX}/bin/ # associated scripts -chmod +x utilities/* -cp utilities/* ${PREFIX}/bin/ +chmod +x workflow/scripts/* +cp workflow/scripts/* ${PREFIX}/bin/ # reports -cp reports/*.Rmd ${PREFIX}/bin/ \ No newline at end of file +cp workflow/report/*.Rmd ${PREFIX}/bin/ diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index 616da31c08dfc..f5a78e0b92088 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.0" %} -{% set sha256 = "6062ece4701b6de964d1f25fc6e9e0d6b6525f3b04f9ca22d8b90191c7767928" %} +{% set version = "0.5.0" %} +{% set sha256 = "77ba116665fd00a945b65072b86b4c54f672b1b74912309709f580f7329b4adf" %} package: name: harpy @@ -12,63 +12,50 @@ source: build: skip: True # [osx] number: 0 + missing_dso_whitelist: + - /lib64/libstdc++.so.6 + - /lib64/libc.so.6 run_exports: - {{ pin_subpackage('harpy', max_pin="x.x") }} requirements: host: - - python =3.9 + - python =3.10 + - pip run: - - bcftools - - bioconductor-complexheatmap - - bwa - - fastp - - fastqc - - hapcut2 - - icu - - libzlib - - leviathan - - llvm-openmp + - bcftools =1.19 - multiqc - - naibr-plus - - python =3.9 - - pysam - - r-base - - r-circlize - - r-dplyr - - r-dt - - r-ggplot2 - - r-ggridges - - r-knitr - - r-magrittr - - r-plotly - - r-rmarkdown - - r-stitch - - r-tidyr - - r-viridislite + - pandas + - pysam =0.22 + - python =3.10 - rich-click - - snakemake >=7 - - sambamba + - snakemake-minimal - samtools - seqtk - tabix - - xz test: commands: - "snakemake --version" - - "R --version" - "harpy --version" + about: home: "https://github.com/pdimens/harpy/" - license: MIT + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE summary: "Process raw haplotagging data, from raw sequences to phased haplotypes." + description: | + Harpy is a command-line tool to easily process haplotag or 10x linked-read data. It uses + Snakemake under the hood to execute different workflows (quality control, trimming, + alignment, variant calling, phasing, etc.), but the user is rarely, if ever, exposed + to Snakemake directly. With an emphasis on user-friendliness, parallelization, transparency, + and reproducibility, Harpy aims to quickly handle data processing so that you can focus more + on analyzing your data. doc_url: https://pdimens.github.io/harpy/ dev_url: https://github.com/pdimens/harpy extra: - container: - extended-base: True recipe-maintainers: - pdimens skip-lints: From fbf5e5009ebf8af6ab3c10d16f0adf910c490dea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 14:24:36 -0500 Subject: [PATCH 0482/1813] Update amdirt to 1.5.0 (#45813) * Update amdirt to 1.5.0 * Fix run export linting --------- Co-authored-by: James A. Fellows Yates --- recipes/amdirt/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/amdirt/meta.yaml b/recipes/amdirt/meta.yaml index 897c231a4e148..32fcaf104f35f 100644 --- a/recipes/amdirt/meta.yaml +++ b/recipes/amdirt/meta.yaml @@ -1,5 +1,5 @@ {% set name = "amdirt" %} -{% set version = "1.4.6" %} +{% set version = "1.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/AMDirT-{{ version }}.tar.gz - sha256: dc099a28c68996ea7e8ca087856598e693fa5f780eec166ee9fcac8780b1f930 + sha256: f52028b539767e7d8ae357aa0716716b7b18ee0231612ffc9c4d4a2eb1e74f24 build: entry_points: @@ -15,6 +15,8 @@ build: noarch: python script: {{ PYTHON }} -m pip install . -vv number: 0 + run_exports: + - {{ pin_subpackage("amdirt", max_pin="x.x") }} requirements: host: From 0c7a84b75be1161162aa4a94278b4a62c766f2ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 14:53:00 -0500 Subject: [PATCH 0483/1813] Update sercol to 1.0.0 (#45792) * Update sercol to 1.0.0 * add run_exports --------- Co-authored-by: mencian --- recipes/sercol/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/sercol/meta.yaml b/recipes/sercol/meta.yaml index 47cefcfa8bf95..cedf8663759d9 100644 --- a/recipes/sercol/meta.yaml +++ b/recipes/sercol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sercol" %} -{% set version = "0.1.4" %} +{% set version = "1.0.0" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: eab962cf60bccb3c500b0eac7f51e865efefc4203d0323da3c4d5414e0b4e577 + sha256: 6507f5efcee4596eb77c45f1580ff562533ef5d115918a6a28bc4eac09ec191c build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('sercol', max_pin="x") }} requirements: host: @@ -30,7 +32,8 @@ test: about: home: "https://github.com/openvax/sercol" - license: Apache Software + license: Apache-2.0 + license_file: LICENSE license_family: APACHE summary: "Rich collection class with grouping and filtering helpers" From dc83c93824e12c701b08932f334d6e0f2ffb0c22 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 18:25:46 -0500 Subject: [PATCH 0484/1813] Update snakemake-executor-plugin-googlebatch to 0.3.0 (#45819) --- recipes/snakemake-executor-plugin-googlebatch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml index 2b428cb274a58..1cc605247f4ba 100644 --- a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml +++ b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-googlebatch" %} -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_googlebatch-{{ version }}.tar.gz - sha256: 3cccef6db07f47d53c0863db960c36d24c6336caabbea2b7fd3f2fc42c95edc4 + sha256: b143fcaeffceec682bc0f7e3f13eece3596a5d6faaf41fab94977f4a93948c16 build: noarch: python From 002004816b0c99e4955fe1f67dfd5086367775e7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 18:25:56 -0500 Subject: [PATCH 0485/1813] Update snakemake-storage-plugin-s3 to 0.2.9 (#45820) --- recipes/snakemake-storage-plugin-s3/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-storage-plugin-s3/meta.yaml b/recipes/snakemake-storage-plugin-s3/meta.yaml index 9bc32ac5fff7f..f846ede5119a0 100644 --- a/recipes/snakemake-storage-plugin-s3/meta.yaml +++ b/recipes/snakemake-storage-plugin-s3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-s3" %} -{% set version = "0.2.8" %} +{% set version = "0.2.9" %} package: name: {{ name|lower }} @@ -7,12 +7,12 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_s3-{{ version }}.tar.gz - sha256: 4006be9cec5113aaead77a0c9f362be4f3af5409a5da1a3a0f7d69675b222605 + sha256: 41cb23326f37dc576d4a1deac15b3f5a647e26ca957a69ae06b128c044ba2f32 build: noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 1 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} From 178ed9f3c97989ddf31b228f760b7d2488f0677f Mon Sep 17 00:00:00 2001 From: lspindler2509 <83402447+lspindler2509@users.noreply.github.com> Date: Fri, 16 Feb 2024 01:00:06 +0100 Subject: [PATCH 0486/1813] Add recipe for biodigest (#45751) * added recipe for biodigest * added missing properties * corrected name * add graphtools * graphtool import * add install * correct name * different install * different import * addressed changes from review * unnecessary info deleted * clean up recipe --------- Co-authored-by: mencian --- recipes/biodigest/meta.yaml | 49 +++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/biodigest/meta.yaml diff --git a/recipes/biodigest/meta.yaml b/recipes/biodigest/meta.yaml new file mode 100644 index 0000000000000..1f5455223cb84 --- /dev/null +++ b/recipes/biodigest/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "biodigest" %} +{% set version = "0.2.16" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 7618cedf40fedd6dd60aa2fbf8635fb4af0a2c0ae16c01ef9741d30729b6e8bc + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" + noarch: python + run_exports: + - {{ pin_subpackage('biodigest', max_pin="x.x") }} + +requirements: + host: + - pip + - python >=3.7 + run: + - biothings_client ==0.2.6 + - gseapy ==0.10.5 + - graph-tool + - numpy ==1.24.3 + - pandas ==1.5.2 + - psutil ==5.9.0 + - pycairo >=1.21.0 + - python >=3.7 + - requests ==2.28.2 + - scipy ==1.8.0 + - seaborn ==0.12.2 + + +test: + imports: + - biodigest + - biodigest.evaluation + - biodigest.evaluation.d_utils + - biodigest.evaluation.mappers + +about: + home: "http://pypi.python.org/pypi/biodigest/" + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: "In silico Validation of Disease and Gene Sets, Clusterings or Subnetworks (DIGEST)" From 75bf748f09b52708e80b9959c2845beb470ef8e6 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 15 Feb 2024 18:43:35 -0600 Subject: [PATCH 0487/1813] Add recipe for genbank v0.110 (#45822) --- recipes/genbank/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 recipes/genbank/meta.yaml diff --git a/recipes/genbank/meta.yaml b/recipes/genbank/meta.yaml new file mode 100644 index 0000000000000..d5a0c8f267aad --- /dev/null +++ b/recipes/genbank/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "genbank" %} +{% set version = "0.110" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/genbank-{{ version }}.tar.gz + sha256: f9a6ba243d62934e9e5ed283d8b475ab3dd9a3760ba329a054d5f6df54a8ec45 + +build: + number: 0 + skip: True # [py < 36] + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('genbank', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - python + - pip + run: + - python + +test: + imports: + - genbank + +about: + home: https://github.com/deprekate/genbank + summary: Code to work with Genbank files + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE From 5f4ac3af6d965024b97e98a79fbfd3629d170801 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 15 Feb 2024 19:41:20 -0600 Subject: [PATCH 0488/1813] Update peptide-shaker to 3.0.6 (#45823) --- recipes/peptide-shaker/meta.yaml | 4 ++-- recipes/peptide-shaker/peptide-shaker.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index 677a59a7abc65..3c16f06cf6d56 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the peptide-shaker.py file {% set name = "PeptideShaker" %} -{% set version = "3.0.4" %} -{% set sha256 = "e1317b51dda3e10348f74e544832169340939f056576d2f01ed13988e56e8214" %} +{% set version = "3.0.6" %} +{% set sha256 = "9356fb98d8d70bde35d3b37b0de24b5b76943ae9103a1af250018c0204062951" %} package: name: peptide-shaker diff --git a/recipes/peptide-shaker/peptide-shaker.py b/recipes/peptide-shaker/peptide-shaker.py index 98a22145a4cda..54aedb2ae0e6f 100755 --- a/recipes/peptide-shaker/peptide-shaker.py +++ b/recipes/peptide-shaker/peptide-shaker.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'PeptideShaker-3.0.4.jar' +jar_file = 'PeptideShaker-3.0.6.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From 12658df11789debda547fac825587c88cdb06454 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 22:31:54 -0500 Subject: [PATCH 0489/1813] Update phanotate to 1.6.4 (#45809) * Update phanotate to 1.6.4 * add run_exports * add genbank --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/phanotate/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/phanotate/meta.yaml b/recipes/phanotate/meta.yaml index 00d8dc1cede86..7965786cd5199 100644 --- a/recipes/phanotate/meta.yaml +++ b/recipes/phanotate/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phanotate" %} -{% set version = "1.5.1" %} +{% set version = "1.6.4" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "1c3b241d59b801f9023946ef3ba1090e4fc32a4ff5bd06ba0144320ae9693de6" + sha256: "315524223515c88a00b13104c91c1b85f8187e8eec5459bdf66046c30ff1e23f" build: - number: 1 - skip: True # [py27] - script: "{{ PYTHON }} -m pip install . --no-deps -vv " + number: 0 + skip: True # [py < 36] + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('phanotate', max_pin="x") }} requirements: build: @@ -21,6 +23,7 @@ requirements: - pip - python run: + - python - fastpath - matplotlib-base - scipy @@ -28,8 +31,8 @@ requirements: - statsmodels - backports.tempfile - textwrap3 - - setuptools - trnascan-se + - genbank test: commands: From 1ee998e61ca6893bd9f6415250caf25f0e5a88e3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 23:05:15 -0500 Subject: [PATCH 0490/1813] Update primer3-py to 2.0.3 (#45825) --- recipes/primer3-py/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primer3-py/meta.yaml b/recipes/primer3-py/meta.yaml index f9a31011d0db2..7eec666088e21 100644 --- a/recipes/primer3-py/meta.yaml +++ b/recipes/primer3-py/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primer3-py" %} -{% set version = "2.0.2" %} +{% set version = "2.0.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/primer3-py-{{ version }}.tar.gz - sha256: 1fa140cab651a2841ec71f3e29ef347e6546f644884e3cac1fe536c4feb8eb5c + sha256: 1ec6ce99ea149b1c82361c654a0eab824e698ce32d5f9ed2dd8f8f37564b3f5f build: number: 0 From daedd1782290f85126fee89a79ae75742d673890 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 15 Feb 2024 22:56:09 -0600 Subject: [PATCH 0491/1813] Update searchgui to 4.3.6 (#45824) * Update searchgui to 4.3.6 * restore build variable --- recipes/searchgui/meta.yaml | 4 ++-- recipes/searchgui/searchgui.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index 6108e9779ef2a..5f489c4eb2479 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the searchgui.py file {% set name = "SearchGUI" %} -{% set version = "4.3.5" %} -{% set sha256 = "51458d20745f83c88fe1041d0e3ff64b148538c63795a0b548c1aa3f7ca8f67d" %} +{% set version = "4.3.6" %} +{% set sha256 = "76c3662165e929a82d49408d344409b62057cb0c0cf6a4834b54585a756cf894" %} {% set build = "0" %} package: diff --git a/recipes/searchgui/searchgui.py b/recipes/searchgui/searchgui.py index f697c358d602e..c6c3cfb7c386d 100755 --- a/recipes/searchgui/searchgui.py +++ b/recipes/searchgui/searchgui.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'SearchGUI-4.3.5.jar' +jar_file = 'SearchGUI-4.3.6.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From 43485c94469f65574e8c8cad98b72cf7ba0884ed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 00:58:54 -0500 Subject: [PATCH 0492/1813] Update pbsim3 to 3.0.2 (#45827) --- recipes/pbsim3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbsim3/meta.yaml b/recipes/pbsim3/meta.yaml index 5a166dcaeb058..8b4d4a835b177 100644 --- a/recipes/pbsim3/meta.yaml +++ b/recipes/pbsim3/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbsim3" %} -{% set version = "3.0.1" %} -{% set sha256 = "4d2d0cabc1adfd1ade0cde983fb37f7e8af477c0fd7b09ef3e753742b89cc541" %} +{% set version = "3.0.2" %} +{% set sha256 = "db938d58bbe3003f36b0b6f9fdc5a190816ff1c30e1d7da53b87e0fb6aee4795" %} package: name: {{ name }} From 8170f6d428939d8c0715ad0a659c48a25a1d390e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 03:39:53 -0500 Subject: [PATCH 0493/1813] Update insilicoseq to 2.0.0 (#45816) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update insilicoseq to 2.0.0 * add run_exports * update checksums --------- Co-authored-by: mencian Co-authored-by: Hadrien Gourlé --- recipes/insilicoseq/checksums.md5 | 4 ++-- recipes/insilicoseq/meta.yaml | 12 +++++++++--- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/recipes/insilicoseq/checksums.md5 b/recipes/insilicoseq/checksums.md5 index 62eea9823d41f..d0cfecf9e2afb 100644 --- a/recipes/insilicoseq/checksums.md5 +++ b/recipes/insilicoseq/checksums.md5 @@ -1,2 +1,2 @@ -80319ebef7bd8f98c3d589c42ba852da bogus-reads_R1.fastq -f883f153efbbc1a1519c21f4829ba8dd bogus-reads_R2.fastq +9aeb0f7da8af96b9ce20270a50b20aec bogus-reads_R1.fastq +638e4fe4e8470feeb40e359995d803db bogus-reads_R2.fastq diff --git a/recipes/insilicoseq/meta.yaml b/recipes/insilicoseq/meta.yaml index 7270ab4cc77fe..d212e177e6070 100644 --- a/recipes/insilicoseq/meta.yaml +++ b/recipes/insilicoseq/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.6.0" %} -{% set sha256 = "4cbd8e30a17e9591899be42aaa776e0748907709ac56db8133050335f24d35e5" %} +{% set version = "2.0.0" %} +{% set sha256 = "1eb851ea345aaf46d8a5924516bbd55c8f957bb83ada8e9a995c1aae001d5d2a" %} package: name: insilicoseq @@ -13,8 +13,10 @@ build: noarch: python entry_points: - iss = iss.app:main - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv number: 0 + run_exports: + - {{ pin_subpackage('insilicoseq', max_pin="x") }} requirements: host: @@ -33,6 +35,8 @@ requirements: test: imports: - iss + commands: + - iss --help files: - bogus-genome.fasta.gz - checksums.md5 @@ -41,8 +45,10 @@ about: home: https://github.com/HadrienG/InSilicoSeq license: MIT license_family: MIT + license_file: LICENSE summary: A sequencing simulator. dev_url: https://github.com/HadrienG/InSilicoSeq + doc_url: https://insilicoseq.readthedocs.io/en/latest/ extra: recipe-maintainers: From e0fef40c9128cdf6c897a509eb94040975434234 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 09:24:11 -0500 Subject: [PATCH 0494/1813] Update badread to 0.4.1 (#45826) * Update badread to 0.4.1 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/badread/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/badread/meta.yaml b/recipes/badread/meta.yaml index 00bef0af70ac4..f787041f5d582 100644 --- a/recipes/badread/meta.yaml +++ b/recipes/badread/meta.yaml @@ -1,5 +1,5 @@ -{% set version='0.4.0' %} -{% set sha256='1920f1efc1eae7b17f1fd9c6878795b5ba8d7fd910c933999aad349672a994b0' %} +{% set version='0.4.1' %} +{% set sha256='236dee5ac99b8d0c1997c482df5b805908b0c34f75277ef706e897af71db1f9a' %} package: name: badread @@ -10,9 +10,11 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: python script: {{ PYTHON }} -m pip install . --no-deps -vv + run_exports: + - {{ pin_subpackage('badread', max_pin='x.x') }} requirements: host: From c5be54e785fd332f8747f3bb5171982ad9e864b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 10:15:31 -0500 Subject: [PATCH 0495/1813] Update bigscape to 1.1.9 (#45829) --- recipes/bigscape/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bigscape/meta.yaml b/recipes/bigscape/meta.yaml index 7915ed0a1a506..0809408af242a 100644 --- a/recipes/bigscape/meta.yaml +++ b/recipes/bigscape/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.8" %} -{% set sha256 = "9a9c256cb0464ca23408fe5a1738db21b8818b487216fb939d7aef037339a598" %} +{% set version = "1.1.9" %} +{% set sha256 = "ef0ddb5b433e0b1467ae5f96037fd6d23ebcba6bc08201d1421eba35d072e534" %} package: name: bigscape From ec73db304263a58405b3c5e46fdd8bc72c165738 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 11:39:00 -0500 Subject: [PATCH 0496/1813] Update pyhmmer to 0.10.5 (#45833) --- recipes/pyhmmer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 65622ccd0e60d..314fea094cdc4 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.4" %} +{% set version = "0.10.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 08bc02aadf0f113df2b2912478bb02be9daf5d322df9c72bcd07fa01fe53a87b + sha256: 1c9c6bb5600b96eb3386c524b24bf6eb1f51610017e82b585fe0f3b3c7cdbe03 build: number: 0 From afda3d1e73a18e605164c64793424e5bde316423 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 12:13:37 -0500 Subject: [PATCH 0497/1813] Update deeplcretrainer to 0.2.11 (#45831) * Update deeplcretrainer to 0.2.9 * Update deeplcretrainer to 0.2.10 * Update deeplcretrainer to 0.2.11 --- recipes/deeplcretrainer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/deeplcretrainer/meta.yaml b/recipes/deeplcretrainer/meta.yaml index 5d602ecfa1aa3..e3ad13723e94d 100644 --- a/recipes/deeplcretrainer/meta.yaml +++ b/recipes/deeplcretrainer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLCRetrainer" %} -{% set version = "0.2.8" %} -{% set sha256 = "73a9052d186921df42cfefce6215ee50f2a0abb3c4b1cef4a67126a59dfa7c9b" %} +{% set version = "0.2.11" %} +{% set sha256 = "99b1b2f41abb8d79638cc0731095e4b12bb7ca07ab1d64d87923e6b00154996b" %} package: name: {{ name|lower }} From 3776e777ec2cfebb6ff8601d6a98caddabaa1aab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 15:41:55 -0500 Subject: [PATCH 0498/1813] Update ucsc-cell-browser to 1.2.5 (#45841) --- recipes/ucsc-cell-browser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ucsc-cell-browser/meta.yaml b/recipes/ucsc-cell-browser/meta.yaml index a86e0702e4f9c..1dfd309f10ef8 100644 --- a/recipes/ucsc-cell-browser/meta.yaml +++ b/recipes/ucsc-cell-browser/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.2.4' %} +{% set version = '1.2.5' %} {% set name = "cellbrowser" %} package: @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "9c7414dd377ce36c290b1eef0763d0e9d0b8fa9ddc697f6bcfd1e2efa49e67f9" + sha256: "76757ff00f806f48d47831b0bd9df82aa9e170e4ce96629993a0e8ea5f539bf5" build: number: 0 From b185c34f5f905c12f92de539404e7caf04c0100d Mon Sep 17 00:00:00 2001 From: tlacroix Date: Fri, 16 Feb 2024 22:56:47 +0100 Subject: [PATCH 0499/1813] Update icescreen v1.3.2 (#45839) --- recipes/icescreen/meta.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/recipes/icescreen/meta.yaml b/recipes/icescreen/meta.yaml index a1d4fdde1d551..09c46a851ab4f 100644 --- a/recipes/icescreen/meta.yaml +++ b/recipes/icescreen/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ICEscreen" %} -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/archive/v{{ version }}/icescreen-v{{ version }}.tar.gz - sha256: 283fb2bf95eb9066a535a25f7df94f6ec9d4b78083d62bd5237f801e94ac02d5 + sha256: f8d691891bd92e2dc4a72b14a5404645d26f30d3fbe09d407b45c548d37f2ca3 build: number: 0 @@ -23,11 +23,11 @@ requirements: run: - python - pandas >=2.1.0 - - snakemake-minimal >=7.32 - - biopython =1.81 - - bcbio-gff =0.7.0 - - blast =2.12 - - hmmer =3.3.2 + - snakemake-minimal >=8.4 + - biopython =1.83 + - blast =2.15 + - hmmer =3.4 + - pyarrow test: commands: @@ -38,7 +38,7 @@ about: license: AGPL-3.0-or-later license_family: AGPL summary: "ICEscreen detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes." - doc_url: icescreen.migale.inrae.fr + doc_url: https://icescreen.migale.inrae.fr extra: recipe-maintainers: From 9bfd2cbae7c2ba9f881af8b581f45264f6820a8d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 16:57:43 -0500 Subject: [PATCH 0500/1813] Update ncbi-datasets-pylib to 16.4.8 (#45838) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index adb9708118530..dcd72174fd033 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.7" %} -{% set sha256 = "6d637d0b730426a35fa89f8107ada4573abe374214a1c93f9bafdb265986c9f4" %} +{% set version = "16.4.8" %} +{% set sha256 = "5c08fc546170079034be19f53468667114d0695ab348bb2c04794141a9a6ed3c" %} package: name: {{ name|lower }} From bd25bc559e2a311a22dea8fff3fb7b9e22ca3697 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Fri, 16 Feb 2024 22:58:18 +0100 Subject: [PATCH 0501/1813] fix: pin gffutils python to <3.12 (#45828) * fix: pin gffutils python to <3.12 * fix: add run_exports following best practices from docs * do as I'm told... --- recipes/gffutils/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/gffutils/meta.yaml b/recipes/gffutils/meta.yaml index f1f35d06d9903..30f72adae5628 100644 --- a/recipes/gffutils/meta.yaml +++ b/recipes/gffutils/meta.yaml @@ -12,8 +12,10 @@ source: build: noarch: python - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: @@ -23,7 +25,7 @@ requirements: - argcomplete >=1.9.4 - argh >=0.26.2 - pyfaidx >=0.5.5.2 - - python + - python <3.12 - simplejson - six >=1.12.0 From 2a710bda4eba5fd000be175a534979baac076406 Mon Sep 17 00:00:00 2001 From: SantaMcCloud <100047964+SantaMcCloud@users.noreply.github.com> Date: Fri, 16 Feb 2024 22:58:30 +0100 Subject: [PATCH 0502/1813] Update bigscape to 1.1.9 (#45836) * update bigscape to the newest version * Update bigscape to 1.1.8 * Update bigscape recipe From 0ef3d3e69e3e535b185adccd6dade1b587f3a38e Mon Sep 17 00:00:00 2001 From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com> Date: Fri, 16 Feb 2024 13:58:38 -0800 Subject: [PATCH 0503/1813] Update/fix kb-python (#45808) * kb python compatibility kb build fails due to obscure pysam incompatibilities on python 3.9. * Update meta.yaml --- recipes/kb-python/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/kb-python/meta.yaml b/recipes/kb-python/meta.yaml index 23a0ad79fcaaa..840469c6ff8be 100644 --- a/recipes/kb-python/meta.yaml +++ b/recipes/kb-python/meta.yaml @@ -11,7 +11,7 @@ source: patches: config.py.patch build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" entry_points: @@ -21,10 +21,10 @@ build: requirements: host: - - python >=3.7 + - python >=3.7, <3.9 - pip run: - - python >=3.7 + - python >=3.7, <3.9 - anndata >=0.6.22.post1 - h5py >=2.10.0 - jinja2 >2.10.1 From f08a1a340ed7f0e8d65c63b1b037ea0c4086979b Mon Sep 17 00:00:00 2001 From: Ryan James Kennedy <67742838+ryanjameskennedy@users.noreply.github.com> Date: Fri, 16 Feb 2024 22:58:48 +0100 Subject: [PATCH 0504/1813] Add git to serotypefinder (#45837) --- recipes/serotypefinder/build.sh | 8 ++++---- recipes/serotypefinder/meta.yaml | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/serotypefinder/build.sh b/recipes/serotypefinder/build.sh index 448adcd673160..bdcf3a4a8221e 100644 --- a/recipes/serotypefinder/build.sh +++ b/recipes/serotypefinder/build.sh @@ -5,10 +5,6 @@ mkdir -p ${PREFIX}/bin chmod +x serotypefinder.py cp serotypefinder.py ${PREFIX}/bin/serotypefinder -# copy script to download database -chmod +x ${RECIPE_DIR}/update-serotypefinder-db.sh -cp ${RECIPE_DIR}/update-serotypefinder-db.sh ${PREFIX}/bin/update-serotypefinder-db - # create folder for database download target=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION} mkdir -p ${target}/db/ @@ -18,6 +14,10 @@ touch ${target}/db/.empty cp ${RECIPE_DIR}/download-db.sh ${PREFIX}/bin chmod +x ${PREFIX}/bin/download-db.sh +# copy script to download database +chmod +x ${RECIPE_DIR}/update-serotypefinder-db.sh +cp ${RECIPE_DIR}/update-serotypefinder-db.sh ${PREFIX}/bin/update-serotypefinder-db + # set SEROTYPEFINDER_DB variable on env activation mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d cat <> ${PREFIX}/etc/conda/activate.d/serotypefinder.sh diff --git a/recipes/serotypefinder/meta.yaml b/recipes/serotypefinder/meta.yaml index 6fb2ab6ca1434..9bbaafbbaa65d 100644 --- a/recipes/serotypefinder/meta.yaml +++ b/recipes/serotypefinder/meta.yaml @@ -12,7 +12,7 @@ source: - database_path.patch build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('serotypefinder', max_pin="x") }} @@ -27,7 +27,7 @@ requirements: - kma - python >=3.8 - tabulate >=0.8.9 - + - git test: commands: From 5b3a21f9dd00e777da23397df139ecb8bfddac3d Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" <19176506+pdimens@users.noreply.github.com> Date: Fri, 16 Feb 2024 17:01:44 -0500 Subject: [PATCH 0505/1813] Update harpy build to use smaller release instead of source (#45843) * Update harpy build to use smaller release instead of source * add license to tarball --- recipes/harpy/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index f5a78e0b92088..83fd39527998c 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,17 +1,17 @@ {% set version = "0.5.0" %} -{% set sha256 = "77ba116665fd00a945b65072b86b4c54f672b1b74912309709f580f7329b4adf" %} +{% set sha256 = "58d407059057f6f3aa6213e2bbb00bf9d920b405fe435baf88837d60b5cc0d08" %} package: name: harpy version: '{{ version }}' source: - url: https://github.com/pdimens/harpy/archive/{{ version }}.tar.gz + url: https://github.com/pdimens/harpy/releases/download/{{ version }}/harpy.{{ version }}.tar.gz sha256: '{{ sha256 }}' build: skip: True # [osx] - number: 0 + number: 1 missing_dso_whitelist: - /lib64/libstdc++.so.6 - /lib64/libc.so.6 From 87ba75b0a8f6fb9d75dcf47762f3b571a7c42670 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Fri, 16 Feb 2024 23:05:52 +0000 Subject: [PATCH 0506/1813] added recipe for tracegroomer (#45814) * added recipe for tracegroomer * added home and summary --- recipes/tracegroomer/meta.yaml | 59 ++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 recipes/tracegroomer/meta.yaml diff --git a/recipes/tracegroomer/meta.yaml b/recipes/tracegroomer/meta.yaml new file mode 100644 index 0000000000000..d6ea7f2606309 --- /dev/null +++ b/recipes/tracegroomer/meta.yaml @@ -0,0 +1,59 @@ +{% set name = "tracegroomer" %} +{% set version = "0.1.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/tracegroomer-{{ version }}.tar.gz + sha256: 87728daf011976062eabb7967b3b286d7905b4cd5b92387bc1b3f07abfd6cf16 + +build: + entry_points: + - tracegroomer = tracegroomer.__main__:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('tracegroomer', max_pin="x") }} + +requirements: + host: + - python >=3.10,<4.0 + - poetry-core + - pip + run: + - python >=3.10.0,<4.0.0 + - sphinx >=7.2.6,<8.0.0 + - click >=8.1.7,<9.0.0 + - matplotlib-base >=3.8.2,<4.0.0 + - mypy >=1.8.0,<2.0.0 + - numpy >=1.26.4,<2.0.0 + - pandas >=2.2.0,<3.0.0 + - scipy >=1.12.0,<2.0.0 + - scikit-learn >=1.4.0,<2.0.0 + - seaborn >=0.13.2,<0.14.0 + - openpyxl >=3.1.2,<4.0.0 + - pyyaml >=6.0.1,<7.0.0 + - python-dotenv >=1.0.1,<2.0.0 + - pydantic >=1.10.8,<2.0.0 + +test: + imports: + - tracegroomer + commands: + - pip check + - tracegroomer --help + requires: + - pip + +about: + summary: 'Format and normalise tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet analysis.' + license: MIT + license_file: LICENSE + home: 'https://github.com/cbib/TraceGroomer' + +extra: + recipe-maintainers: + - hechth From a748dd766d220512a31d691437a7588a6cec77e6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 17 Feb 2024 02:48:43 -0500 Subject: [PATCH 0507/1813] Update viralmsa to 1.1.44 (#45850) --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 8c476c2293244..7f8cf82f1cbac 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.43" %} +{% set version = "1.1.44" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: 15adaed42f65e2b6a0ba7e6db498fd67f3227b4658f555313194d5b73234ed89 + sha256: a3f90307b86e6171beadc61bfc09309570d51d9b21085a6c74054b86a8991026 requirements: run: From 5dc4c4d9f0d9619a282568753d11d13bc44ed14a Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Sat, 17 Feb 2024 10:11:25 -0800 Subject: [PATCH 0508/1813] Update nextclade to 3.2.1 (#45853) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index b53743caebf7f..174aad8dc0c36 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.2.0" %} +{% set version = "3.2.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 392f5b980f291f1580cfc09abc51779955c83811aa0537f6dba7d755e03c8fa9 # [linux64] + sha256: 797d9dab371dad8fcd65d6fe8347f8e3caa21243a930b0b422cb0e68f2039b57 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: deabdd06b1e6b6052c0ae50985b36db9839dfd8393de3a8d44b812b4b8b52cf6 # [osx and x86_64] + sha256: 9be0cca8dcf580bed2aa1746d8117a29711b72c96029ac960ca29e715f51abf3 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: 3b6185ff3741da4f15bd382f2f3c9cefb342e8add90a29be6050e20e4b3e66d2 # [arm64] + sha256: e2dbf3d2fa624f8926068dee7a678d867bfbe607fa2efefe7ca0d2f478f8df1a # [arm64] build: number: 0 From 384d509988a4f136023d180dd9bbeac0d6f32640 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 17 Feb 2024 13:27:17 -0500 Subject: [PATCH 0509/1813] Update harpy to 0.6.0 (#45844) --- recipes/harpy/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index 83fd39527998c..f51726858a1c8 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.5.0" %} -{% set sha256 = "58d407059057f6f3aa6213e2bbb00bf9d920b405fe435baf88837d60b5cc0d08" %} +{% set version = "0.6.0" %} +{% set sha256 = "3b7010054c3cafb19ae6973154015e17cd4688966237af90f5584d933eec86b3" %} package: name: harpy @@ -11,7 +11,7 @@ source: build: skip: True # [osx] - number: 1 + number: 0 missing_dso_whitelist: - /lib64/libstdc++.so.6 - /lib64/libc.so.6 From 904e5f3200a594782ea6975a78048a9b4bb2082a Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Sat, 17 Feb 2024 13:57:40 -0500 Subject: [PATCH 0510/1813] Create build.sh (#45849) * Create build.sh * Create meta.yaml * Update meta.yaml * add oarfish * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml Add dash --- recipes/oarfish/build.sh | 7 +++++++ recipes/oarfish/meta.yaml | 30 ++++++++++++++++++++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 recipes/oarfish/build.sh create mode 100644 recipes/oarfish/meta.yaml diff --git a/recipes/oarfish/build.sh b/recipes/oarfish/build.sh new file mode 100644 index 0000000000000..3c3929c054e07 --- /dev/null +++ b/recipes/oarfish/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash -euo +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . diff --git a/recipes/oarfish/meta.yaml b/recipes/oarfish/meta.yaml new file mode 100644 index 0000000000000..d571d3d5e4b3f --- /dev/null +++ b/recipes/oarfish/meta.yaml @@ -0,0 +1,30 @@ +{% set version = "0.2.0" %} + +package: + name: oarfish + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("oarfish", max_pin="x.x") }} + +source: + url: https://github.com/COMBINE-lab/oarfish/archive/v{{ version }}.tar.gz + sha256: 47e9ad6ae8af5f96eac16f294052319948a25892a9554c36ac5fe73646f20c2e + +requirements: + build: + - {{ compiler('rust') }} + host: + run: + +test: + commands: + - oarfish --help + +about: + home: https://github.com/COMBINE-lab/oarfish + license: BSD-3-Clause + license_file: LICENSE + summary: oarfish is a tool for fast, accurate and versatile transcript quantification from long-read RNA-seq data From f91528660bbe699d24fe92b828a7d0c395f1a85a Mon Sep 17 00:00:00 2001 From: pirovc <4673375+pirovc@users.noreply.github.com> Date: Sun, 18 Feb 2024 09:28:40 +0100 Subject: [PATCH 0511/1813] Update ganon to 2.1.0 (#45760) * ganon version 2.1.0 * add dep. test * add dep. test * Update meta.yaml * Update meta.yaml --------- Co-authored-by: James A. Fellows Yates --- recipes/ganon/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/ganon/meta.yaml b/recipes/ganon/meta.yaml index 3f42b377f4284..8138ce24f94e8 100755 --- a/recipes/ganon/meta.yaml +++ b/recipes/ganon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ganon" %} -{% set version = "2.0.1" %} +{% set version = "2.1.0" %} package: name: "{{ name|lower }}" @@ -8,7 +8,7 @@ package: source: - folder: ganon url: https://github.com/pirovc/{{ name }}/archive/{{ version }}.tar.gz - sha256: e8050f9522e35fe41abd5425ebe35a292081ff179a6a42cd285002ba0ef89f5f + sha256: bba93f9c45c922d6d309fcb81dfeddac6ef5439852ff1c48a1e6fed299e29f8b - folder: robin-hood-hashing url: https://github.com/martinus/robin-hood-hashing/archive/refs/tags/3.11.3.tar.gz sha256: dcf2b7fa9ef9dd0c67102d94c28e8df3effbe1845e0ed1f31f4772ca5e857fc4 @@ -30,7 +30,7 @@ requirements: - catch2 ==2.* - cxxopts >=2.2.0 - python - - pandas >=1.1.0 + - pandas >=1.2.0 - multitax >=1.3.1 - genome_updater >=0.6.3 - grep @@ -38,10 +38,12 @@ requirements: - curl - diffutils - zlib + - parameterized >=0.9.0 + - raptor ==3.* run: - bzip2 - python - - pandas >=1.1.0 + - pandas >=1.2.0 - multitax >=1.3.1 - genome_updater >=0.6.3 - grep @@ -49,7 +51,7 @@ requirements: - curl - diffutils - zlib - - raptor ==3.0.1 + - raptor ==3.* test: commands: From f509ec5519baaf13597469b3d308cd9563ca91c9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 03:29:02 -0500 Subject: [PATCH 0512/1813] Update tsebra to 1.1.2.3 (#45854) --- recipes/tsebra/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tsebra/meta.yaml b/recipes/tsebra/meta.yaml index d0c23407dc092..025b3cec0dc83 100644 --- a/recipes/tsebra/meta.yaml +++ b/recipes/tsebra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.2.2" %} +{% set version = "1.1.2.3" %} {% set name = "tsebra" %} -{% set sha256 = "e055efea29d3b73a6202c56fb9256bf6006005ef54c8a5de83b9aa0377fff27c" %} +{% set sha256 = "bdba8f114a75bd822e7af475f09bc433d1b673902ec09e1ed1f735d21ea80222" %} package: name: "{{ name }}" From 30162a617d26c62336565efb87d774b8e23eeaa7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 03:29:42 -0500 Subject: [PATCH 0513/1813] Update braker3 to 3.0.8 (#45856) --- recipes/braker3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/braker3/meta.yaml b/recipes/braker3/meta.yaml index cbf46b0d20506..174a5deb011ec 100644 --- a/recipes/braker3/meta.yaml +++ b/recipes/braker3/meta.yaml @@ -1,6 +1,6 @@ {% set name = "BRAKER3" %} -{% set version = "3.0.7" %} -{% set sha256 = "578b51538e9d18c6f4d8892452d05d59b9126dcfbb6a32a1fe6f70c210370c96" %} +{% set version = "3.0.8" %} +{% set sha256 = "f2623290c3007a3e42719a0bb2713bec7226db222bfef742895a9d5d0b4ee526" %} package: name: "{{ name|lower }}" From 3c30769f404a42ecb1cf7664b3b28380d6a1366b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 04:03:55 -0500 Subject: [PATCH 0514/1813] Update f5c to 1.4 (#45857) --- recipes/f5c/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/f5c/meta.yaml b/recipes/f5c/meta.yaml index 55b96f9534adf..5b8c3e4ee649d 100644 --- a/recipes/f5c/meta.yaml +++ b/recipes/f5c/meta.yaml @@ -1,5 +1,5 @@ {% set name = "f5c" %} -{% set version = "1.3" %} +{% set version = "1.4" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/hasindu2008/f5c/releases/download/v{{ version }}/f5c-v{{ version }}-release.tar.gz - sha256: 5688016fe92c8dc6dc5124d4d81bf2ad0ed5fcd78ea0d0a1995f5c868ea1f819 + sha256: 9336b35caf6486f9fffc791591ef7b40bea9156ecfb1d315fe222b6e9957d632 build: number: 0 From ab4b62aafcde57973aa11147d20a7b7e2ae3c24f Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Sun, 18 Feb 2024 04:04:25 -0500 Subject: [PATCH 0515/1813] add piscem-infer (#45852) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * add piscem-infer * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Rename build.sh to build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/piscem-infer/build.sh | 8 ++++++++ recipes/piscem-infer/meta.yaml | 31 +++++++++++++++++++++++++++++++ 2 files changed, 39 insertions(+) create mode 100644 recipes/piscem-infer/build.sh create mode 100644 recipes/piscem-infer/meta.yaml diff --git a/recipes/piscem-infer/build.sh b/recipes/piscem-infer/build.sh new file mode 100644 index 0000000000000..fd9c0897999fd --- /dev/null +++ b/recipes/piscem-infer/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -euo +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . + diff --git a/recipes/piscem-infer/meta.yaml b/recipes/piscem-infer/meta.yaml new file mode 100644 index 0000000000000..01b9ea8560cea --- /dev/null +++ b/recipes/piscem-infer/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "0.5.2" %} + +package: + name: piscem-infer + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("piscem-infer", max_pin="x.x") }} + +source: + url: https://github.com/COMBINE-lab/piscem-infer/archive/v{{ version }}.tar.gz + sha256: 95bdab6724428ebb05dc7459ea717857e2c90fb3fe1065d131858a70273a16c5 + +requirements: + build: + - rust >=1.75 + - {{ compiler('rust') }} + host: + run: + +test: + commands: + - piscem-infer --help + +about: + home: https://github.com/COMBINE-lab/piscem-infer + license: BSD-3-Clause + license_file: LICENSE + summary: piscem-infer is a flexible tool to perform target quantification from bulk-sequencing data From b010c5d6842c4057ce94ab368e60568a66203503 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 04:05:03 -0500 Subject: [PATCH 0516/1813] Update tracegroomer to 0.1.2 (#45848) --- recipes/tracegroomer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tracegroomer/meta.yaml b/recipes/tracegroomer/meta.yaml index d6ea7f2606309..5b435366e63af 100644 --- a/recipes/tracegroomer/meta.yaml +++ b/recipes/tracegroomer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tracegroomer" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/tracegroomer-{{ version }}.tar.gz - sha256: 87728daf011976062eabb7967b3b286d7905b4cd5b92387bc1b3f07abfd6cf16 + sha256: a1b951583f6016d96799a270def0472b6b7a93c5fe94e685fb30916f73d32662 build: entry_points: From 5f8b68840262f175a39da0a83b3de64b32c215cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 04:05:16 -0500 Subject: [PATCH 0517/1813] Update augur to 24.2.2 (#45847) --- recipes/augur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index acab680fa5d8b..ab32c10e43f51 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.2.1" %} +{% set version = "24.2.2" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: c1fe7c357357d9b73dd614db7641695bbd780d884bebe2fb6082f19a28bb0f3b + sha256: f15359e193163ce397a2bc056d0f495fbddb223544af1b5956204cf135b79c11 build: number: 0 From 484130cb4fd11f852e972dad3b9a72cf2e72418f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 11:13:10 -0500 Subject: [PATCH 0518/1813] Update snakemake to 8.4.9 (#45858) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 9fc08ce4c7cbd..a226a8f3ff36b 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.8" %} +{% set version = "8.4.9" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: ab64a4f402f78ec252f211d9cc900344fdc2a000dadcec91833efb5fd0f275e7 + sha256: 6bd24c39110a8d6744d09aab5ca71bde0c4559542ec7f58e52a6c4d360120171 build: number: 0 From 1739f1aa2e51b413844c4a7e10cf527bdba701a7 Mon Sep 17 00:00:00 2001 From: Tim Dunn <13918078+TimD1@users.noreply.github.com> Date: Sun, 18 Feb 2024 11:26:32 -0500 Subject: [PATCH 0519/1813] Add vcfdist package (#45815) * First vcfdist recipe build attempt. * Added pin_subpackage() * Added 'cd src' * Update build.sh Added 'cd src' * Updated vcfdist version with more compatible Makefile. * Add BASH path exports * C++ version of path variables * Updated vcfdist source to v2.4.0 * Update meta.yaml --- recipes/vcfdist/build.sh | 9 ++++++ recipes/vcfdist/conda_build_config.yaml | 4 +++ recipes/vcfdist/meta.yaml | 42 +++++++++++++++++++++++++ 3 files changed, 55 insertions(+) create mode 100644 recipes/vcfdist/build.sh create mode 100644 recipes/vcfdist/conda_build_config.yaml create mode 100644 recipes/vcfdist/meta.yaml diff --git a/recipes/vcfdist/build.sh b/recipes/vcfdist/build.sh new file mode 100644 index 0000000000000..ba9402cf841f3 --- /dev/null +++ b/recipes/vcfdist/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +export CPATH="${PREFIX}/include" +export CPLUS_INCLUDE_PATH="${PREFIX}/include" +export LD_LIBRARY_PATH="${PREFIX}/lib" + +cd src && make +install -d "${PREFIX}/bin" +install vcfdist "${PREFIX}/bin" diff --git a/recipes/vcfdist/conda_build_config.yaml b/recipes/vcfdist/conda_build_config.yaml new file mode 100644 index 0000000000000..50a90b77e33c2 --- /dev/null +++ b/recipes/vcfdist/conda_build_config.yaml @@ -0,0 +1,4 @@ +htslib: + - 1.17 +pin_run_as_build: + htslib: x.x diff --git a/recipes/vcfdist/meta.yaml b/recipes/vcfdist/meta.yaml new file mode 100644 index 0000000000000..bd4e85ad61cf7 --- /dev/null +++ b/recipes/vcfdist/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "2.4.0" %} +{% set sha256 = "bdb1bc84229f2bb81c9a4b5ee005b4f586895c320f504fbd1f983a0ef1cd6bb6" %} + +package: + name: vcfdist + version: {{ version }} + +source: + url: https://github.com/TimD1/vcfdist/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("vcfdist", max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + - htslib + run: + - htslib + +test: + commands: + - vcfdist --version + +about: + summary: 'vcfdist: benchmarking phased germline variant calls in VCF format' + home: https://github.com/TimD1/vcfdist + license: GPL-3.0-only + license_family: GPL3 + license_file: LICENSE + doc_url: https://github.com/TimD1/vcfdist/wiki + +extra: + maintainers: + - TimD1 + identifiers: + - doi:10.5281/zenodo.8368282 From c39ede249700fef5578b3ceac5025d1e69e4cb04 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 14:49:46 -0500 Subject: [PATCH 0520/1813] Update r-pscbs to 0.67.0 (#45855) * Update r-pscbs to 0.67.0 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-pscbs/meta.yaml | 51 +++++++++++++++++++++------------------ 1 file changed, 27 insertions(+), 24 deletions(-) diff --git a/recipes/r-pscbs/meta.yaml b/recipes/r-pscbs/meta.yaml index dba0c9851e2ea..6b9486d7121bf 100644 --- a/recipes/r-pscbs/meta.yaml +++ b/recipes/r-pscbs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.66.0' %} +{% set version = '0.67.0' %} package: name: r-pscbs @@ -8,48 +8,51 @@ source: url: - {{ cran_mirror }}/src/contrib/PSCBS_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/PSCBS/PSCBS_{{ version }}.tar.gz - sha256: 58805636e55e0fd3f57bd4a0e296a8bb3d57a7bdd0fdd5868a73ddc83d173a93 + sha256: 2695d18d197a3bd729cca0940248ddc1880e4f54da95b9ecc5eda002a715cdbe build: noarch: generic - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-pscbs', max_pin="x") }} requirements: host: - r-base - - bioconductor-dnacopy - - r-r.cache >=0.13.0 - - r-r.methodss3 >=1.7.1 - - r-r.oo >=1.22.0 - - r-r.utils >=2.8.0 - - bioconductor-aroma.light - - r-future >=1.12.0 - - r-listenv >=0.7.0 - - r-matrixstats >=0.54.0 + - bioconductor-dnacopy >=1.42.0 + - r-r.cache >=0.16.0 + - r-r.methodss3 >=1.8.2 + - r-r.oo >=1.25.0 + - r-r.utils >=2.12.0 + - bioconductor-aroma.light >=2.4.0 + - r-future >=1.28.0 + - r-listenv >=0.8.0 + - r-matrixstats >=0.62.0 run: - r-base - - bioconductor-dnacopy - - r-r.cache >=0.13.0 - - r-r.methodss3 >=1.7.1 - - r-r.oo >=1.22.0 - - r-r.utils >=2.8.0 - - bioconductor-aroma.light - - r-future >=1.12.0 - - r-listenv >=0.7.0 - - r-matrixstats >=0.54.0 + - bioconductor-dnacopy >=1.42.0 + - r-r.cache >=0.16.0 + - r-r.methodss3 >=1.8.2 + - r-r.oo >=1.25.0 + - r-r.utils >=2.12.0 + - bioconductor-aroma.light >=2.4.0 + - r-future >=1.28.0 + - r-listenv >=0.8.0 + - r-matrixstats >=0.62.0 test: commands: - - $R -e "library('PSCBS')" # [not win] - - "\"%R%\" -e \"library('PSCBS')\"" # [win] + - $R -e "library('PSCBS')" about: home: https://github.com/HenrikBengtsson/PSCBS - license: GPL (>= 2) + license: GPL-2.0-or-later summary: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported. license_family: GPL3 + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' From d9b316841debf8e0eb1b446157e8c0ec6e0c43cb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 15:50:38 -0500 Subject: [PATCH 0521/1813] Update panaroo to 1.4.1 (#45863) --- recipes/panaroo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/panaroo/meta.yaml b/recipes/panaroo/meta.yaml index 8d83ad1beb7c2..a85cb44af1e88 100644 --- a/recipes/panaroo/meta.yaml +++ b/recipes/panaroo/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.0" %} +{% set version = "1.4.1" %} {% set name = "panaroo" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/gtonkinhill/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 651a11c9326bf885709ad555722ffefc5f67a365dce8a6475c09cd8d3537a89c + sha256: 5ff88a48b339083bcbf843e84eeff3be5f9eda3808394da436386ce0cdfc0111 build: number: 0 From d0bdddf995f4f863d3b4fb1eaed7c4b06b2a3f7b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 05:58:18 -0500 Subject: [PATCH 0522/1813] Update clipkit to 2.2.2 (#45864) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index 63fb201258cb4..7c62e3cce5c85 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.2.0" %} +{% set version = "2.2.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7f973cec1842a3066c1478752b8692012174f5a58df870c1518a56cd37264605 + sha256: 76e13db515a951490e9ed6a86955c6207fae3292fb62b6d8adef7ac4a235077a build: number: 0 From 2bd3ef33f80a6c81b2cd0839c396fc6ded662f4a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 06:02:50 -0500 Subject: [PATCH 0523/1813] Update r-aroma.affymetrix to 3.2.2 (#45866) * Update r-aroma.affymetrix to 3.2.2 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-aroma.affymetrix/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/r-aroma.affymetrix/meta.yaml b/recipes/r-aroma.affymetrix/meta.yaml index b28a7de9263f0..c8237d9eb4f99 100644 --- a/recipes/r-aroma.affymetrix/meta.yaml +++ b/recipes/r-aroma.affymetrix/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '3.2.1' %} +{% set version = '3.2.2' %} package: name: r-aroma.affymetrix @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/aroma.affymetrix_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/aroma.affymetrix/aroma.affymetrix_{{ version }}.tar.gz - sha256: 7aefbbddf94f6fc0ee2dec261f0caa6ca28d5f36aa7f7534ffb5f4e10ec4f5fb + sha256: 18e1c9479e3e41bdfff06769d0ff2d85fcae16042cfd0eefa4dbcd0c4f3c9c40 build: noarch: generic - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-aroma.affymetrix', max_pin="x.x") }} requirements: host: @@ -60,3 +62,5 @@ about: Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006. license_family: LGPL + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' From 3fdc25c682fc79fadd3cf62f7cbb02d419d97430 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 19 Feb 2024 12:28:12 +0100 Subject: [PATCH 0524/1813] add snakemake-interface-report-plugins (#45871) --- .../meta.yaml | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 recipes/snakemake-interface-report-plugins/meta.yaml diff --git a/recipes/snakemake-interface-report-plugins/meta.yaml b/recipes/snakemake-interface-report-plugins/meta.yaml new file mode 100644 index 0000000000000..16c4632e6a84d --- /dev/null +++ b/recipes/snakemake-interface-report-plugins/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "snakemake-interface-report-plugins" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_report_plugins-{{ version }}.tar.gz + sha256: 02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage("snakemake-interface-report-plugins", max_pin="x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.16.0,<2.0.0 + +test: + imports: + - snakemake_interface_report_plugins + commands: + - pip check + requires: + - pip + +about: + summary: This package provides a stable interface for interactions between Snakemake and its report plugins. + home: https://github.com/snakemake/snakemake-interface-report-plugins + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab From e3eb1d648b5afac66443e835a3d9a0b0d5fc2d3d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:15:12 -0500 Subject: [PATCH 0525/1813] Update genoboo to 0.4.13 (#45620) * Update genoboo to 0.4.13 * fix build * fix osx --------- Co-authored-by: Anthony Bretaudeau --- recipes/genoboo/build.sh | 7 +++++-- recipes/genoboo/meta.yaml | 4 ++-- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/genoboo/build.sh b/recipes/genoboo/build.sh index 76a76236e8b16..d42cfaa60bf28 100644 --- a/recipes/genoboo/build.sh +++ b/recipes/genoboo/build.sh @@ -11,17 +11,20 @@ export ARCH=$(uname -m) export HOME="$(mktemp -d)" # Install meteor here (instead of in npm run bundle) because we need to patch the install script -curl "https://install.meteor.com/?release=2.8.0" > meteor.sh +curl "https://install.meteor.com/?release=2.13.3" > meteor.sh chmod a+x meteor.sh sed -i.bak 's|PREFIX=|#PREFIX=|' meteor.sh ./meteor.sh +sed -i.bak 's/"preinstall".*/"preinstall":"",/g' package.json + npm install --unsafe-perm export PATH=$PATH:"$HOME/.meteor" # Now run the normal gnb install -METEOR_ALLOW_SUPERUSER=1 METEOR_DISABLE_OPTIMISTIC_CACHING=1 npm run bundle + +TOOL_NODE_FLAGS="--max-old-space-size=2048" METEOR_ALLOW_SUPERUSER=1 METEOR_DISABLE_OPTIMISTIC_CACHING=1 npm run bundle cp -R genoboo_v${PKG_VERSION}/* $outdir diff --git a/recipes/genoboo/meta.yaml b/recipes/genoboo/meta.yaml index 1ea6112da89ba..5a1a8efef34fd 100644 --- a/recipes/genoboo/meta.yaml +++ b/recipes/genoboo/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'genoboo' %} -{% set version = '0.4.12' %} -{% set sha256 = 'd8c280a174360c03ad4be4292e628ccf416a170771a369aa4bf32a5cebf1085e' %} +{% set version = '0.4.13' %} +{% set sha256 = '7a300f2cc9d885e2c5bf51ddcbdd9c952ef3f74d5801918e0f9114cdc3991b41' %} package: name: {{ name|lower }} From 0f6f34ce1bff1e48b0ca4e9476e17b838c664f42 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:26:23 -0500 Subject: [PATCH 0526/1813] Update last to 1542 (#45868) --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 9298623f84248..8c7b6b9fae609 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1541" %} +{% set version = "1542" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 80165ad97bd651b038ca187cc990c930ec96a0a9f5715a2179b5b75304ed64f9 + sha256: ee26e762fe76d167241f7e85b5e72ef8d17ed243c405e38dbbd06de97003596a build: number: 0 From df1a6dce2ad3256dc7e455de5f4a32763e2c5d2e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:26:29 -0500 Subject: [PATCH 0527/1813] Update pybiolib to 1.1.1749 (#45870) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 4d20a5881de64..1b55ef019fc9c 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1747" %} +{% set version = "1.1.1749" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: b6e014d302e0551db14697ec438ec07fecbf7bdd3634ccd22a47c4410a7a7839 + sha256: ec24fc1418b84918ffa85a9bf7a251e102e3dd025eb9460745ba19ba32600bf3 build: noarch: python From 7c475b97a8f01118629dfea63cc39616baf2b9df Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:26:42 -0500 Subject: [PATCH 0528/1813] Update snakemake-interface-storage-plugins to 3.1.0 (#45874) --- recipes/snakemake-interface-storage-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-storage-plugins/meta.yaml b/recipes/snakemake-interface-storage-plugins/meta.yaml index f3ebb462501db..8ca9b30fbc900 100644 --- a/recipes/snakemake-interface-storage-plugins/meta.yaml +++ b/recipes/snakemake-interface-storage-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-storage-plugins" %} -{% set version = "3.0.0" %} +{% set version = "3.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_storage_plugins-{{ version }}.tar.gz - sha256: f20d85ee7e86a1e2ffa3f72e2385dd5abb17fa7b58a26cba8ba59096872fe169 + sha256: 26e95be235ef2a9716b890ea96c3a9a2e62061c5d72fbb89c2fad2afada87304 build: noarch: python From fecd00da9403514558df82e2478521020e235e6a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:27:06 -0500 Subject: [PATCH 0529/1813] Update reframed to 1.5.1 (#45875) --- recipes/reframed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/reframed/meta.yaml b/recipes/reframed/meta.yaml index 5bc8f8eec8325..257bf77160da5 100644 --- a/recipes/reframed/meta.yaml +++ b/recipes/reframed/meta.yaml @@ -1,5 +1,5 @@ {% set name = "reframed" %} -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/reframed-{{ version }}.tar.gz - sha256: 2f40e631080be7aa8f2ea1c1f4b1ffa5cf52e87e4279978b6c72c7bb690dc1c1 + sha256: cded8ba31fa1dcddb358f79122cbe5d1f4562a538a4058045d462b50d7fc71c8 build: noarch: python From 9b4e5709319db9990b6144852261ae5c80e40677 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:27:19 -0500 Subject: [PATCH 0530/1813] Update snakemake-interface-common to 1.17.0 (#45876) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index f7298deb2e3a2..38e66d2a7ae0f 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.16.0" %} +{% set version = "1.17.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: b0780b9c3525435031815fd1f01079828d55c83fef18b5a0b05caa965408046b + sha256: d1f0cb83611f24f62ec5af852cee1cef429dd4e86c55bf373092fc682acac133 build: noarch: python From 8f2c8a65d655fd42e2d01c4bb2a4b45ff360543b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:28:41 -0500 Subject: [PATCH 0531/1813] Update nanomotif to 0.1.19 (#45878) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index afe275f534641..8620e63a0f280 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.18" %} +{% set version = "0.1.19" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: a8a4e7bfe21617c51003ae9d0ed056b1a5380d7df83b3d115cd079d06e8cd116 + sha256: e62cc67dc23bc185aa9af77420e53be0d820fa70880d1b048c522d646def75ef build: entry_points: From dad94383c4afe3189f74b0151dac80cc0fe5717f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:29:23 -0500 Subject: [PATCH 0532/1813] Update harpy to 0.6.1 (#45885) --- recipes/harpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index f51726858a1c8..8ceac942c5b01 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.0" %} -{% set sha256 = "3b7010054c3cafb19ae6973154015e17cd4688966237af90f5584d933eec86b3" %} +{% set version = "0.6.1" %} +{% set sha256 = "82841865d78362b084f76031329b30ff82521160d7ebdfb64386bfd32dac131c" %} package: name: harpy From 9cb82b9674baf5f26301eb22034f4cc605418c8d Mon Sep 17 00:00:00 2001 From: Christian Atallah <34323164+chrisAta@users.noreply.github.com> Date: Mon, 19 Feb 2024 18:50:27 +0000 Subject: [PATCH 0533/1813] Add mgnify-pipelines-toolkit recipe (#45872) * initial mgnify-pipelines-toolkit bioconda commit * fix lint by adding homepage and run_exports * fix argv error with new release of toolkit * update sha256 --- recipes/mgnify-pipelines-toolkit/meta.yaml | 70 ++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 recipes/mgnify-pipelines-toolkit/meta.yaml diff --git a/recipes/mgnify-pipelines-toolkit/meta.yaml b/recipes/mgnify-pipelines-toolkit/meta.yaml new file mode 100644 index 0000000000000..424f194a0dfc0 --- /dev/null +++ b/recipes/mgnify-pipelines-toolkit/meta.yaml @@ -0,0 +1,70 @@ +{% set name = "mgnify-pipelines-toolkit" %} +{% set version = "0.0.9" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgnify_pipelines_toolkit-{{ version }}.tar.gz + sha256: 6140dd322824086169cebd6ba2a22c9be9276920f3ea04c6fe6e96c7848c3d1d + +build: + entry_points: + - get_subunits = mgnify_pipelines_toolkit.analysis.shared.get_subunits:main + - get_subunits_coords = mgnify_pipelines_toolkit.analysis.shared.get_subunits_coords:main + - mapseq2biom = mgnify_pipelines_toolkit.analysis.shared.mapseq2biom:main + - are_there_primers = mgnify_pipelines_toolkit.analysis.amplicon.are_there_primers:main + - assess_inflection_point_mcp = mgnify_pipelines_toolkit.analysis.amplicon.assess_inflection_point_mcp:main + - assess_mcp_proportions = mgnify_pipelines_toolkit.analysis.amplicon.assess_mcp_proportions:main + - classify_var_regions = mgnify_pipelines_toolkit.analysis.amplicon.classify_var_regions:main + - find_mcp_inflection_points = mgnify_pipelines_toolkit.analysis.amplicon.find_mcp_inflection_points:main + - make_asv_count_table = mgnify_pipelines_toolkit.analysis.amplicon.make_asv_count_table:main + - remove_ambiguous_reads = mgnify_pipelines_toolkit.analysis.amplicon.remove_ambiguous_reads:main + - rev_comp_se_primers = mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('mgnify-pipelines-toolkit', max_pin="x.x") }} + +requirements: + host: + - python >=3.9 + - setuptools >=61.0 + - pip + run: + - python >=3.9 + - biopython ==1.82 + - numpy ==1.26.0 + - pandas ==2.0.2 + - regex ==2023.12.25 + +test: + imports: + - mgnify_pipelines_toolkit + commands: + - pip check + - get_subunits --help + - get_subunits_coords --help + - mapseq2biom --help + - are_there_primers --help + - assess_inflection_point_mcp --help + - assess_mcp_proportions --help + - classify_var_regions --help + - find_mcp_inflection_points --help + - make_asv_count_table --help + - remove_ambiguous_reads --help + - rev_comp_se_primers --help + requires: + - pip + +about: + home: https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit + summary: Collection of scripts and tools for MGnify pipelines + license: Apache-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - chrisAta From 05831bc7b9584a7bd15162302ec93de763eef8c3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:24:58 -0500 Subject: [PATCH 0534/1813] Update snakemake to 8.4.11 (#45882) * Update snakemake to 8.4.10 * Update snakemake to 8.4.11 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index a226a8f3ff36b..d25d92a34cfe4 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.9" %} +{% set version = "8.4.11" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 6bd24c39110a8d6744d09aab5ca71bde0c4559542ec7f58e52a6c4d360120171 + sha256: 6c176d2f3e9cb163a81d1b0e9876b2178c6d8187971d95c9ac2be3470d94d246 build: number: 0 From 44986b1bdd94517e4a54bd2ad96fe4de4cddd69d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:25:34 -0500 Subject: [PATCH 0535/1813] Update mirmachine to 0.2.13 (#45877) * Update mirmachine to 0.2.13 * Update mirmachine meta.yaml (#45879) * Update mirmachine meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Sinan U. Umu --- recipes/mirmachine/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/mirmachine/meta.yaml b/recipes/mirmachine/meta.yaml index 0d9b2844285c3..aeb3d30ca4d51 100644 --- a/recipes/mirmachine/meta.yaml +++ b/recipes/mirmachine/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MirMachine" %} -{% set version = "0.2.12" %} +{% set version = "0.2.13" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 5e55e5d4358d44e5f59f610476f1420a565c1bb916d1de1323d984d02313232c + sha256: 0a2d7d466a391b07a358ee543c34814974f8273cd42ce37f5ccb757169649411 build: noarch: python number: 0 script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_compatible("MirMachine", max_pin="x.x") }} requirements: host: From a766d548a0671aeb786488733628ed817feed801 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:41:48 -0500 Subject: [PATCH 0536/1813] Update r-aroma.core to 3.3.1 (#45873) * Update r-aroma.core to 3.3.1 * add run_exports --------- Co-authored-by: mencian --- recipes/r-aroma.core/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/r-aroma.core/meta.yaml b/recipes/r-aroma.core/meta.yaml index c2ec781553729..5d9c36cd653b2 100644 --- a/recipes/r-aroma.core/meta.yaml +++ b/recipes/r-aroma.core/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '3.3.0' %} +{% set version = '3.3.1' %} package: name: r-aroma.core @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/aroma.core_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/aroma.core/aroma.core_{{ version }}.tar.gz - sha256: 7b6ab7cc6079f6783b0eaa2c10a29492e53cfb3f05b7a298588491b35a472188 + sha256: fa26bca509750eb44e85cae2d78b03870c003d4f7e0360977e924a7838805e44 build: noarch: generic - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-aroma.core', max_pin="x") }} requirements: host: @@ -54,10 +56,11 @@ test: - $R -e "library('aroma.core')" about: - home: https://github.com/HenrikBengtsson/aroma.core, http://www.aroma-project.org/ + home: https://www.aroma-project.org/ license: LGPL-2.1-or-later summary: Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'. + dev_url: https://github.com/HenrikBengtsson/aroma.core license_family: LGPL license_file: - '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' From e2a579e90ebaad9fd22063aaee5eaae5eac79634 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:41:55 -0500 Subject: [PATCH 0537/1813] Update tissuumaps to 3.2.0.5 (#45834) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index 5f81144cf6ced..50e6992dce10d 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.0.4" %} +{% set version = "3.2.0.5" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 02ce7e575075fd5b401c322ade25ed9f52cc4b7af944a9c29441c1784506a1ed + sha256: 2d0cefff0aa54a8f9bb040cf5537a77c5fec2a40954b8c1b2b2af8a07bb181d9 build: number: 0 From eb92e56bfe9fa75964d8673d9093cb154ff135bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:43:47 -0500 Subject: [PATCH 0538/1813] Update snakemake-storage-plugin-s3 to 0.2.10 (#45835) * Update snakemake-storage-plugin-s3 to 0.2.10 * retrigger CI --------- Co-authored-by: mencian --- recipes/snakemake-storage-plugin-s3/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-storage-plugin-s3/meta.yaml b/recipes/snakemake-storage-plugin-s3/meta.yaml index f846ede5119a0..55783267920c3 100644 --- a/recipes/snakemake-storage-plugin-s3/meta.yaml +++ b/recipes/snakemake-storage-plugin-s3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-s3" %} -{% set version = "0.2.9" %} +{% set version = "0.2.10" %} package: name: {{ name|lower }} @@ -7,11 +7,11 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_s3-{{ version }}.tar.gz - sha256: 41cb23326f37dc576d4a1deac15b3f5a647e26ca957a69ae06b128c044ba2f32 + sha256: a4554d170b5621751aba20ee08e6357090471a0a68b173525b118580c287a12e build: noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -40,7 +40,9 @@ about: summary: A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.) home: https://github.com/snakemake/snakemake-storage-plugin-s3 license: MIT + license_family: MIT license_file: LICENSE + doc_url: https://snakemake.github.io/snakemake-plugin-catalog/plugins/storage/s3.html extra: recipe-maintainers: From 7099834e87352236b6366a661652bb76be6ec83e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:52:04 -0500 Subject: [PATCH 0539/1813] Update vcf2parquet to 0.5.0 (#45881) * Update vcf2parquet to 0.5.0 * add run_exports --------- Co-authored-by: mencian --- recipes/vcf2parquet/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/vcf2parquet/meta.yaml b/recipes/vcf2parquet/meta.yaml index f5b5e47b394db..ad6addc3938bc 100644 --- a/recipes/vcf2parquet/meta.yaml +++ b/recipes/vcf2parquet/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.1" %} -{% set sha256 = "c0eb32658e4ec05433b265c78c158e216e2e464a15174615c1e6d39380019a46" %} +{% set version = "0.5.0" %} +{% set sha256 = "61cba26e418d33af994bc85c4e5174ed115fc15bcf94f4f54e14a31ab839c82f" %} package: name: vcf2parquet @@ -11,17 +11,18 @@ source: build: number: 0 + run_exports: + - {{ pin_subpackage('vcf2parquet', max_pin="x.x") }} requirements: build: - {{ compiler("c") }} - - rust + - {{ compiler("rust") }} - pkg-config # [osx] host: - xz - zlib - bzip2 - run: test: commands: From 59dfe5ddb7714981b131405eb82b3a739358d781 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:56:17 -0500 Subject: [PATCH 0540/1813] Update anglerfish to 0.6.1 (#45830) * Update anglerfish to 0.6.1 * add requirements.txt * copy requirements.txt to SRC_DIR --------- Co-authored-by: Brandon Seah Co-authored-by: mencian --- recipes/anglerfish/meta.yaml | 10 ++++++---- recipes/anglerfish/requirements.txt | 6 ++++++ 2 files changed, 12 insertions(+), 4 deletions(-) create mode 100644 recipes/anglerfish/requirements.txt diff --git a/recipes/anglerfish/meta.yaml b/recipes/anglerfish/meta.yaml index ee4d25f033fc1..d15537aa287a2 100644 --- a/recipes/anglerfish/meta.yaml +++ b/recipes/anglerfish/meta.yaml @@ -1,5 +1,5 @@ {% set name = "anglerfish" %} -{% set version = "0.6.0" %} +{% set version = "0.6.1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,12 @@ package: source: url: "https://pypi.io/packages/source/b/bio-{{ name }}/bio-{{ name }}-{{ version }}.tar.gz" - sha256: b67a0c77680f85ebdf88622382bb271655e807c60dc3bdcd01997d336e6574fa + sha256: 91a62cbbc388009bd503df0d3f64441c0e86ab377da46f721f5fcf82b9cce331 build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: "cp ${RECIPE_DIR}/requirements.txt ${SRC_DIR} && {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" entry_points: - anglerfish=anglerfish.anglerfish:anglerfish run_exports: @@ -24,11 +24,13 @@ requirements: - python >=3.7 run: - biopython + - click + - minimap2 - numpy + - pandas - python >=3.7 - python-levenshtein - pyyaml - - minimap2 test: imports: diff --git a/recipes/anglerfish/requirements.txt b/recipes/anglerfish/requirements.txt new file mode 100644 index 0000000000000..db39464867253 --- /dev/null +++ b/recipes/anglerfish/requirements.txt @@ -0,0 +1,6 @@ +biopython==1.83 +click==8.1.7 +levenshtein==0.23.0 +numpy==1.26.3 +pandas==2.1.4 +pyyaml==6.0.1 \ No newline at end of file From 31dcf0ece95d95c9b0a0c76559ed45bf6b39bdef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 15:23:33 -0500 Subject: [PATCH 0541/1813] Update snakemake-storage-plugin-fs to 0.2.0 (#45884) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake-storage-plugin-fs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-storage-plugin-fs/meta.yaml b/recipes/snakemake-storage-plugin-fs/meta.yaml index 2f0f622a761d0..996d529132ccb 100644 --- a/recipes/snakemake-storage-plugin-fs/meta.yaml +++ b/recipes/snakemake-storage-plugin-fs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-fs" %} -{% set version = "0.1.5" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_fs-{{ version }}.tar.gz - sha256: f1a54248008b6c65102a1fde2064e3b66aadd9f6795522bacb452deecfe181ad + sha256: cad1859036cbf429ea6fdb97f242567ec54a36d0b6ff900ce0d3ecfb6a824ae7 build: noarch: python From bd89e8a5c5937f68510dc881d0e56c7a7c3036db Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:52:10 -0600 Subject: [PATCH 0542/1813] Add recipe for sctriangulate v0.13.0 (#45889) * Add recipe for sctriangulate v0.13.0 * edit dependencies --- recipes/sctriangulate/LICENSE | 21 +++++++++++++++++ recipes/sctriangulate/meta.yaml | 41 +++++++++++++++++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 recipes/sctriangulate/LICENSE create mode 100644 recipes/sctriangulate/meta.yaml diff --git a/recipes/sctriangulate/LICENSE b/recipes/sctriangulate/LICENSE new file mode 100644 index 0000000000000..f8836ff0edea6 --- /dev/null +++ b/recipes/sctriangulate/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2021 Guangyuan(Frank) Li + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/recipes/sctriangulate/meta.yaml b/recipes/sctriangulate/meta.yaml new file mode 100644 index 0000000000000..9d3d2eb7a402a --- /dev/null +++ b/recipes/sctriangulate/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "sctriangulate" %} +{% set version = "0.13.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sctriangulate-{{ version }}.tar.gz + sha256: dc24a47c912c15d06465ea6ec87599e5bcdf06d18955d964f96eebce445a7bc2 + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('sctriangulate', max_pin="x.x") }} + +requirements: + host: + - python >=3.7 + - pip + run: + - python >=3.7 + - squidpy + - gseapy ==0.10.4 + - scrublet ==0.2.3 + - yattag + - anytree + - mygene ==3.2.2 + +test: + imports: + - sctriangulate + +about: + home: https://github.com/frankligy/scTriangulate + summary: A Python package to mix-and-match conflicting clustering results in single cell analysis, and generate reconciled clustering solutions. + license: MIT + license_family: MIT + license_file: LICENSE From c8beb534241ce97c0a19d96de2b3c819725a7a48 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 17:14:12 -0500 Subject: [PATCH 0543/1813] Update jbrowse2 to 2.10.2 (#45890) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 48774c686d68b..49ca9eeb5caee 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.10.1" %} +{% set version = "2.10.2" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 9495e73d98e4eb287c8a48d8d4a61f2523755a4582681ce4e8e09b9e0fbef291 + sha256: 06e6054086ae0a1aa3bcd55ed6fe475fc23b5960a9907c25c0d3cadfab2c6db7 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From 03d48c54bd3daa6306afd4f79d745cbe9f5882b9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 17:14:19 -0500 Subject: [PATCH 0544/1813] Update oakvar to 2.9.88 (#45891) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 2054f16001ab9..8e67b03ac181a 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.87" %} -{% set sha256 = "3ee4c24b0d1f8995b7f41ec2ba2c6948c9bd6bed4166715a1fe3b0e4436fba44" %} +{% set version = "2.9.88" %} +{% set sha256 = "ebb19910d3c3b0eff179430ea175072c21a658557b72b11dc5c5d45ddddab7c2" %} package: name: {{ name|lower }} From aea83824a47b3eed67e03d696e0eb7a1c79822b4 Mon Sep 17 00:00:00 2001 From: Christian Atallah <34323164+chrisAta@users.noreply.github.com> Date: Mon, 19 Feb 2024 23:09:16 +0000 Subject: [PATCH 0545/1813] Update mgnify-pipelines-toolkit package to add missing alias for standard_primer_matching script (#45893) * add missing alias for standard_primer_matching * add description --- recipes/mgnify-pipelines-toolkit/meta.yaml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/mgnify-pipelines-toolkit/meta.yaml b/recipes/mgnify-pipelines-toolkit/meta.yaml index 424f194a0dfc0..180d73ca19264 100644 --- a/recipes/mgnify-pipelines-toolkit/meta.yaml +++ b/recipes/mgnify-pipelines-toolkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mgnify-pipelines-toolkit" %} -{% set version = "0.0.9" %} +{% set version = "0.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgnify_pipelines_toolkit-{{ version }}.tar.gz - sha256: 6140dd322824086169cebd6ba2a22c9be9276920f3ea04c6fe6e96c7848c3d1d + sha256: ec70929a119207c866b2eeb92323a30d82998a983ef0364ecaf288d5994dfb00 build: entry_points: @@ -22,6 +22,7 @@ build: - make_asv_count_table = mgnify_pipelines_toolkit.analysis.amplicon.make_asv_count_table:main - remove_ambiguous_reads = mgnify_pipelines_toolkit.analysis.amplicon.remove_ambiguous_reads:main - rev_comp_se_primers = mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main + - standard_primer_matching = mgnify_pipelines_toolkit.analysis.amplicon.standard_primer_matching:main noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 @@ -56,12 +57,16 @@ test: - make_asv_count_table --help - remove_ambiguous_reads --help - rev_comp_se_primers --help + - standard_primer_matching --help requires: - pip about: home: https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit summary: Collection of scripts and tools for MGnify pipelines + description: | + This package contains a collection of scripts used by MGnify + pipelines license: Apache-2.0 license_file: LICENSE From 55055d0386215f1d1a1b16a670abbb50d8c3bf88 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 04:07:54 -0500 Subject: [PATCH 0546/1813] Update gxf2bed to 0.2.0 (#45900) --- recipes/gxf2bed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gxf2bed/meta.yaml b/recipes/gxf2bed/meta.yaml index 0104d86e074a6..b95b9777d8ddb 100644 --- a/recipes/gxf2bed/meta.yaml +++ b/recipes/gxf2bed/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gxf2bed" %} -{% set version = "0.1.0" %} +{% set version = "0.2.0" %} package: name: gxf2bed @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 75aa006736b7e03a16bf7cb1dd1e2a7fef87a5cc9d114b2ea603df79042cd2a9 + sha256: 5bd42033a2b72fe8e4a6dd467fb97ca3cd4ebd71d2f4466467cec384c5acbf9c build: number: 0 From cd31028dea3455a83e9710040ad0763c57cb4bee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 04:13:26 -0500 Subject: [PATCH 0547/1813] Update decoupler to 1.6.0 (#45888) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update decoupler to 1.6.0 * clean up recipe * Delete recipes/decoupler/meta.yaml --------- Co-authored-by: mencian Co-authored-by: Björn Grüning --- recipes/decoupler/meta.yaml | 52 ------------------------------------- 1 file changed, 52 deletions(-) delete mode 100644 recipes/decoupler/meta.yaml diff --git a/recipes/decoupler/meta.yaml b/recipes/decoupler/meta.yaml deleted file mode 100644 index d8c9c0a826d9f..0000000000000 --- a/recipes/decoupler/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set name = "decoupler" %} -{% set version = "1.5.0" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/decoupler-{{ version }}.tar.gz - sha256: 1278b0912df0eb22618b720a7c862e6babd874472290e7c81c27dcf65c5bd48a - -build: - noarch: python - script: {{ PYTHON }} -m pip install . -vv - number: 0 - run_exports: - - {{ pin_subpackage(name, max_pin="x") }} - -requirements: - host: - - python >=3.6 - - pip - run: - - python >=3.6 - - numba - - tqdm - - anndata - - typing-extensions - - seaborn - - skranger - - scikit-learn - - omnipath - - adjusttext - - scanpy - -test: - imports: - - decoupler - commands: - - pip check - requires: - - pip - -about: - home: https://github.com/saezlab/decoupler-py - summary: Ensemble of methods to infer biological activities from omics data - license: GPL-3.0 - license_file: LICENSE - -extra: - recipe-maintainers: - - pcm32 From 6a54e64870530bf82c4b8c13b2ccf13efb2f92ae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 20 Feb 2024 12:04:11 +0100 Subject: [PATCH 0548/1813] fix: snakemake dependencies (#45903) --- recipes/snakemake/meta.yaml | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index d25d92a34cfe4..b5e3f12330276 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,3 +1,5 @@ +# Attention: when upgrading the version, please compare below dependencies with +# https://github.com/snakemake/snakemake/blob/{version}/setup.cfg {% set version = "8.4.11" %} package: @@ -9,7 +11,7 @@ source: sha256: 6c176d2f3e9cb163a81d1b0e9876b2178c6d8187971d95c9ac2be3470d94d246 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage("snakemake", max_pin="x") }} @@ -81,16 +83,14 @@ outputs: run: # Keep in sync with snakemake/setup.cfg - python >=3.11,<3.13 - - immutables - appdirs - - conda-inject >=1.3.1,<2.0 + - immutables - configargparse - connection_pool >=0.0.3 - datrie - docutils - gitpython - humanfriendly - - immutables - jinja2 >=3.0,<4.0 - jsonschema - nbformat @@ -100,17 +100,18 @@ outputs: - pyyaml - requests >=2.8.1 - reretry - - smart_open >=3.0 + - smart_open >=3.0,<4.0 - snakemake-interface-executor-plugins >=8.1.3,<9.0 - - snakemake-interface-common >=1.15.0,<2.0 - - snakemake-interface-storage-plugins >=3.0.0,<4.0 + - snakemake-interface-common >=1.17.0,<2.0 + - snakemake-interface-storage-plugins >=3.1.0,<4.0 - stopit - tabulate - throttler - - toposort >=1.10 - - yte >=1.5.1,<2.0 + - toposort >=1.10,<2.0 - wrapt + - yte >=1.5.1,<2.0 - dpath >=2.1.6,<3.0.0 + - conda-inject >=1.3.1,<2.0 test: imports: From 0cbff61f88bc11d0b98c00c19c2c16058bae958f Mon Sep 17 00:00:00 2001 From: George Bouras <84495559+gbouras13@users.noreply.github.com> Date: Wed, 21 Feb 2024 00:59:36 +1030 Subject: [PATCH 0549/1813] fix phanotate to lower than 1.6.4 (#45906) --- recipes/pharokka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pharokka/meta.yaml b/recipes/pharokka/meta.yaml index fad8abba9cbc1..21fb6adf06685 100644 --- a/recipes/pharokka/meta.yaml +++ b/recipes/pharokka/meta.yaml @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-build-isolation --use-pep517 --no-deps -vvv" run_exports: @@ -26,7 +26,7 @@ requirements: - python >=3.5 - bcbio-gff >=0.7.0 - biopython >=1.78,<1.82 - - phanotate >=1.5.0 + - phanotate >=1.5.0,<1.6.4 - mmseqs2 ==13.45111 - trnascan-se >=2.0.9 - minced >=0.4.2 From cbd2e0d5c8f9ac7a242b4e2c71336d5961849613 Mon Sep 17 00:00:00 2001 From: mwaldl Date: Tue, 20 Feb 2024 17:01:07 +0100 Subject: [PATCH 0550/1813] Add initial RRIkinDP recipe (#45821) * add initial RRIkinDP recipes * add run export section * use matplotlib-base instead of matplotlib in dependencies * fix typo in test/commands * add boost and openmp as run requirement * debugging boost location * use compiler flags to solve issue of not found boost lib * add compiler flags to make call * switch to release that supports passing of CXXFLAGS and LDFLAGS when running make * define path to output executable * switch to lower case name space for python module * use $PYTHON instead of python in build.sh * update to source release with license file * Change bin installation path * change source release to fix return value of RRIkinDP --version --------- Co-authored-by: Sebastian Will --- recipes/rrikindp/build.sh | 8 +++++ recipes/rrikindp/meta.yaml | 71 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 recipes/rrikindp/build.sh create mode 100644 recipes/rrikindp/meta.yaml diff --git a/recipes/rrikindp/build.sh b/recipes/rrikindp/build.sh new file mode 100644 index 0000000000000..0f8e3cfde1a94 --- /dev/null +++ b/recipes/rrikindp/build.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +$PYTHON -m pip install . --no-deps --ignore-installed -vv + +cd src/rrikindp + +make -j ${CPU_COUNT} CXXFLAGS+="-I${CONDA_PREFIX}/include" LDFLAGS+="-L${CONDA_PREFIX}/lib" +install RRIkinDP "${PREFIX}/bin" diff --git a/recipes/rrikindp/meta.yaml b/recipes/rrikindp/meta.yaml new file mode 100644 index 0000000000000..18246c4e9a938 --- /dev/null +++ b/recipes/rrikindp/meta.yaml @@ -0,0 +1,71 @@ + +{% set name = "RRIkinDP" %} +{% set version = "0.0.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/mwaldl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 75f6f0dd0c993796423ca812ab4926225c44d718ab3bbe90c0be856aa5d83d2f + +build: + number: 0 + run_exports: + - {{ pin_subpackage('rrikindp', max_pin="x.x,x") }} + +requirements: + build: + - python + - pip + - make + - {{ compiler('cxx') }} + host: + - python + - boost-cpp + - viennarna >=2.6.0 + - intarna + - llvm-openmp + run: + - boost-cpp + - llvm-openmp + - python >=3.6 + - intarna + - viennarna >=2.6.0 + - matplotlib-base >=3.7.0 + - seaborn >=0.12.0 + - pandas >=2.0.0 + + +output: + files: + - src/RRIkinDP/RRIkinDP + py_modules: + - rrikindp + +test: + commands: + - RRIkinDP --version + imports: + - rrikindp + +about: + home: "https://github.com/mwaldl/RRIkinDP" + license: "GPL-3.0-only" + license_family: GPL + license_file: COPYING + summary: 'Evaluation of thermodynamic and kinetic features of RNA-RNA interactions.' + description: | + RRIkinDP evaluated thermodynamic and kinetic features of RNA-RNA interactions. As input, two RNA + sequences as well as their interaction structure is provided. The tool generates the state space of + all intermediate interactions from single base pair interactions to the full input interaction. + On top of this state space it computes the barrier energy for the best direct path from a given + start interaction to the full input interaction. + doc_url: https://doi.org/10.1101/2023.07.28.548983 + dev_url: https://github.com/mwaldl/RRIkinDP + +extra: + recipe-maintainers: + - mwaldl + - s-will From 8fb4d6c58a7364d62fc730ca37238bea9c40b0c2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 11:50:46 -0500 Subject: [PATCH 0551/1813] Update nf-core to 2.13 (#45912) --- recipes/nf-core/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index bdfc0e175394a..af43d2adb35cf 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nf-core" %} -{% set version = "2.12.1" %} -{% set sha256 = "29503365111d5f760fe178cb0db317f9196af5340e649e68e345eb06c95be211" %} +{% set version = "2.13" %} +{% set sha256 = "7e0eb09bd56b2dd2861ea162204c6c0b2c966be29cacde2bb758831423ce7c81" %} package: name: {{ name|lower }} From 5fb1566f71b9215062e83197345697315b7f8df4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 12:36:07 -0500 Subject: [PATCH 0552/1813] Update annosine2 to 2.0.7 (#45901) --- recipes/annosine2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annosine2/meta.yaml b/recipes/annosine2/meta.yaml index 8e3f769b95e18..e3e0c6c3e22fc 100644 --- a/recipes/annosine2/meta.yaml +++ b/recipes/annosine2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "annosine2" %} -{% set version = "1.0.5" %} +{% set version = "2.0.7" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4b51d569f064657d31ad70893723ce1809e0be22d9be0fa23bb4c9924645a423 + sha256: 94387b895e2b011125211039598b8c426124aa43be6915697243497eefb7fff8 build: number: 0 From 6a25d6c59c8171616cd0c2b67d5f0ceb29ec8ae2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 12:36:43 -0500 Subject: [PATCH 0553/1813] Update biocommons.seqrepo to 0.6.9 (#45898) * Update biocommons.seqrepo to 0.6.8 * Update biocommons.seqrepo to 0.6.9 --- recipes/biocommons.seqrepo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biocommons.seqrepo/meta.yaml b/recipes/biocommons.seqrepo/meta.yaml index 190a81d3545ba..0009a20f469c5 100644 --- a/recipes/biocommons.seqrepo/meta.yaml +++ b/recipes/biocommons.seqrepo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biocommons.seqrepo" %} -{% set version = "0.6.7" %} +{% set version = "0.6.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/biocommons.seqrepo-{{ version }}.tar.gz - sha256: 2c3f982c1ed3adb1971a0dd2e7a554d096a1c5801075e384a62dd3f73d5e8c81 + sha256: b08d616c6ab5c4bc8e1ef5e09e94c5c274c6da41f75a435323eddc716c9b5575 build: number: 0 From c65423ed88107d3c80763e0c7f00dc7f155b5ff4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 12:41:01 -0500 Subject: [PATCH 0554/1813] Update sevenbridges-python to 2.10.3 (#45907) --- recipes/sevenbridges-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index 34b191fef1cfc..346b24f70a44f 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.10.2" %} -{% set sha256 = "4402b7b874f97532c5156a68b45ebb9554a774ffd182ef346876cca83db791a9" %} +{% set version = "2.10.3" %} +{% set sha256 = "eb49e2300eaba7d4f50d07cfb10e9706079741a7964e36f9158c2f4efa3ea3c4" %} package: name: sevenbridges-python From bd8acb8b43b6e028cf9f2f234bdaf6b06f91b022 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 15:14:31 -0500 Subject: [PATCH 0555/1813] Update pyfastani to 0.5.1 (#45908) * Update pyfastani to 0.5.1 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/pyfastani/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/pyfastani/meta.yaml b/recipes/pyfastani/meta.yaml index 7f8c1496bd166..d85b7057c9ad7 100644 --- a/recipes/pyfastani/meta.yaml +++ b/recipes/pyfastani/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyfastani" %} -{% set version = "0.4.1" %} +{% set version = "0.5.1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 44d86cbe8581d4891748ebe9851ae0a0c27489bb9f77728131415ed6b90cc35a + sha256: ad6c28303290a2389c29ed20db8266bbc4bf89a5b1bf64a7514d1bc9c6ba2d92 build: - number: 3 + number: 0 skip: True #[py2k] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: From 8e4e75091469bda8abab74909863c70e7ed68909 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 15:20:14 -0500 Subject: [PATCH 0556/1813] Update snakemake to 8.4.12 (#45911) --- recipes/snakemake/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index b5e3f12330276..a2220d2f22c9b 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.4.11" %} +{% set version = "8.4.12" %} package: name: snakemake @@ -8,10 +8,10 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 6c176d2f3e9cb163a81d1b0e9876b2178c6d8187971d95c9ac2be3470d94d246 + sha256: 1320590f24d3ef08d63ac91f1b3f634b27e4cfef21c7bbb3f267a79d75327621 build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage("snakemake", max_pin="x") }} From fcc0167a47654580eb631f83a4d393aca70fcc71 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 03:47:11 -0500 Subject: [PATCH 0557/1813] Update annotsv to 3.4 (#45916) --- recipes/annotsv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annotsv/meta.yaml b/recipes/annotsv/meta.yaml index c729ada9c6038..8b2d6880cc386 100644 --- a/recipes/annotsv/meta.yaml +++ b/recipes/annotsv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "annotsv" %} -{% set version = "3.3.9" %} -{% set sha256 = "698db38f70aaf7e839fbe090fc647b5dd7584c71a9b6397e38bf5af83a4e4c44" %} +{% set version = "3.4" %} +{% set sha256 = "98dcdbaf93525380e6c9c9dd0d501bf1af21b68155f635e4422a955970ca8f83" %} package: name: {{ name }} From 435f5c92459e3b918fc79b72ad9d52d95c82fe7d Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Wed, 21 Feb 2024 10:51:23 +0000 Subject: [PATCH 0558/1813] Update scanpy-scripts to 1.9.301 (#45913) --- recipes/scanpy-scripts/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index 6cad46ec670b5..990206e2e559f 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -1,14 +1,13 @@ {% set name = "scanpy-scripts" %} -{% set version = "1.9.0" %} +{% set version = "1.9.301" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - # - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - - url: https://github.com/ebi-gene-expression-group/scanpy-scripts/archive/refs/heads/develop.tar.gz - sha256: 669fb6f12e23a689e2e889d160c3f4f09d05d33068bef36a88bb94f9053c7b9c + - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: c681d9cf5670d8b771b7327684f19d52f9661ee31e685241af4d960220a5d63b folder: scanpy-scripts build: From 7e04e4141465aeb7362988101b25ffb9d592e03f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 06:17:39 -0500 Subject: [PATCH 0559/1813] Update mehari to 0.23.0 (#45928) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index e410ddacac824..f198f9be47627 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.22.0" %} -{% set sha256 = "1240ac7d026eebfa6a4396548f748848501fd0128e3ca81cc890ee70faf33fac" %} +{% set version = "0.23.0" %} +{% set sha256 = "296ba1df8bfa2bd7ce6efe4d109af9214f1b6ac921563ab537c87ade827e01ad" %} package: name: mehari From 1f654e4e7588f59ea5900e164858f5e9811c3340 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 06:21:08 -0500 Subject: [PATCH 0560/1813] Update r-ontologyplot to 1.7 (#45920) * Update r-ontologyplot to 1.7 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-ontologyplot/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/r-ontologyplot/meta.yaml b/recipes/r-ontologyplot/meta.yaml index 8b6b1b81d83ed..94c88333bac20 100644 --- a/recipes/r-ontologyplot/meta.yaml +++ b/recipes/r-ontologyplot/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.6' %} +{% set version = '1.7' %} package: name: r-ontologyplot @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/ontologyPlot_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/ontologyPlot/ontologyPlot_{{ version }}.tar.gz - sha256: 41a601e2201f32673c6830adc770a877be1ba4003b7352d4c09c8c50a3e8a158 + sha256: d508b861cfd596555f1b7bea681de71c9674fa7b708bb00b7a55744fb2cfd61b build: - number: 4 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-ontologyplot', max_pin="x") }} requirements: host: @@ -35,7 +37,8 @@ test: about: home: https://CRAN.R-project.org/package=ontologyPlot - license: GPL (>= 2) + license: GPL-2.0-or-later summary: Functions for visualising sets of ontological terms using the 'graphviz' layout system. license_family: GPL3 - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' From c05c005e1c2aa0e7ce1152226f95a972b702cfd5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 06:43:37 -0500 Subject: [PATCH 0561/1813] Update metaphlan to 4.1.0 (#45926) * Update metaphlan to 4.1.0 * Update meta.yaml * Fixing strainphlan -h --------- Co-authored-by: Francesco Asnicar --- recipes/metaphlan/meta.yaml | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/recipes/metaphlan/meta.yaml b/recipes/metaphlan/meta.yaml index 26ea15ee0a30e..362577e6f15ae 100644 --- a/recipes/metaphlan/meta.yaml +++ b/recipes/metaphlan/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metaphlan" %} -{% set version = "4.0.6" %} +{% set version = "4.1.0" %} package: name: {{ name }} @@ -7,13 +7,15 @@ package: source: url: https://github.com/biobakery/MetaPhlAn/archive/{{version}}.tar.gz - sha256: f69e9499056a259829a50f4eb5ab8e62e76f57852df921784d66fb5d7c4379a4 + sha256: 7552ee617a1ca7d862cc07bbb4f238ab0a8872f2702fb49192bee0461264d376 build: noarch: python number: 0 script: {{ PYTHON }} -m pip install -vv --no-deps . + run_exports: + - {{ pin_subpackage('metaphlan', max_pin='x.x') }} requirements: host: @@ -24,10 +26,9 @@ requirements: run: - python >=3.7 - bowtie2 >=2.3.0 - - cmseq - - phylophlan - dendropy - numpy + - phylophlan >=3.1 - biom-format - matplotlib-base - biopython @@ -39,7 +40,15 @@ requirements: - pysam - raxml >=8.2.10 - samtools >=1.9 - + - r-base >=4 + - r-essentials + - r-optparse + - r-rbiom + - r-ape + - r-compositions + - r-biocmanager + - bioconductor-microbiome + - hclust2 test: commands: - metaphlan -v @@ -51,6 +60,12 @@ test: - plot_tree_graphlan.py -h - sample2markers.py -h - strain_transmission.py -h + - sgb_to_gtdb_profile.py -h + - metaphlan2krona.py -h + - hclust2.py -h + - run_treeshrink.py -h + - treeshrink.py -h + - create_toy_database.py -h - bowtie2-align-s --help about: From 31a641e365dabc8c0f579b171bce350d69ff94fc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 07:54:29 -0500 Subject: [PATCH 0562/1813] Update snakemake-interface-common to 1.17.1 (#45930) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 38e66d2a7ae0f..5d1078964b88a 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.17.0" %} +{% set version = "1.17.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: d1f0cb83611f24f62ec5af852cee1cef429dd4e86c55bf373092fc682acac133 + sha256: 555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae build: noarch: python From 080bcfd4253c64c49d4cbbbd3aa907373b79f3ba Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 12:19:33 -0500 Subject: [PATCH 0563/1813] Update cramino to 0.14.3 (#45935) --- recipes/cramino/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cramino/meta.yaml b/recipes/cramino/meta.yaml index 5647f84ea1049..d7ba67ed1e831 100644 --- a/recipes/cramino/meta.yaml +++ b/recipes/cramino/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.1" %} +{% set version = "0.14.3" %} package: name: cramino @@ -12,7 +12,7 @@ build: source: url: https://github.com/wdecoster/cramino/archive/v{{ version }}.tar.gz - sha256: 57e15afb113808c327a4ec843ae1677f37c35f692e04927cfcc3823affac6cff + sha256: 10bf8574892077915b314422c18690ec141d8c934e8446502761601f4ab78303 requirements: build: From aa35507407ae964dc1e674b436f125f8bb24c054 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 12:48:39 -0500 Subject: [PATCH 0564/1813] Update ngs-chew to 0.9.4 (#45934) * Update ngs-chew to 0.9.3 * Update meta.yaml * Update ngs-chew to 0.9.4 --------- Co-authored-by: Manuel Holtgrewe --- recipes/ngs-chew/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/ngs-chew/meta.yaml b/recipes/ngs-chew/meta.yaml index 70a556610a8a9..f6df359de7c2e 100644 --- a/recipes/ngs-chew/meta.yaml +++ b/recipes/ngs-chew/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.9.2" %} -{% set sha256 = "5220182a9b2e6d2c2adf8ca6053c5a8ebf917942c6486eeee19aa2ccc6bea561" %} +{% set version = "0.9.4" %} +{% set sha256 = "7ea102e92268d9db07f9361735da6da1ebf433dbd5bff0766f8a9aaf6b93c279" %} package: name: ngs-chew @@ -37,6 +37,7 @@ requirements: - vcfpy - bcftools - samtools + - pyarrow test: commands: From 10b32b71cde0ae1261c7ad07e447776e1dc9fa7e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 13:41:28 -0500 Subject: [PATCH 0565/1813] Update trtools to 6.0.0 (#45915) * Update trtools to 6.0.0 * Update trtools to 6.0.0 (#45894) * sync dependency version constraints with pyproject.toml https://github.com/gymrek-lab/TRTools/blob/daaa0271e052248dcbbe594b1c4c08a69db9d353/pyproject.toml#L34-L44 * add poetry-core as a build dependency * add patch * remove script entry points which are only valid in pyproject.toml and not meta.yaml recipes --------- Co-authored-by: mencian --------- Co-authored-by: Arya Massarat <23412689+aryarm@users.noreply.github.com> Co-authored-by: mencian --- recipes/trtools/meta.yaml | 35 +++++++++++++++------------ recipes/trtools/test_trtools.sh.patch | 13 ++++++++++ 2 files changed, 33 insertions(+), 15 deletions(-) create mode 100644 recipes/trtools/test_trtools.sh.patch diff --git a/recipes/trtools/meta.yaml b/recipes/trtools/meta.yaml index f0431f6c1f2ec..7e885105b91e8 100644 --- a/recipes/trtools/meta.yaml +++ b/recipes/trtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trtools" %} -{% set version = "5.1.1" %} +{% set version = "6.0.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,9 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: e3b107d3d4a2ba2f0df49c382df911ab79bfbdf04aa15c84d3093bed67e4220d + sha256: afb0337a27aab41a9974ce3390e5d3d0932f5740631db8a91f7cb3c3c10ad148 + patches: + - test_trtools.sh.patch build: noarch: python @@ -27,20 +29,20 @@ build: requirements: host: - - python >=3.5 - - pip >=20.1.1 + - python >=3.7.1 + - poetry-core >=1.0.0 + - pip >=20.3 run: - - cyvcf2 >=0.30.1 - - matplotlib-base >=3.2.2 - - numpy >=1.18.5 - - pandas >=1.0.5 - - pybedtools >=0.8.1 - - pysam >=0.16.0.1 - - python >=3.5 + - python >=3.7.1,<4.0 + - cyvcf2 >=0.30.4 + - matplotlib-base >=3.1.2 + - numpy >=1.17.3,<2.0 + - pandas >=1.2.0 + - pysam >=0.15.4 - scikit-learn >=0.23.1 - - scipy >=1.4.1 - - statsmodels >=0.13.5 - - pyfaidx >=0.5.3 + - scipy >=1.3.3 + - statsmodels >=0.10.2 + - pyfaidx >=0.5.6 - ART >=2016.06.05 test: @@ -71,7 +73,7 @@ test: - simTR --help about: - home: http://github.com/gymreklab/TRTools + home: https://github.com/gymreklab/TRTools license: MIT license_family: MIT license_file: LICENSE.txt @@ -83,3 +85,6 @@ extra: recipe-maintainers: - LiterallyUniqueLogin - aryarm + identifiers: + - biotools:trtools + - doi:10.1093/bioinformatics/btaa736 diff --git a/recipes/trtools/test_trtools.sh.patch b/recipes/trtools/test_trtools.sh.patch new file mode 100644 index 0000000000000..b4c6bf6b3f284 --- /dev/null +++ b/recipes/trtools/test_trtools.sh.patch @@ -0,0 +1,13 @@ +diff --git a/trtools/testsupport/test_trtools.sh b/trtools/testsupport/test_trtools.sh +index 67eb46d5..09e1bf3b 100755 +--- a/trtools/testsupport/test_trtools.sh ++++ b/trtools/testsupport/test_trtools.sh +@@ -15,7 +15,7 @@ if [ ! -d "$TMP" ] ; then + echo "Downloading test data ..." + mkdir $TMP + pushd $TMP +- git clone -b v$(dumpSTR --version) https://github.com/gymrek-lab/TRTools.git ++ git clone -b v$(dumpSTR --version) https://github.com/gymrek-lab/TRTools.git . + popd + echo "Download done" + else From 732815eaaae05ad5a0445d9f39c3cc0d8160b5da Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 13:56:16 -0500 Subject: [PATCH 0566/1813] Update pytrf to 1.3.0 (#45932) --- recipes/pytrf/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pytrf/meta.yaml b/recipes/pytrf/meta.yaml index 14cbbf40ed6d3..209d0d802eb4b 100644 --- a/recipes/pytrf/meta.yaml +++ b/recipes/pytrf/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pytrf" %} -{% set version = "1.2.1" %} -{% set sha256 = "47d201d0cb2dad705f9a4e6030d374878c4b6e30762eefd08f159c28db7402df" %} +{% set version = "1.3.0" %} +{% set sha256 = "624497536b4e9a5cb8bbddb7ead7a2253a89b27ccf872178e9a8d975e21695f6" %} package: name: "{{ name|lower }}" @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 1 + number: 0 skip: True # [py < 36] script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" run_exports: From fb729e7375f149049d304cd9a740de906aedb062 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 13:59:55 -0500 Subject: [PATCH 0567/1813] Update earlgrey to 4.1.0 (#45927) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index e53bf3657fabd..f7fcf4ea41de7 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.8" %} -{% set sha256 = "ae68c9bc464320d07ee026079c7fc2819d5768f29b7742224fc481fd03c46615" %} +{% set version = "4.1.0" %} +{% set sha256 = "682fe5115294b48ac663c3ebe3260811d490d011565f4ad876218ca0417a33cd" %} package: name: {{ name|lower }} From 82418ecbe0d9c15ad67aa66a234e982a561deaba Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:00:01 -0500 Subject: [PATCH 0568/1813] Update ncbi-datasets-pylib to 16.4.9 (#45918) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index dcd72174fd033..8f1be91eac4f5 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.8" %} -{% set sha256 = "5c08fc546170079034be19f53468667114d0695ab348bb2c04794141a9a6ed3c" %} +{% set version = "16.4.9" %} +{% set sha256 = "7a6973469573d8b029f89a52d4f3f6a9612f4bd28c1d8975ba03640fbcf9f1bd" %} package: name: {{ name|lower }} From 20dd62fde637c3224ebdeda62c141f6217e32cb6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:00:26 -0500 Subject: [PATCH 0569/1813] Update ampcombi to 0.2.0 (#45909) * Update ampcombi to 0.2.0 * run_exports * lowercase software name --------- Co-authored-by: Thanh Lee --- recipes/ampcombi/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ampcombi/meta.yaml b/recipes/ampcombi/meta.yaml index 463325c2d636f..dd27f1ed0b8e9 100644 --- a/recipes/ampcombi/meta.yaml +++ b/recipes/ampcombi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "AMPcombi" %} -{% set version = "0.1.7" %} +{% set version = "0.2.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a73ab40cc80670f403aa629d1c1d7318ce21cc952618fdc1eba0ef667fae3578 + sha256: 96ddff5067279d3da05a662d627e793b040764560c6b6a6464bfe01a0768a27b build: noarch: python @@ -15,6 +15,8 @@ build: entry_points: - ampcombi = ampcombi:main script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage("ampcombi", max_pin="x.x") }} requirements: host: From eff4f1a1cca1ba69c3169335cd46256088f13be4 Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren Date: Wed, 21 Feb 2024 14:01:28 -0500 Subject: [PATCH 0570/1813] Update bed2gff v.0.1.4 (#45923) * new: gtfsort recipe * new: bed2gtf recipe * new: bed2gff recipe * fix: clean recipe * feat: add build.sh * fix: clean recipe; add build.sh * fix: delete other recipes already in PRs * fix spacing * Update meta.yaml * feat: bed2gff v.0.1.4 * feat: bed2gff v.0.1.4 --------- Co-authored-by: mencian --- recipes/bed2gff/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bed2gff/meta.yaml b/recipes/bed2gff/meta.yaml index 8dd9a3b9338c3..f7e17ea6ec0dd 100644 --- a/recipes/bed2gff/meta.yaml +++ b/recipes/bed2gff/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bed2gff" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: bed2gff @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz - sha256: c278185aba8c352ec2b14cc7db6eb08afb5b81e000b0acb9330bfccdad10506c + sha256: 171c4e334faf50bd7a75d47faaf7e0adda52b820f9af02db282b185af000a0a0 build: number: 0 From 434462c879a34179ae59115df150f91c2f4fffd8 Mon Sep 17 00:00:00 2001 From: miguelteixeira <92163520+lhtxa@users.noreply.github.com> Date: Wed, 21 Feb 2024 20:08:32 +0100 Subject: [PATCH 0571/1813] CarveMe recipe (#45799) * CarveMe recipe * carveme recipe * carveme recipe * fk * updated recipe and license * asd * relax pinning * relax pinning * scip fix * fix reframed scip dependencies * reframed version * missing requests --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/carveme/LICENSE.txt | 16 +++++++++ recipes/carveme/meta.yaml | 65 +++++++++++++++++++++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 recipes/carveme/LICENSE.txt create mode 100644 recipes/carveme/meta.yaml diff --git a/recipes/carveme/LICENSE.txt b/recipes/carveme/LICENSE.txt new file mode 100644 index 0000000000000..e9b0f54ede839 --- /dev/null +++ b/recipes/carveme/LICENSE.txt @@ -0,0 +1,16 @@ + +Apache Software License 2.0 + +Copyright (c) 2017, Daniel Machado + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. diff --git a/recipes/carveme/meta.yaml b/recipes/carveme/meta.yaml new file mode 100644 index 0000000000000..3a9692325ff17 --- /dev/null +++ b/recipes/carveme/meta.yaml @@ -0,0 +1,65 @@ +{% set name = "carveme" %} +{% set version = "1.6.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 3f58e2519af378b15b7e0d175aefa94566793503e32856d690720213a1a9d478 + +build: + number: 0 + entry_points: + - build_universe=carveme.cli.build_universe:main + - curate_universe=carveme.cli.curate_universe:main + - carve=carveme.cli.carve:main + - gapfill=carveme.cli.gapfill:main + - merge_community=carveme.cli.merge_community:main + - benchmark=carveme.cli.benchmark:main + script: "{{ PYTHON }} -m pip install --use-pep517 . -vv" + noarch: python + build: + run_exports: + - {{ pin_subpackage('carveme', max_pin="x.x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - pandas + - python >=3.8 + - reframed >=1.5.1 + - diamond + - pyscipopt + - scip + - numpy + - requests +test: + imports: + - carveme + - carveme.cli + - carveme.reconstruction + - carveme.universe + - tests + commands: + - build_universe --help + - curate_universe --help + - carve --help + - gapfill --help + - merge_community --help + - benchmark --help + +about: + home: "https://github.com/cdanielmachado/carveme" + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE.txt + summary: "CarveMe: automated genome-scale metabolic model reconstruction" + +extra: + recipe-maintainers: + - lhtxa + - cdanielmachado From 5b29c0e65f2f5034eb07aa473f8222b92e836f52 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:11:37 -0500 Subject: [PATCH 0572/1813] Update bed2gtf to 1.9.1 (#45925) --- recipes/bed2gtf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bed2gtf/meta.yaml b/recipes/bed2gtf/meta.yaml index 9ce15cb1fe6a5..90543d51d327f 100644 --- a/recipes/bed2gtf/meta.yaml +++ b/recipes/bed2gtf/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bed2gtf" %} -{% set version = "1.9.0" %} +{% set version = "1.9.1" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz - sha256: ae09861fa3474b3298a0469ad6d58bced91667792b5a20fdafe7b0dde6a05351 + sha256: 7acf7dff631a4d724420110a7a4e28a8324ae9040311567c0feeeec6a33fe661 build: number: 0 From a55340aeda64f9955de5a27f8baab4e051b035af Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:12:18 -0500 Subject: [PATCH 0573/1813] Update pcaone to 0.4.2 (#45937) --- recipes/pcaone/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 3f67d9dbac7c4..78f7aad64ada9 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.1" %} -{% set sha256 = "03f8afa9870507e03aa90a349a00f70f56bbf202b05a4d3d648148f3c30b6518" %} +{% set version = "0.4.2" %} +{% set sha256 = "94d8d41b251dbe2f1dab2aaa80e96ebf51753033ba01a43aae995069554c5a82" %} package: From f697f2395669bf40b09fe0bdf83bf796e639294e Mon Sep 17 00:00:00 2001 From: Guy Assa <78320514+theAguy@users.noreply.github.com> Date: Wed, 21 Feb 2024 21:30:57 +0200 Subject: [PATCH 0574/1813] ver 2.0.8 (#45862) * ver 2.0.8 * Pin python, biopython typing.Protocol introduced in python 3.8 Bio.SubsMat removed in biopython 1.80 --------- Co-authored-by: Brandon Seah --- recipes/crispector2/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/crispector2/meta.yaml b/recipes/crispector2/meta.yaml index 8b47e82f104df..cf882e1b1ee03 100644 --- a/recipes/crispector2/meta.yaml +++ b/recipes/crispector2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.7" %} +{% set version = "2.0.8" %} package: name: crispector2 @@ -15,15 +15,15 @@ build: source: url: https://github.com/theAguy/crispector2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3531fd5cad957c046a54355a18552453bf1dac7141b3e7b7c13b40ccf5599a86 + sha256: 9ca7823cbd4decdd3b1bbe3bd4bb7c77e87142ce4d1df21f06565ee9ee465177 requirements: host: - - python 3.7 + - python >=3.8 - pip run: - - python 3.7 - - biopython >=1.74 + - python >=3.8 + - biopython >=1.74, <=1.79 # Bio.SubsMat - fastp - python-edlib - click >=7.0 From 1d9a521d63b1514774ba2dfcb6a35d8947a10db6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:43:25 -0500 Subject: [PATCH 0575/1813] Update pronto to 2.5.6 (#45936) * Update pronto to 2.5.6 * add run_exports --------- Co-authored-by: mencian --- recipes/pronto/meta.yaml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/recipes/pronto/meta.yaml b/recipes/pronto/meta.yaml index ed42fc4d9781c..4651abcbc0bd9 100644 --- a/recipes/pronto/meta.yaml +++ b/recipes/pronto/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pronto" %} -{% set version = "2.5.5" %} +{% set version = "2.5.6" %} package: name: "{{ name }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8f9a0917156248b2cce05d238c5d76a7b49ee07619f2bce3c73796bff82d5b4f + sha256: eacdaa9b629042d1a07c59470241576c111751229ac052a05bfce8180df33bf8 build: noarch: python number: 0 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps -vvv + run_exports: + - {{ pin_subpackage('pronto', max_pin="x") }} requirements: host: @@ -35,10 +37,13 @@ test: - pronto.serializers about: - home: http://github.com/althonos/pronto + home: https://github.com/althonos/pronto license: MIT summary: 'Python frontend to ontologies' license_family: MIT + license_file: COPYING + doc_url: https://pronto.readthedocs.io/en/stable/ + dev_url: https://github.com/althonos/pronto extra: recipe-maintainers: From 5b57f473099b69e084da3b8c149a57658c440377 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 15:25:21 -0500 Subject: [PATCH 0576/1813] Update r-metacoder to 0.3.7 (#45904) * Update r-metacoder to 0.3.7 * add run_exports --------- Co-authored-by: mencian --- recipes/r-metacoder/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/r-metacoder/meta.yaml b/recipes/r-metacoder/meta.yaml index d4dcb0e8b2ae0..82b9450e80aaf 100644 --- a/recipes/r-metacoder/meta.yaml +++ b/recipes/r-metacoder/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.3.6' %} +{% set version = '0.3.7' %} package: name: r-metacoder @@ -8,10 +8,12 @@ source: url: - {{ cran_mirror }}/src/contrib/metacoder_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/metacoder/metacoder_{{ version }}.tar.gz - sha256: a2ab9675e1b08f4bf7027a74c4e7a1777e71850420e0a901784da0ddbdc5f896 + sha256: a48bf05b526cc3125605fcb221e96f55c74fd18d535c1a0e55982e3cbf3ffe38 build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage('r-metacoder', max_pin="x.x") }} rpaths: - lib/R/lib/ - lib/ @@ -73,7 +75,8 @@ test: - $R -e "library('metacoder')" about: - home: https://grunwaldlab.github.io/metacoder_documentation/ + home: https://github.com/grunwaldlab/metacoder + doc_url: https://grunwaldlab.github.io/metacoder_documentation/ license: GPL-2 | GPL-3 summary: A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy). From 6117151226f1578b1d11dfd9b2bf85041384aebd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 16:22:21 -0500 Subject: [PATCH 0577/1813] Update ncbi-datasets-pylib to 16.5.0 (#45938) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 8f1be91eac4f5..ca968a0c85017 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.9" %} -{% set sha256 = "7a6973469573d8b029f89a52d4f3f6a9612f4bd28c1d8975ba03640fbcf9f1bd" %} +{% set version = "16.5.0" %} +{% set sha256 = "df952921dac4244df9e40d467bd441169f95c2435846b1ab55f2ccfcce805acc" %} package: name: {{ name|lower }} From 0b231c56268141ad29bd14ad0f0976f9e4c1b3e3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 18:26:53 -0500 Subject: [PATCH 0578/1813] Update humid to 1.0.4 (#45704) * Update humid to 1.0.3 * add run_exports * edit license_file line * Update humid to 1.0.4 --------- Co-authored-by: mencian Co-authored-by: Redmar van den Berg <15814544+Redmar-van-den-Berg@users.noreply.github.com> --- recipes/humid/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/humid/meta.yaml b/recipes/humid/meta.yaml index bbc1e7ba47dc4..77f3ae3e1d436 100644 --- a/recipes/humid/meta.yaml +++ b/recipes/humid/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.0.2" %} +{% set version = "1.0.4" %} package: name: humid @@ -6,10 +6,12 @@ package: source: url: https://github.com/jfjlaros/HUMID/releases/download/v{{ version }}/humid-v{{ version }}.tar.gz - sha256: 3e35f663884cb47b089740629a61537e56536479c0c9b560819e599fd047d34e + sha256: 5da8a2a95514304b7a32a6525bb6047bae16b96e56a9737a57a745470eac7733 build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('humid', max_pin="x") }} requirements: build: @@ -17,7 +19,6 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} - isa-l - - libdeflate host: - isa-l - libdeflate @@ -32,4 +33,6 @@ test: about: home: https://github.com/jfjlaros/HUMID license: MIT + license_family: MIT summary: HUMID -- High-performance UMI Deduplicator + doc_url: https://humid.readthedocs.io/en/latest/usage.html From cde6ee04b55e9960fb6d03bf7e0b468c618c2f09 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 19:06:06 -0500 Subject: [PATCH 0579/1813] Update trtools to 6.0.1 (#45940) * Update trtools to 6.0.1 * remove patch --------- Co-authored-by: mencian --- recipes/trtools/meta.yaml | 6 ++---- recipes/trtools/test_trtools.sh.patch | 13 ------------- 2 files changed, 2 insertions(+), 17 deletions(-) delete mode 100644 recipes/trtools/test_trtools.sh.patch diff --git a/recipes/trtools/meta.yaml b/recipes/trtools/meta.yaml index 7e885105b91e8..9cd7d82dec675 100644 --- a/recipes/trtools/meta.yaml +++ b/recipes/trtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trtools" %} -{% set version = "6.0.0" %} +{% set version = "6.0.1" %} package: name: "{{ name|lower }}" @@ -7,9 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: afb0337a27aab41a9974ce3390e5d3d0932f5740631db8a91f7cb3c3c10ad148 - patches: - - test_trtools.sh.patch + sha256: 915e5f1e2ee490ad2e78294014da71cb103182277fc075ee0ccc1d27aab8bece build: noarch: python diff --git a/recipes/trtools/test_trtools.sh.patch b/recipes/trtools/test_trtools.sh.patch deleted file mode 100644 index b4c6bf6b3f284..0000000000000 --- a/recipes/trtools/test_trtools.sh.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/trtools/testsupport/test_trtools.sh b/trtools/testsupport/test_trtools.sh -index 67eb46d5..09e1bf3b 100755 ---- a/trtools/testsupport/test_trtools.sh -+++ b/trtools/testsupport/test_trtools.sh -@@ -15,7 +15,7 @@ if [ ! -d "$TMP" ] ; then - echo "Downloading test data ..." - mkdir $TMP - pushd $TMP -- git clone -b v$(dumpSTR --version) https://github.com/gymrek-lab/TRTools.git -+ git clone -b v$(dumpSTR --version) https://github.com/gymrek-lab/TRTools.git . - popd - echo "Download done" - else From 54cb4a151c5d9778d6c170a8f28a96278c1d468b Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 22 Feb 2024 13:11:24 +1300 Subject: [PATCH 0580/1813] Added ltr_harvest_parallel (#45867) * Added ltr_harvest_parallel * Fixed pin_subpackage * Removed version for perl --- recipes/ltr_harvest_parallel/build.sh | 15 ++++++++++ recipes/ltr_harvest_parallel/meta.yaml | 41 ++++++++++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 recipes/ltr_harvest_parallel/build.sh create mode 100644 recipes/ltr_harvest_parallel/meta.yaml diff --git a/recipes/ltr_harvest_parallel/build.sh b/recipes/ltr_harvest_parallel/build.sh new file mode 100644 index 0000000000000..ebadfe1bb70e0 --- /dev/null +++ b/recipes/ltr_harvest_parallel/build.sh @@ -0,0 +1,15 @@ +#!/bin/sh +set -x -e + +LTR_HARVEST_PARALLEL_DIR=${PREFIX}/share/LTR_HARVEST_parallel + +mkdir -p ${PREFIX}/bin +mkdir -p ${LTR_HARVEST_PARALLEL_DIR} +cp -r bin/LTR_HARVEST_parallel/* ${LTR_HARVEST_PARALLEL_DIR} + +cat <>${PREFIX}/bin/LTR_HARVEST_parallel +#!/bin/bash +perl ${LTR_HARVEST_PARALLEL_DIR}/LTR_HARVEST_parallel \$@ +END + +chmod a+x ${PREFIX}/bin/LTR_HARVEST_parallel diff --git a/recipes/ltr_harvest_parallel/meta.yaml b/recipes/ltr_harvest_parallel/meta.yaml new file mode 100644 index 0000000000000..0c0366ea3aca4 --- /dev/null +++ b/recipes/ltr_harvest_parallel/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "LTR_HARVEST_parallel" %} +{% set version = "1.1" %} +{% set edta_version = "2.2.0" %} +{% set sha256 = "3515667804437f749f0bb934812ca83b23ec5472c221786f6e5a0d4b613a1a7a" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/oushujun/EDTA/archive/v{{ edta_version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('ltr_harvest_parallel', max_pin='x') }} + +requirements: + run: + - perl + - genometools-genometools ==1.6.5 + +test: + commands: + - LTR_HARVEST_parallel -check_dependencies > /dev/null + +about: + home: https://github.com/oushujun/EDTA/tree/8980f498f05ad63dbffa3241842d3d38e939531b/bin/LTR_HARVEST_parallel + license: MIT + license_family: MIT + license_file: LICENSE + summary: Perl wrapper for parallel execution of LTR_harvest + dev_url: https://github.com/oushujun/EDTA/tree/8980f498f05ad63dbffa3241842d3d38e939531b/bin/LTR_HARVEST_parallel + doc_url: https://github.com/oushujun/EDTA/tree/8980f498f05ad63dbffa3241842d3d38e939531b/bin/LTR_HARVEST_parallel + +extra: + identifiers: + - doi:10.1186/s13059-019-1905-y + - doi:10.1101/2022.10.09.511471 From 2e0adbc1ba979a8b79eaaf23bb30a1bca33d2f1b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 22 Feb 2024 02:56:34 -0500 Subject: [PATCH 0581/1813] Update mehari to 0.23.1 (#45947) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index f198f9be47627..2357b0b532a06 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.23.0" %} -{% set sha256 = "296ba1df8bfa2bd7ce6efe4d109af9214f1b6ac921563ab537c87ade827e01ad" %} +{% set version = "0.23.1" %} +{% set sha256 = "fd025d56c0d13c6e48c4fcfff799bace96ec267317993c255bfbbfe8bb7dafac" %} package: name: mehari From 771846b253a44f9cef4a96deb2de79ca5bb93ace Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 22 Feb 2024 09:47:50 -0500 Subject: [PATCH 0582/1813] Update varlociraptor to 8.4.5 (#45950) --- recipes/varlociraptor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index 98b3bb7d447fc..c7c24a4b76bf6 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.4" %} +{% set version = "8.4.5" %} package: name: varlociraptor @@ -11,7 +11,7 @@ build: source: url: https://github.com/varlociraptor/varlociraptor/archive/v{{ version }}.tar.gz - sha256: e95294fb7dcefc1f61e26fac3fceedb8355138ff386e5ffd76236f3aea083cb3 + sha256: 96141350ba0eeaf57731f654f2c33b7044a3b64a433d863e6c659b82d1ca3526 requirements: build: From 0337e2553056167d604569e725b833d5e563b464 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 22 Feb 2024 09:51:53 -0500 Subject: [PATCH 0583/1813] Update ppanggolin to 2.0.3 (#45951) --- recipes/ppanggolin/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ppanggolin/meta.yaml b/recipes/ppanggolin/meta.yaml index 16e09e9ca169c..85280b93ba3e0 100644 --- a/recipes/ppanggolin/meta.yaml +++ b/recipes/ppanggolin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.2" %} +{% set version = "2.0.3" %} package: name: ppanggolin @@ -6,7 +6,7 @@ package: source: url: https://github.com/labgem/PPanGGOLiN/archive/{{ version }}.tar.gz - sha256: a655b378b05da41c5d2b7e8e8269af722681854c5d6c7c9589d01bea636035a1 + sha256: 0cd44aa30868387fb3617c52658674e57d9bd73efab636e7d8690f5d1a144c5f build: number: 0 From 03f2828fd1f041032ca4800f5d45164ca3ed3346 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 22 Feb 2024 09:55:46 -0500 Subject: [PATCH 0584/1813] Update mehari to 0.23.2 (#45956) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 2357b0b532a06..9273c9e42a05b 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.23.1" %} -{% set sha256 = "fd025d56c0d13c6e48c4fcfff799bace96ec267317993c255bfbbfe8bb7dafac" %} +{% set version = "0.23.2" %} +{% set sha256 = "d6b25df465fd6da7423c54b254b8506bfb39f647a45378b3cd1d6221db8040cd" %} package: name: mehari From f5e43b68126a1d4ba630cbeb4dc35d4a101473cb Mon Sep 17 00:00:00 2001 From: pirovc <4673375+pirovc@users.noreply.github.com> Date: Thu, 22 Feb 2024 19:48:19 +0100 Subject: [PATCH 0585/1813] Update dudes to 0.10.0 (#45959) * dudes v0.10.0 * python310 * matplotlib-base * poetry * license --- recipes/dudes/meta.yaml | 45 ++++++++++++++++++++++++++++------------- 1 file changed, 31 insertions(+), 14 deletions(-) diff --git a/recipes/dudes/meta.yaml b/recipes/dudes/meta.yaml index af2174caed477..31bf5937c52ae 100644 --- a/recipes/dudes/meta.yaml +++ b/recipes/dudes/meta.yaml @@ -1,30 +1,47 @@ +{% set name = "dudes" %} +{% set version = "0.10.0" %} + package: - name: dudes - version: "0.08" + name: "{{ name|lower }}" + version: "{{ version }}" source: - url: https://github.com/pirovc/dudes/archive/dudes_v0.08.tar.gz - md5: b569094e73ad2d40dccac7a26554a839 + url: https://github.com/pirovc/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: cb53be14da0c9d40e4ac758a6de7fe98e494c5bff3847d5aa6568a1ea8781180 build: noarch: python - number: 2 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + number: 0 + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed --no-cache-dir -vvv . + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - - python >=3 + - python >=3.10 - pip + - poetry run: - - python >=3 - - numpy - - pandas + - python >=3.10 + - matplotlib-base >=3.5.1 + - numpy >=1.21.0 + - pandas >=1.4.1 test: commands: - - DUDes.py -h 2>&1 | echo $? + - dudes -h + - dudesdb -h about: - home: https://github.com/pirovc/dudes/ - license: The MIT License (MIT) - summary: 'DUDes: a top-down taxonomic profiler for metagenomics' + home: https://github.com/pirovc/dudes + summary: "DUDes: a top-down taxonomic profiler for metagenomics and metaproteomics" + license: MIT License + license_family: MIT + license_file: LICENSE.md + +extra: + identifiers: + - doi:10.1093/bioinformatics/btw150 + recipe-maintainers: + - pirovc + - rababerladuseladim From 31b5f5c8f6663bb0efaa316808bc9535aac9fab3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 04:08:54 -0500 Subject: [PATCH 0586/1813] Update fasten to 0.8.3 (#45962) --- recipes/fasten/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fasten/meta.yaml b/recipes/fasten/meta.yaml index 79537796084c4..07b12a9b9b61f 100644 --- a/recipes/fasten/meta.yaml +++ b/recipes/fasten/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.1" %} -{% set sha256 = "35314fa8b6c8d2139338ed070f1c171b06bb7760efecf3e06064bc521399e2cd" %} +{% set version = "0.8.3" %} +{% set sha256 = "ae4d56cb81ae1e5ead734aaf3727ae595bb6c8703707f408915b992ee6ba08f1" %} package: name: fasten From 9680c8276ae6f08e2a19dd12a8290bf63bfce396 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 05:51:13 -0500 Subject: [PATCH 0587/1813] Update cramino to 0.14.4 (#45972) --- recipes/cramino/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cramino/meta.yaml b/recipes/cramino/meta.yaml index d7ba67ed1e831..dedfeb0ffcfa5 100644 --- a/recipes/cramino/meta.yaml +++ b/recipes/cramino/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.3" %} +{% set version = "0.14.4" %} package: name: cramino @@ -12,7 +12,7 @@ build: source: url: https://github.com/wdecoster/cramino/archive/v{{ version }}.tar.gz - sha256: 10bf8574892077915b314422c18690ec141d8c934e8446502761601f4ab78303 + sha256: b07a40180dae4d413ba1cb3ea1307bcf5208634cab38ede352e70e8edd84e6ba requirements: build: From c2fa481bafdfbd23cbb4240079e109373ce09843 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 05:52:10 -0500 Subject: [PATCH 0588/1813] Update insilicoseq to 2.0.1 (#45971) --- recipes/insilicoseq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/insilicoseq/meta.yaml b/recipes/insilicoseq/meta.yaml index d212e177e6070..9839e23b74ac0 100644 --- a/recipes/insilicoseq/meta.yaml +++ b/recipes/insilicoseq/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.0.0" %} -{% set sha256 = "1eb851ea345aaf46d8a5924516bbd55c8f957bb83ada8e9a995c1aae001d5d2a" %} +{% set version = "2.0.1" %} +{% set sha256 = "a1b452fbb6781c5c04bad269836893bf8d2103215e8d131c37baa95a74b2cbaa" %} package: name: insilicoseq From be7bd7687adcff874e95e621c6400efeda3f5ada Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 23 Feb 2024 15:14:05 +0100 Subject: [PATCH 0589/1813] Bump multiqc to do another build (#45969) See https://github.com/MultiQC/MultiQC/issues/2283 --- recipes/multiqc/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index cb8edecf3f5a4..2f3097c7e9847 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 46e01394ee4c213eee3c14fde01afcb0da3e87a29b09a119e5aaeabf2817313d build: - number: 1 + number: 2 entry_points: - multiqc=multiqc.__main__:run_multiqc noarch: python From 45edb1b61b31fac61c489085d375521c6a7036ca Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 09:34:19 -0500 Subject: [PATCH 0590/1813] Update pydeseq2 to 0.4.5 (#45970) * Update pydeseq2 to 0.4.5 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/pydeseq2/meta.yaml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml index 5086ace06d91f..c66af03900ccf 100644 --- a/recipes/pydeseq2/meta.yaml +++ b/recipes/pydeseq2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydeseq2" %} -{% set version = "0.4.4" %} +{% set version = "0.4.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz - sha256: ebd978d51d4d66b40e6dce8826029d9551fec9946c2a75793e75eb748cc3b207 + sha256: 51b32980f1959bb14c8830b151f60493fff7d8c5e0a1774889ef09de5aa194f1 build: noarch: python @@ -18,18 +18,17 @@ build: requirements: host: - - python >=3.8 + - python >=3.9 - pip run: - - python >=3.8 + - python >=3.9 - anndata >=0.8.0 - jupyter - ipython - numpy >=1.23.0 - pandas >=1.4.0 - scikit-learn >=1.1.0 - - scipy >=1.8.0 - - statsmodels + - scipy >=1.11.0 - matplotlib-base >=3.6.2 test: From a92a259bb39e49b9cd6917ba17a52e1936b54306 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 10:52:01 -0500 Subject: [PATCH 0591/1813] Update panaroo to 1.4.2 (#45978) --- recipes/panaroo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/panaroo/meta.yaml b/recipes/panaroo/meta.yaml index a85cb44af1e88..5fbf153632352 100644 --- a/recipes/panaroo/meta.yaml +++ b/recipes/panaroo/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.1" %} +{% set version = "1.4.2" %} {% set name = "panaroo" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/gtonkinhill/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 5ff88a48b339083bcbf843e84eeff3be5f9eda3808394da436386ce0cdfc0111 + sha256: 7f3e06d19dfc8b65e761ea0199e0a1363ee8b708bab327679000e770de9f3af3 build: number: 0 From 00bac45a8de87afa8ffa4b3db13177a7fed502a8 Mon Sep 17 00:00:00 2001 From: Reid Wagner <74672860+reid-wagner@users.noreply.github.com> Date: Fri, 23 Feb 2024 10:24:04 -0600 Subject: [PATCH 0592/1813] Add IonQuant recipe. (#45126) * Add IonQuant recipe. * Add maintainer field. Co-authored-by: M Bernt --------- Co-authored-by: M Bernt --- recipes/ionquant/academic_install.py | 74 ++++++++++++++++++++++++ recipes/ionquant/build.sh | 33 +++++++++++ recipes/ionquant/ionquant.py | 86 ++++++++++++++++++++++++++++ recipes/ionquant/meta.yaml | 50 ++++++++++++++++ 4 files changed, 243 insertions(+) create mode 100755 recipes/ionquant/academic_install.py create mode 100644 recipes/ionquant/build.sh create mode 100755 recipes/ionquant/ionquant.py create mode 100644 recipes/ionquant/meta.yaml diff --git a/recipes/ionquant/academic_install.py b/recipes/ionquant/academic_install.py new file mode 100755 index 0000000000000..fb4adafac6868 --- /dev/null +++ b/recipes/ionquant/academic_install.py @@ -0,0 +1,74 @@ +#!/usr/bin/env python3 + +# Automates accepting the academic license agreements in order to download IonQuant. A user of this package is then expected to accept the terms themselves when they download a license key from the IonQuant site, which is enforced by the wrapper script and IonQuant jar file. + +import argparse +import hashlib +import os +import re +import sys +import urllib.request +import urllib.parse + +IONQUANT_URL = 'http://msfragger-upgrader.nesvilab.org/ionquant/upgrade_download.php' +DOWNLOAD_READ_SIZE = 1000000 + +def download_url(url, post_dict, dest): + data = urllib.parse.urlencode(post_dict).encode('ascii') + with open(dest, 'wb') as wh: + size = 0 + m = hashlib.sha256() + with urllib.request.urlopen(url, data) as f: + while True: + seg = f.read(DOWNLOAD_READ_SIZE) + m.update(seg) + bytes_read = len(seg) + if bytes_read < 1: + break + size += bytes_read + wh.write(seg) + + return m.hexdigest() + +def parse_version(version_string): + version_pattern = '([\\d.]+)' + m = re.search(version_pattern, version_string.strip()) + if m: + return m.groups()[0] + return None + +parser = argparse.ArgumentParser( + description="Download IonQuant zip file." +) +parser.add_argument( + '-n', '--name', help='user name' +) +parser.add_argument( + '-e', '--email', help='email' +) +parser.add_argument( + '-o', '--organization', help='institutional organization' +) +parser.add_argument( + '-i', '--ionquant_version', help='IonQuant version', required=True +) +parser.add_argument( + '-p', '--path', default='.', help='path in which to install' +) +parser.add_argument( + '--hash', default='.', help='SHA256 hash of downloaded zip' +) + +args = parser.parse_args() +iq_ver = parse_version(args.ionquant_version) +if iq_ver == None: + print(f'Could not find version: {args.ionquant_version}', file=sys.stderr) + sys.exit(1) + +iq_zip = iq_ver + '$zip' +dest = os.path.join(args.path, 'IonQuant-' + iq_ver + '.zip') +data = {'transfer': 'academic', 'agreement1': 'true', 'name': args.name, 'email' : args.email, 'organization' : args.organization, 'download': iq_zip} + +if download_url(IONQUANT_URL, data, dest) != args.hash: + print('Invalid hash calculated.', file=sys.stderr) + sys.exit(1) diff --git a/recipes/ionquant/build.sh b/recipes/ionquant/build.sh new file mode 100644 index 0000000000000..9a487d861c802 --- /dev/null +++ b/recipes/ionquant/build.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +# These values are submitted to the IonQuant site when downloading the application zip. +if [[ -z "$NAME" ]]; then + NAME="${USERNAME:-bioconda}"; +fi +if [[ -z "$EMAIL" ]]; then + EMAIL="${NAME}@${HOSTNAME:-bioconda.org}"; +fi +if [[ -z "$INSTITUTION" ]]; then + INSTITUTION="${HOSTNAME:-bioconda.org}"; +fi + +# Create directories +TARGET="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +mkdir -p "$TARGET" + +# Add wrapper python script and link to unprefixed name. +cp "$RECIPE_DIR/ionquant.py" "$TARGET" +ln -s "$TARGET/ionquant.py" "$PREFIX/bin/ionquant" +chmod 0755 "${PREFIX}/bin/ionquant" + +# This script automates accepting the academic license agreements in order to download the software and build the package. A user of this package is then expected to accept the terms themselves when they download a license key from the IonQuant site, which is enforced by the wrapper script and IonQuant jar file. +"${RECIPE_DIR}/academic_install.py" -n galaxy -e "$EMAIL" -o "$INSTITUTION" -i "$PKG_VERSION" -p "$TARGET" --hash "$SHA256SUM" +if [[ $? -ne 0 ]]; then + echo "Problem downloading jar file." > /dev/stderr + exit 1; +fi + +# Unzip and link jar. +cd "$TARGET" +unzip "IonQuant-$PKG_VERSION.zip" +ln -s "IonQuant-$PKG_VERSION/IonQuant-$PKG_VERSION.jar" "IonQuant.jar" diff --git a/recipes/ionquant/ionquant.py b/recipes/ionquant/ionquant.py new file mode 100755 index 0000000000000..b9de0803001e1 --- /dev/null +++ b/recipes/ionquant/ionquant.py @@ -0,0 +1,86 @@ +#!/usr/bin/env python +# +# Wrapper script for Java Conda packages that ensures that the java runtime +# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). +# + +import os +import sys +import subprocess +from os import access, getenv, X_OK + +jar_file = os.path.join(os.path.dirname(__file__), "IonQuant.jar") + +default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] + +license_agreement_text = ''' +Please provide pass a license key with the --key argument. You may obtain a key by agreeing to the terms at https://msfragger.arsci.com/ionquant/. +''' + +def real_dirname(path): + """Return the symlink-resolved, canonicalized directory-portion of path.""" + return os.path.dirname(os.path.realpath(path)) + + +def java_executable(): + """Return the executable name of the Java interpreter.""" + java_home = getenv('JAVA_HOME') + java_bin = os.path.join('bin', 'java') + + if java_home and access(os.path.join(java_home, java_bin), X_OK): + return os.path.join(java_home, java_bin) + else: + return 'java' + + +def jvm_opts(argv): + """Construct list of Java arguments based on our argument list. + + The argument list passed in argv must not include the script name. + The return value is a 3-tuple lists of strings of the form: + (memory_options, prop_options, passthrough_options) + """ + mem_opts = [] + prop_opts = [] + pass_args = [] + + for arg in argv: + if arg.startswith('-D'): + prop_opts.append(arg) + elif arg.startswith('-XX'): + prop_opts.append(arg) + elif arg.startswith('-Xm'): + mem_opts.append(arg) + else: + pass_args.append(arg) + + # In the original shell script the test coded below read: + # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] + # To reproduce the behaviour of the above shell code fragment + # it is important to explictly check for equality with None + # in the second condition, so a null envar value counts as True! + + if mem_opts == [] and getenv('_JAVA_OPTIONS') == None: + mem_opts = default_jvm_mem_opts + + return (mem_opts, prop_opts, pass_args) + + +def main(): + java = java_executable() + jar_dir = real_dirname(sys.argv[0]) + jar_path = os.path.join(jar_dir, jar_file) + jar_arg = '-jar' + + (mem_opts, prop_opts, pass_args) = jvm_opts(sys.argv[1:]) + + if '--key' not in sys.argv: + print(license_agreement_text) + sys.exit(1) + + java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args + + sys.exit(subprocess.call(java_args)) + +if __name__ == '__main__': + main() diff --git a/recipes/ionquant/meta.yaml b/recipes/ionquant/meta.yaml new file mode 100644 index 0000000000000..3b87b49eeac8c --- /dev/null +++ b/recipes/ionquant/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.10.12" %} + +# This key was generated ONLY for the testing of this bioconda package. +# Users must generate their own key by agreeing to the terms at https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf. +{% set academic_use_only_key = "47cb2953-b4bf7726-2c96f5fe-8f1013aa" %} +{% set sha256sum = "861a633ab815a34ea54e6e26f318e19b510b25cb8955f3daeb83d6d10c6938ea" %} + +package: + name: ionquant + version: {{ version }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('ionquant', max_pin="x.x") }} + script_env: + - SHA256SUM={{ sha256sum }} + +requirements: + host: + - python >=3.9 + - unzip + run: + - openjdk >=11 + - python >=3.8 + +test: + commands: + - ionquant --key {{ academic_use_only_key }} -Xms512m -Xmx1g --help 2>&1 | grep 'IonQuant' + +about: + home: https://github.com/Nesvilab/IonQuant + license: Academic License (https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf) + summary: A label free quantification tool + description: | + IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. + It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). + It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. + + IonQuant is available freely for academic research and educational purposes only, in accordance with the terms at https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf. + +extra: + recipe-maintainers: + - reid-wagner + notes: | + The "ionquant" command runs the IonQuant java program. + identifiers: + - biotools:fragpipe + - doi:10.1074/mcp.TIR120.002048 From 4c8b1762790917ec65d633c20b4edcc65db393ad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 11:34:17 -0500 Subject: [PATCH 0593/1813] Update chewbbaca to 3.3.3 (#45975) --- recipes/chewbbaca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index fae78e05f24ed..770e27d49c701 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,5 +1,5 @@ {% set name = 'chewBBACA' %} -{% set version = '3.3.2' %} +{% set version = '3.3.3' %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4e282320ce8b6b3b6e71d2db8961911c523d970f8b06e16c7c42b2aff0ae5f03 + sha256: c29e34bdca769b38f8e9c7f7bd3547563f9e1e1effe5266e7b00674d9a7ca12a build: number: 0 From 1cdb6ba29b508e2ae594baadd75260f3b034b40e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 11:52:46 -0500 Subject: [PATCH 0594/1813] Update defense-finder to 1.2.2 (#45960) --- recipes/defense-finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/defense-finder/meta.yaml b/recipes/defense-finder/meta.yaml index 3bb41bf1ac853..8b03555254ce6 100644 --- a/recipes/defense-finder/meta.yaml +++ b/recipes/defense-finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "defense-finder" %} -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/mdmparis/defense-finder/archive/v{{ version }}.tar.gz - sha256: bff50fce7442e1bcc7fb7dd9ed202176662e5e02205551eee5ca05e4172cd2cd + sha256: e34e59cf1329e26c9cb6e42bb5cb6a7a051e09ca4bf981b9334f73a08d354625 # patches: 0001-fix-no-results.patch build: From 1cb5d5559bcc3b18028f92412cf7bd299f1345fb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 12:42:01 -0500 Subject: [PATCH 0595/1813] Update oakvar to 2.9.89 (#45981) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 8e67b03ac181a..a8f76bc238221 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.88" %} -{% set sha256 = "ebb19910d3c3b0eff179430ea175072c21a658557b72b11dc5c5d45ddddab7c2" %} +{% set version = "2.9.89" %} +{% set sha256 = "1c55c4d0bf7b849c14deaaa213591ca825ff33f8cb5d4b17b787e49bb60f11a3" %} package: name: {{ name|lower }} From c2ab9facde298db80a54083da48c2b3ed45693d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 12:42:10 -0500 Subject: [PATCH 0596/1813] Update bionumpy to 1.0.4 (#45977) --- recipes/bionumpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index e150ab834eebc..eb79aa91be613 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.2" %} +{% set version = "1.0.4" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 0052120fb3c07a83d5064b680246b2b8ddf251dac526ac60d6d1c18f4ee944eb + sha256: 88d84fd1f18c4406c79bc492963267e837673d961af2dfceb45f65ef27430823 build: noarch: python From b54bda8ccde08eacb50efc5c5cff59a8084e75d0 Mon Sep 17 00:00:00 2001 From: Benjamin Linard <22132778+blinard-BIOINFO@users.noreply.github.com> Date: Fri, 23 Feb 2024 19:15:42 +0100 Subject: [PATCH 0597/1813] Add recipe epik (#45973) * Adds recipe for epik --------- Co-authored-by: Benjamin Linard --- recipes/epik/build.sh | 24 +++++++++++++++++++++++ recipes/epik/meta.yaml | 42 ++++++++++++++++++++++++++++++++++++++++ recipes/epik/run_test.sh | 36 ++++++++++++++++++++++++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 recipes/epik/build.sh create mode 100644 recipes/epik/meta.yaml create mode 100644 recipes/epik/run_test.sh diff --git a/recipes/epik/build.sh b/recipes/epik/build.sh new file mode 100644 index 0000000000000..7bdd89211df09 --- /dev/null +++ b/recipes/epik/build.sh @@ -0,0 +1,24 @@ +#!/bin/bash +set -ex + +export CPLUS_INCLUDE_PATH=${PREFIX}/include +export CPP_INCLUDE_PATH=${PREFIX}/include +export CXX_INCLUDE_PATH=${PREFIX}/include + +#to ensure zlib location +export CFLAGS="$CFLAGS -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" + +mkdir -p $PREFIX/bin +mkdir -p $PREFIX/lib + +cmake -B build -DBUILD_SHARED_LIBS=ON --install-prefix=$PREFIX +cmake --build build --target all +cmake --install build + +ls $PREFIX/bin +ls $PREFIX/lib + +chmod +x $PREFIX/bin/epik-aa +chmod +x $PREFIX/bin/epik-dna +chmod +x $PREFIX/bin/epik.py diff --git a/recipes/epik/meta.yaml b/recipes/epik/meta.yaml new file mode 100644 index 0000000000000..438e50ab8cc17 --- /dev/null +++ b/recipes/epik/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "EPIK" %} +{% set version = "0.2.0" %} +{% set sha256 = "33db0a0fec8e89950110ea8c910947e00e224117dcba2a78d9347f61da4fe1cb" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/phylo42/{{ name|lower }}/releases/download/v{{ version }}/EPIK-v{{ version }}_src_for_bioconda.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('epik', max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + - cmake + - llvm-openmp # [osx] + host: + - boost-cpp >=1.67 + - zlib + - rapidjson + run: + - boost-cpp >=1.67 + - llvm-openmp # [osx] + - python + - click + + +about: + home: https://github.com/phylo42/epik + license: MIT + license_family: MIT + license_file: LICENSE + summary: "EPIK is a tool for fast alignement-free phylogenetic placements." + description: "EPIK uses pre-computed phylo-k-mers indexes (see package IPK) to rapidly place large amounts of sequences on a fixed phylogenetic tree. Please cite: doi.org/10.1093/bioinformatics/btad692" + diff --git a/recipes/epik/run_test.sh b/recipes/epik/run_test.sh new file mode 100644 index 0000000000000..d35e1baf13fad --- /dev/null +++ b/recipes/epik/run_test.sh @@ -0,0 +1,36 @@ +#!/usr/bin/env bash + +PASS=true + +# A +echo "test A" +command -v epik-dna +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + +# B +echo "test B" +command -v epik-aa +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + +# C +echo "test C" +epik-dna 2>&1 | grep "Evolutionary Placement with Informative K-mers" +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + +#D +echo "test D" +epik.py place --help +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + From 13f7b937ab6f2d940f889c7693e11ac2e7df96ce Mon Sep 17 00:00:00 2001 From: Qiyun Zhu Date: Fri, 23 Feb 2024 11:19:06 -0700 Subject: [PATCH 0598/1813] Update Woltka to 0.1.6 (#45967) * Update Woltka to 0.1.6 * Update Woltka to 0.1.6 * Update Woltka to 0.1.6 * Update Woltka to 0.1.6 * updated license --- recipes/woltka/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/woltka/meta.yaml b/recipes/woltka/meta.yaml index 0eb7ddeaedf5b..f5fdbff852898 100644 --- a/recipes/woltka/meta.yaml +++ b/recipes/woltka/meta.yaml @@ -1,5 +1,5 @@ {% set name = "woltka" %} -{% set version = "0.1.5" %} +{% set version = "0.1.6" %} package: name: "{{ name|lower }}" @@ -7,14 +7,16 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e97f84ba5044aec8aae7f54dc42a4172c0972a3ca008e4cf7909d364496fa16d + sha256: d1ffe069515284f6350e3129b5fa3a65b4a583105282c5af0a3997c30b7f8e99 build: number: 0 noarch: python entry_points: - woltka=woltka.cli:cli - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + run_exports: + - {{ pin_subpackage("woltka", max_pin="x.x") }} requirements: host: @@ -37,9 +39,9 @@ test: about: home: "https://github.com/qiyunzhu/woltka" - license: BSD + license: BSD-3-Clause license_family: BSD - license_file: + license_file: LICENSE summary: "versatile meta-omic data classifier" doc_url: dev_url: From 22370c0dd50db2320f1467c63d94eecb0a34b4bb Mon Sep 17 00:00:00 2001 From: Marc Sturm Date: Fri, 23 Feb 2024 19:23:21 +0100 Subject: [PATCH 0599/1813] Update of ngs-bits to version 2024_02 (#45961) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2024_02 --- recipes/ngs-bits/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ngs-bits/meta.yaml b/recipes/ngs-bits/meta.yaml index 5fa12dddf0aa1..36577f5655986 100755 --- a/recipes/ngs-bits/meta.yaml +++ b/recipes/ngs-bits/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2023_11" %} +{% set version = "2024_02" %} package: name: ngs-bits @@ -11,7 +11,7 @@ build: source: url: https://github.com/imgag/ngs-bits/releases/download/{{ version }}/ngs-bits-{{ version }}.tgz - sha256: bb994eb9a74043fa173a3b0ee6b9eafdf3e7b1aeb1ebcc2ba3e73888e1e61fa4 + sha256: 29f95f6e4e5c1cd57e463730312464bb2b632758c46abd5e1531a1d75a26a782 requirements: build: From f6a59d6203b495105d72ebabaa2f8d6c2be5480b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 14:47:06 -0500 Subject: [PATCH 0600/1813] Update hmftools-mark-dups to 1.1.1 (#45968) --- recipes/hmftools-mark-dups/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-mark-dups/meta.yaml b/recipes/hmftools-mark-dups/meta.yaml index c1fc3b06c02b4..e85200d715b60 100644 --- a/recipes/hmftools-mark-dups/meta.yaml +++ b/recipes/hmftools-mark-dups/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1" %} -{% set sha256 = "f2939d64ef5d96c638264074cf28eaf140d85ff5a21b537dbb156b54ab142047" %} +{% set version = "1.1.1" %} +{% set sha256 = "053440f3aac22a6bd627795bd5968180c0e6b7dcce43e45dab1a5536e1220abd" %} package: name: hmftools-mark-dups From 93f86d03442d8142e756c2a67e1ae8be6cecfee7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 17:17:33 -0500 Subject: [PATCH 0601/1813] Update pyhmmer to 0.10.6 (#45931) --- recipes/pyhmmer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 314fea094cdc4..38c369f3a8ce2 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.5" %} +{% set version = "0.10.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1c9c6bb5600b96eb3386c524b24bf6eb1f51610017e82b585fe0f3b3c7cdbe03 + sha256: 47e017ccc523046400312afc937d4d68306f6ca0ed82e313deb3697d4fd8ccff build: number: 0 From c2695f83ce1bc728ce3b5cf90b7fbcf89ad126a5 Mon Sep 17 00:00:00 2001 From: Leonid Kostrykin Date: Sat, 24 Feb 2024 08:38:39 +0100 Subject: [PATCH 0602/1813] Update segmetrics to 1.4.1 (#45964) * Bump segmetrics to 1.4.1 * minor consistency changes --------- Co-authored-by: Robert A. Petit III --- recipes/segmetrics/meta.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/recipes/segmetrics/meta.yaml b/recipes/segmetrics/meta.yaml index 73bb5a142078f..085a15459bbea 100644 --- a/recipes/segmetrics/meta.yaml +++ b/recipes/segmetrics/meta.yaml @@ -1,20 +1,20 @@ {% set name = "segmetrics" %} -{% set version = "1.4" %} -{% set repo_url = "https://github.com/BMCV/segmetrics.py" %} -{% set docs_url = "https://segmetrics.readthedocs.io" %} +{% set version = "1.4.1" %} package: name: "{{ name }}" version: "{{ version }}" source: - url: "{{ repo_url }}/archive/refs/tags/{{ version }}.zip" - sha256: 65fce3cd45c4f1fa0f83013a3f7c245e8ea2698ed94a75454b5f5dc833c97ad5 + url: "https://github.com/BMCV/segmetrics/archive/refs/tags/{{ version }}.zip" + sha256: a9c2eec155cc3cc3028fed4e9cf97d08fe1ef666100bb50f251f2b63b8377616 build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv " + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: @@ -39,11 +39,11 @@ test: - python -m segmetrics.cli --help about: - home: "{{ repo_url }}" + home: "https://github.com/BMCV/segmetrics" license: MIT summary: "A Python package implementing image segmentation and object detection performance measures, for biomedical image analysis and beyond." - dev_url: "{{ repo_url }}" - doc_url: "{{ docs_url }}" + dev_url: "https://github.com/BMCV/segmetrics" + doc_url: "https://segmetrics.readthedocs.io" extra: recipe-maintainers: From 4d5aebde3f6df017db29114539ac2a20258cf7f4 Mon Sep 17 00:00:00 2001 From: Dillon Roach Date: Sat, 24 Feb 2024 01:30:11 -0800 Subject: [PATCH 0603/1813] Delete recipes/r-harmony directory for transfer to conda-forge (#45982) Adding the package to CF in this PR: https://github.com/conda-forge/staged-recipes/pull/25268 --- recipes/r-harmony/build.sh | 1 - recipes/r-harmony/meta.yaml | 59 ------------------------------------- 2 files changed, 60 deletions(-) delete mode 100644 recipes/r-harmony/build.sh delete mode 100644 recipes/r-harmony/meta.yaml diff --git a/recipes/r-harmony/build.sh b/recipes/r-harmony/build.sh deleted file mode 100644 index 5bf492ab9fc06..0000000000000 --- a/recipes/r-harmony/build.sh +++ /dev/null @@ -1 +0,0 @@ -$R CMD INSTALL --build . diff --git a/recipes/r-harmony/meta.yaml b/recipes/r-harmony/meta.yaml deleted file mode 100644 index 2fde7c768fbde..0000000000000 --- a/recipes/r-harmony/meta.yaml +++ /dev/null @@ -1,59 +0,0 @@ -{% set version = '0.1' %} - -package: - name: r-harmony - version: {{ version }} - -source: - url: https://github.com/immunogenomics/harmony/archive/{{ version }}.tar.gz - sha256: 1243bec2c9cd96d32ee48cafc74795bf18c3b50789e388ef8d80e4440940ae2b - -build: - # https://github.com/immunogenomics/harmony/issues/180 - skip: True # [osx] - number: 6 - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - build: - - {{ compiler('cxx') }} - host: - - r-base - - r-rcpp - - r-dplyr - - r-cowplot - - r-tidyr - - r-ggplot2 - - r-irlba - - r-matrix - - r-tibble - - bioconductor-singlecellexperiment - - r-rlang - - r-rcpparmadillo - - r-rcppprogress - run: - - r-base - - r-dplyr - - r-cowplot - - r-tidyr - - r-ggplot2 - - r-irlba - - r-matrix - - r-tibble - - bioconductor-singlecellexperiment - - r-rlang - - r-rcpparmadillo - - r-rcppprogress - -test: - commands: - - $R -e "library('harmony')" - -about: - home: https://github.com/immunogenomics/harmony - dev_url: https://github.com/immunogenomics/harmony - license: GPL-3.0-only - license_file: LICENSE - summary: Fast, sensitive and accurate integration of single-cell data with Harmony From 59247dc284c14372bcc4420587d53702f21d21f9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 04:39:24 -0500 Subject: [PATCH 0604/1813] Update snakemake-executor-plugin-slurm to 0.3.2 (#45991) --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 38c4d83d70a5c..0e3d1706f16d2 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.3.1" %} +{% set version = "0.3.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 3c45605515f73020d437872e6003de661ddd17a09e2e60780b2d19a5668f0eb5 + sha256: 3912f2895eab1270d7a42959a2e221ce53428dfffb847e03ec6bc4eead88e30b build: noarch: python From ae1a4529c5bed66857fe5adfd1c6a11f4da8bf94 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 06:00:06 -0500 Subject: [PATCH 0605/1813] Update snakemake to 8.5.1 (#45993) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake to 8.5.1 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index a2220d2f22c9b..60287b09c96b7 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.4.12" %} +{% set version = "8.5.1" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 1320590f24d3ef08d63ac91f1b3f634b27e4cfef21c7bbb3f267a79d75327621 + sha256: 1cfc81901047b831aa322a22fe86f3a2191b721a8deeb28d6448ae4eb0a5bc70 build: number: 0 @@ -104,6 +104,7 @@ outputs: - snakemake-interface-executor-plugins >=8.1.3,<9.0 - snakemake-interface-common >=1.17.0,<2.0 - snakemake-interface-storage-plugins >=3.1.0,<4.0 + - snakemake-interface-report-plugins >=1.0.0,<2.0.0 - stopit - tabulate - throttler From 1cbac51a66fcaa354c4fc62d060c08359e4c0cc2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:50:05 -0500 Subject: [PATCH 0606/1813] Update snakemake to 8.5.2 (#45994) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 60287b09c96b7..ab1c0e27635e0 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.5.1" %} +{% set version = "8.5.2" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 1cfc81901047b831aa322a22fe86f3a2191b721a8deeb28d6448ae4eb0a5bc70 + sha256: cc94876263182277e4a429e5d371c867400eeddc791c114dfd090d1bb3158975 build: number: 0 From a6481ca2b7c8c975d15ff41324baf34102a2b608 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:50:13 -0500 Subject: [PATCH 0607/1813] Update fiji-simple_omero_client to 5.17.0 (#45990) --- recipes/fiji-simple_omero_client/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fiji-simple_omero_client/meta.yaml b/recipes/fiji-simple_omero_client/meta.yaml index 1a71aba5be3a5..cf97f12237bf0 100644 --- a/recipes/fiji-simple_omero_client/meta.yaml +++ b/recipes/fiji-simple_omero_client/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fiji-simple_omero_client" %} -{% set version = "5.16.0" %} +{% set version = "5.17.0" %} package: name: {{ name | lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/GReD-Clermont/simple-omero-client/releases/download/{{ version }}/simple-omero-client-{{ version }}.jar - sha256: 577a1edcea00a4f3ad50360e8e53c0f25474b44ae21ffc20afbc757cc6c6c9d3 + sha256: 4dd058185368fb7511e538112bd8edc382409495ce2127ab19405c2b3dcef55a build: number: 0 From aae9c62b9cb4cfc0fbbd5ab2a492ecf5115ebf1d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:50:25 -0500 Subject: [PATCH 0608/1813] Update isospecpy to 2.2.2 (#45986) --- recipes/isospecpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/isospecpy/meta.yaml b/recipes/isospecpy/meta.yaml index a40f7264077e9..a162dafa99b55 100644 --- a/recipes/isospecpy/meta.yaml +++ b/recipes/isospecpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "isospecpy" %} -{% set version = "2.2.1" %} +{% set version = "2.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/IsoSpecPy-{{ version }}.tar.gz - sha256: 5426cd5ff70835b9d6b54de60b8d7b850eb63758c7443378bcb6d84601a69075 + sha256: ca838870d31c4879f7e8d0ff782876858888532b6eb0d501fb9650bf5395578e build: script: {{ PYTHON }} -m pip install . -vv From 9aa52e208e83d803e7206e07b40d1b4dddb45722 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:50:35 -0500 Subject: [PATCH 0609/1813] Update augur to 24.2.3 (#45983) --- recipes/augur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index ab32c10e43f51..afe0aac0b2035 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.2.2" %} +{% set version = "24.2.3" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: f15359e193163ce397a2bc056d0f495fbddb223544af1b5956204cf135b79c11 + sha256: 67f21f0de7d5cbf8e7f95d01f27d6a42d0e8e0c63e373969609d879c5f4785d0 build: number: 0 From 731605864b5b09b94f848565e04c8b955fd8c8c4 Mon Sep 17 00:00:00 2001 From: Marcel Martin Date: Sat, 24 Feb 2024 13:50:55 +0100 Subject: [PATCH 0610/1813] Update minute to 0.6.0 (#45976) --- recipes/minute/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/minute/meta.yaml b/recipes/minute/meta.yaml index ea573baaaef3b..7de1dc0076d35 100644 --- a/recipes/minute/meta.yaml +++ b/recipes/minute/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.4.0" %} +{% set version = "0.6.0" %} package: name: minute version: {{ version }} source: - url: https://github.com/NBISweden/minute/archive/v{{ version }}.tar.gz - sha256: 38156262a2d105774c93f2732ded5af866965a57552969540f29cfe5d03ba62a + url: https://github.com/NBISweden/minute/archive/refs/tags/v{{ version }}.tar.gz + sha256: 168077b9bc369d8e4bbda51133d00a344dc33716e2a070311cfacaf792b131d7 build: number: 0 From b112fc46856c3bfb93af96f812458ccad8cefe4b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:51:02 -0500 Subject: [PATCH 0611/1813] Update pcaone to 0.4.3 (#45974) --- recipes/pcaone/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 78f7aad64ada9..427ea5b26e300 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.2" %} -{% set sha256 = "94d8d41b251dbe2f1dab2aaa80e96ebf51753033ba01a43aae995069554c5a82" %} +{% set version = "0.4.3" %} +{% set sha256 = "91467feef2fa90f168aa2b7d4f4e9b2ec21e255af21c3191bfc9c96a241126c0" %} package: From cc1acbf82678ec07cc94f7a394d28b904335d818 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:51:13 -0500 Subject: [PATCH 0612/1813] Update synapseclient to 4.1.0 (#45965) --- recipes/synapseclient/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/synapseclient/meta.yaml b/recipes/synapseclient/meta.yaml index 58be08dcd1ec8..fa49bf12a5f38 100644 --- a/recipes/synapseclient/meta.yaml +++ b/recipes/synapseclient/meta.yaml @@ -1,5 +1,5 @@ {% set name = "synapseclient" %} -{% set version = "4.0.0" %} +{% set version = "4.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/synapseclient-{{ version }}.tar.gz - sha256: 9b1acfa4fc9d76c3d69fab3a362e80a4f3cb8dbd60cea0dd6ab34fbb120a9b34 + sha256: a3a3bb581a5424d4d57408a6c81505b0c50907b7b88ad1cea59f62bf9ee8919e build: noarch: python From eee42c12717930b0cb78f45a53c2ecce5a74702c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:51:23 -0500 Subject: [PATCH 0613/1813] Update fgpyo to 0.1.3 (#45963) --- recipes/fgpyo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgpyo/meta.yaml b/recipes/fgpyo/meta.yaml index a92669798697a..2082d162ec3a6 100644 --- a/recipes/fgpyo/meta.yaml +++ b/recipes/fgpyo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fgpyo" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/fulcrumgenomics/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: e305049a2961a400519de2426f6b06bac00cd0216ab68e7966ea24420593ab37 + sha256: fbf58a5bb936a7b817c61cd3fb905f7daf48326b9b642a96e16310c14d236715 build: noarch: python From cf52a5e558f582819fd6049816fc54efb5008247 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 24 Feb 2024 14:58:07 +0100 Subject: [PATCH 0614/1813] add libpdf support to EMBOSS (#45992) * add libpdf support * add run_exports --- recipes/emboss/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/emboss/meta.yaml b/recipes/emboss/meta.yaml index 6d391404b6993..f0dc4935fe501 100644 --- a/recipes/emboss/meta.yaml +++ b/recipes/emboss/meta.yaml @@ -3,8 +3,10 @@ package: version: "6.6.0" build: - number: 7 + number: 8 skip: True # [osx] + run_exports: + - {{ pin_subpackage("emboss", max_pin="x.x") }} source: url: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz @@ -19,10 +21,12 @@ requirements: - zlib - libgd - libpng + - libharu run: - zlib - libgd - libpng + - libharu about: home: http://emboss.open-bio.org/ From 1f4be53062c14905e946962c5ca1bc65dd45a581 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 18:14:09 -0500 Subject: [PATCH 0615/1813] Update mgnify-pipelines-toolkit to 0.1.1 (#45949) --- recipes/mgnify-pipelines-toolkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mgnify-pipelines-toolkit/meta.yaml b/recipes/mgnify-pipelines-toolkit/meta.yaml index 180d73ca19264..00a8968f37bce 100644 --- a/recipes/mgnify-pipelines-toolkit/meta.yaml +++ b/recipes/mgnify-pipelines-toolkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mgnify-pipelines-toolkit" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgnify_pipelines_toolkit-{{ version }}.tar.gz - sha256: ec70929a119207c866b2eeb92323a30d82998a983ef0364ecaf288d5994dfb00 + sha256: 925b5b154d2858289fc83339fedeb09e58019c0a319edf20d822bc658ff8825b build: entry_points: From 4ce56012ccce638b52110b42a74f530b3dbf1caa Mon Sep 17 00:00:00 2001 From: heylf Date: Sun, 25 Feb 2024 13:08:36 +0100 Subject: [PATCH 0616/1813] Add COSG (#45952) * Adding cosg recipe * Add run_exports --------- Co-authored-by: Marcel Martin --- recipes/cosg/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 recipes/cosg/meta.yaml diff --git a/recipes/cosg/meta.yaml b/recipes/cosg/meta.yaml new file mode 100644 index 0000000000000..71dc651904859 --- /dev/null +++ b/recipes/cosg/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "cosg" %} +{% set version = "1.0.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cosg-{{ version }}.tar.gz + sha256: 258ca73066ac6cbe5121cf78d5e047b48b9372c9b448ecaeb3fb67dc9f7e759c + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python + - pip + run: + - python + - anndata >=0.7.4 + - numpy >=1.17.0 + - pandas >=0.21 + - scanpy >=1.6.0 + - scikit-learn >=0.21.2 + - scipy >=1.4 + +test: + imports: + - cosg + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/genecell/COSG + summary: Accurate and fast cell marker gene identification with COSG + license: BSD-3-Clause + license_file: LICENSE + +extra: + recipe-maintainers: + - heylf From 00bb1e63426646ac046b7bdef60bb3b17c114ac5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 25 Feb 2024 07:48:42 -0500 Subject: [PATCH 0617/1813] Update galaxy-objectstore to 23.2.1 (#45945) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/galaxy-objectstore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml index 148329751bff0..d2ec30dbfa0d2 100644 --- a/recipes/galaxy-objectstore/meta.yaml +++ b/recipes/galaxy-objectstore/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.1.4" %} -{% set sha256 = "548af50412cac61a38299b5ab6a7e9b787afc51db43370e058e4e58f2d10706b" %} +{% set version = "23.2.1" %} +{% set sha256 = "31deb13282286c4f8baae364049726686559ab2575a8b2360fda12af26146f47" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From c206771f63637411fe58ebb3c4db6c1dc7daced1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 25 Feb 2024 07:51:44 -0500 Subject: [PATCH 0618/1813] Update masurca to 4.1.1 (#45980) * Update masurca to 4.1.1 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/masurca/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml index d9b9f6bd806ec..1663a0fe1c87f 100644 --- a/recipes/masurca/meta.yaml +++ b/recipes/masurca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "masurca" %} -{% set version = "4.1.0" %} +{% set version = "4.1.1" %} package: name: {{ name }} @@ -7,11 +7,13 @@ package: source: url: https://github.com/alekseyzimin/masurca/releases/download/v{{ version }}/MaSuRCA-{{ version }}.tar.gz - sha256: 15078e24c79fe5aabe42748d64f95d15f3fbd7708e84d88fc07c4b7f2e4b0902 + sha256: 8758f6196bf7f57e24e08bda84abddfff08feb4cea204c0eb5e1cb9fe8198573 build: - number: 1 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: build: From 6fb4a32598ae28cce5b989ff7d5270b893274105 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 25 Feb 2024 09:55:22 -0500 Subject: [PATCH 0619/1813] Update pyabpoa to 1.5.1 (#45240) --- recipes/pyabpoa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyabpoa/meta.yaml b/recipes/pyabpoa/meta.yaml index 1a1872e3a6f85..f25d359f54d23 100644 --- a/recipes/pyabpoa/meta.yaml +++ b/recipes/pyabpoa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyabpoa" %} -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/yangao07/abPOA/releases/download/v{{ version }}/abPOA-v{{ version }}.tar.gz - sha256: 221e62c68e4cd728b85ab5f9864f7711f2102ff58c800c1477368cc83fee42d8 + sha256: f0e1b41b1c9e18ecd2096df9b60ad053260ec773d70eecb307b02cca0efab89d build: number: 0 From f8c768315b42bd57e9252ecf6f8631d027426c95 Mon Sep 17 00:00:00 2001 From: Ben J Woodcroft Date: Mon, 26 Feb 2024 00:56:13 +1000 Subject: [PATCH 0620/1813] galah: Loosen fastani version requirement. (#45941) * galah: Loosen fastani version requirement. * bump build --------- Co-authored-by: Robert A. Petit III --- recipes/galah/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galah/meta.yaml b/recipes/galah/meta.yaml index 3259624da0826..f90f03562e182 100644 --- a/recipes/galah/meta.yaml +++ b/recipes/galah/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('galah', max_pin="x.x") }} @@ -22,7 +22,7 @@ requirements: - {{ compiler('c') }} run: - dashing ==0.4.0 - - fastani ==1.31 + - fastani >=1.31 test: commands: From 82aebe584f076ef9761474feaddcf2b4f1d55d58 Mon Sep 17 00:00:00 2001 From: miguelteixeira <92163520+lhtxa@users.noreply.github.com> Date: Sun, 25 Feb 2024 16:26:50 +0100 Subject: [PATCH 0621/1813] Reframed (#45957) * fk * asd * reframed * reframed * update recipe * updata maintainers * update identifiers --- recipes/reframed/LICENSE.txt | 15 +++++++++++++++ recipes/reframed/meta.yaml | 10 +++++++--- 2 files changed, 22 insertions(+), 3 deletions(-) create mode 100644 recipes/reframed/LICENSE.txt diff --git a/recipes/reframed/LICENSE.txt b/recipes/reframed/LICENSE.txt new file mode 100644 index 0000000000000..ea167eefc7532 --- /dev/null +++ b/recipes/reframed/LICENSE.txt @@ -0,0 +1,15 @@ +Apache Software License 2.0 + +Copyright (c) 2019, Daniel Machado + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. diff --git a/recipes/reframed/meta.yaml b/recipes/reframed/meta.yaml index 257bf77160da5..9121cbd0ac6ee 100644 --- a/recipes/reframed/meta.yaml +++ b/recipes/reframed/meta.yaml @@ -11,10 +11,10 @@ source: build: noarch: python - script: {{ PYTHON }} -m pip install . -vv - number: 0 + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 1 run_exports: - - {{ pin_subpackage('reframed', max_pin="x") }} + - {{ pin_subpackage('reframed', max_pin="x.x.x") }} requirements: host: @@ -26,6 +26,8 @@ requirements: - scipy - sympy - python-libsbml + - pyscipopt + - scip test: imports: @@ -43,6 +45,8 @@ about: extra: recipe-maintainers: + - lhtxa + - cdanielmachado - acaprez identifiers: - biotools:reframed From a6754f4c0d30ef659bd2aab5cf41d1744af53a0e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 25 Feb 2024 11:07:08 -0500 Subject: [PATCH 0622/1813] Update ms2rescore to 3.0.1 (#45953) * Update ms2rescore to 3.0.1 * update versions based on upstream --------- Co-authored-by: Ryan Dale --- recipes/ms2rescore/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index e6dd1106f161f..9f6c9fa2eabb6 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms2rescore" %} -{% set version = "3.0.0" %} +{% set version = "3.0.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz - sha256: d59b82f3e8543ab6456126f07dd09c0455daf36a6d226042b87e63aa5cc6cee0 + sha256: c016f64d76cc0fc6d3ed691d1d8350d2d6e52da5e84e4fc258f4445264a4b9ad build: number: 0 @@ -37,19 +37,20 @@ requirements: - click >=7 - cascade-config >=0.4.0 - deeplc >=2.2 - - deeplcretrainer ==0.1.17 + - deeplcretrainer >=0.2 - tomli >=2 # [py<311] - psm-utils >=0.4 - customtkinter >=5,<6 - mokapot >=0.9 - pydantic >=1.8.2,<2 - jinja2 >=3 - - plotly + - plotly >=5 - sqlalchemy <2,>=1.3 - mokapot - statsmodels - matplotlib-base - seaborn + - xgboost <2,>=1.3 # from ms2pip test: imports: From 6bd73a88331f929c780513a3abf45b00e6777af0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 03:51:43 -0500 Subject: [PATCH 0623/1813] Update lamassemble to 1.7.1 (#46009) --- recipes/lamassemble/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/lamassemble/meta.yaml b/recipes/lamassemble/meta.yaml index 1c0464b1f1233..b9864b9b87ac8 100644 --- a/recipes/lamassemble/meta.yaml +++ b/recipes/lamassemble/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.7.0" %} +{% set version = "1.7.1" %} package: name: lamassemble @@ -6,7 +6,7 @@ package: source: url: https://gitlab.com/mcfrith/lamassemble/-/archive/{{ version }}/lamassemble-{{ version }}.tar.gz - sha256: e30c1450fb2d17e9203ff702971e100a2e9e842c4fa06d6c605105d1b895957f + sha256: 74c3965c33d1e8807ff4d7b90b55630e1bf7a2485e1d58615b1ed377958ad6c6 build: number: 0 From 03504c2f6e133f30cd87b7250798cbffb9558a97 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 04:23:57 -0500 Subject: [PATCH 0624/1813] Update pmultiqc to 0.0.24 (#46007) * Update pmultiqc to 0.0.24 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Yasset Perez-Riverol --- recipes/pmultiqc/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pmultiqc/meta.yaml b/recipes/pmultiqc/meta.yaml index bf170ac08f041..b8c4ab6027c61 100644 --- a/recipes/pmultiqc/meta.yaml +++ b/recipes/pmultiqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pmultiqc" %} -{% set version = "0.0.23" %} +{% set version = "0.0.24" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: fc66361d1a9da0e2812ef2ca4bf328ed95ecf9ba925d25afa0d045765d9446ab + sha256: e3d617cdfc4eab4fa8905dab1f4e575db038471659840bf1431b535d610ae136 build: number: 0 @@ -24,9 +24,9 @@ requirements: - python >=3.6 - pytest - lxml - - multiqc + - multiqc ==1.19.0 - pandas - - sdrf-pipelines + - sdrf-pipelines >=0.0.18 - pyteomics - pyopenms >2.7 From 1c91a1f991e363ed28cc87e114892f515f83c4f1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 05:35:24 -0500 Subject: [PATCH 0625/1813] Update ena-upload-cli to 0.7.1 (#46011) --- recipes/ena-upload-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-upload-cli/meta.yaml b/recipes/ena-upload-cli/meta.yaml index 5e31554cbe1b8..cd0ab25f80af4 100644 --- a/recipes/ena-upload-cli/meta.yaml +++ b/recipes/ena-upload-cli/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ena-upload-cli" %} -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e82e086c84435f5c9d53373d1e3e124a87ce1ead0ba75b72050db534cd50eab9 + sha256: ee176f66a3ff7af7091eb45184fd2c1778581fc56d4a96410f14cd19312cce7e build: number: 0 From 207b5fc84e967310e23d71336b2aee4f4c9464ae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 06:48:56 -0500 Subject: [PATCH 0626/1813] Update hmftools-purple to 4.0.2 (#46013) --- recipes/hmftools-purple/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-purple/meta.yaml b/recipes/hmftools-purple/meta.yaml index ec2fb71d6ffb2..ae81543b0e19c 100644 --- a/recipes/hmftools-purple/meta.yaml +++ b/recipes/hmftools-purple/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "4.0.1" %} -{% set sha256 = "e52e98b04dd22ae5b785257f9decb16d4ea270a8de7aaa124ad07e5653b4713c" %} +{% set version = "4.0.2" %} +{% set sha256 = "fb534734b4a0833c8d68591e009caea5b654714211a95f23570c1fca9bfa57a9" %} package: name: hmftools-purple From f02aa10b79e13d5c48c789ce5879d5edc77cfcd5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 08:16:05 -0500 Subject: [PATCH 0627/1813] Update mehari to 0.24.1 (#46010) * Update mehari to 0.24.0 * Update meta.yaml --------- Co-authored-by: Manuel Holtgrewe --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 9273c9e42a05b..1f8536fe1df30 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.23.2" %} -{% set sha256 = "d6b25df465fd6da7423c54b254b8506bfb39f647a45378b3cd1d6221db8040cd" %} +{% set version = "0.24.1" %} +{% set sha256 = "bf130073533d279ca31e51871e3cc4126c9799f2cf08024a18ef7483e719e68f" %} package: name: mehari From e5f19d7233faaa2590b2fc4be2a19d6fcd6e93e5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 08:53:34 -0500 Subject: [PATCH 0628/1813] Update thapbi-pict to 1.0.10 (#46014) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index c643e4772b02d..b2d52e5652b4e 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.9" %} +{% set version = "1.0.10" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: 2b271400901dc7378302c7279416b591f4317d6deb43ae6bb6fa3ae1ee1d1a49 + sha256: 7ffd45fac9ede5fa635e08ff5c36d93918b62c287eff18dbd9b3bfbdf7980524 build: noarch: python From 5d23a3bed90e529754c83fe1c738d6ed58bd16e6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 11:02:09 -0500 Subject: [PATCH 0629/1813] Update snakemake to 8.5.3 (#46016) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index ab1c0e27635e0..e9596071c3f42 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.5.2" %} +{% set version = "8.5.3" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: cc94876263182277e4a429e5d371c867400eeddc791c114dfd090d1bb3158975 + sha256: 6fc39107b395760caf3893106d67859fc70d7de2a8892ddcbcd33611a50abeb1 build: number: 0 From 13981371bece899364d3fdf3b312c59fd55da288 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 11:28:54 -0500 Subject: [PATCH 0630/1813] Update monopogen to 1.5.0 (#46008) --- recipes/monopogen/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/monopogen/meta.yaml b/recipes/monopogen/meta.yaml index 974c5c784f73d..21136e395ad53 100644 --- a/recipes/monopogen/meta.yaml +++ b/recipes/monopogen/meta.yaml @@ -1,6 +1,6 @@ {% set name = "Monopogen" %} -{% set version = "1.1.0" %} -{% set sha256 = "d6d049792ae277327e2c08ba675af3c9ae2bfccfbee14bed4ab2e20da2be4805" %} +{% set version = "1.5.0" %} +{% set sha256 = "dc13817d34a7d5e1294e5b6318fd12e8490c56216fc84ab7ea0f229e96e00053" %} package: name: {{ name|lower }} From e599103de9544b6fa94e4d7311289bae376f5a3a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 13:52:17 -0500 Subject: [PATCH 0631/1813] Update pcst-fast to 1.0.10 (#45463) * Update pcst-fast to 1.0.9 * add run_exports * add setuptools_scm * Update pcst-fast to 1.0.10 * Install from sdist, not GitHub archive --------- Co-authored-by: mencian Co-authored-by: Marcel Martin --- recipes/pcst-fast/meta.yaml | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/recipes/pcst-fast/meta.yaml b/recipes/pcst-fast/meta.yaml index bf2fc543c6499..579a73edb174d 100644 --- a/recipes/pcst-fast/meta.yaml +++ b/recipes/pcst-fast/meta.yaml @@ -1,18 +1,20 @@ {% set name = "pcst-fast" %} -{% set version = "1.0.8" %} +{% set version = "1.0.10" %} package: name: "{{ name }}" version: "{{ version }}" source: - url: https://github.com/fraenkel-lab/pcst_fast/archive/refs/tags/1.0.8.tar.gz - sha256: fea6672830d539ebcf29e8a2f1a7b7771ced332bea6e66b4e1093931e62ce5df + url: https://files.pythonhosted.org/packages/d4/fd/64b51c867bad63e6622ff97cad6230b94b19b5a61e30424cd69c8353091c/pcst_fast-{{ version }}.tar.gz + sha256: 3b5694110ce2e004471f383267d5e4ab7fe1ba9828954e8c42560ac1e42b25e6 build: - number: 1 - skip: True # [ py!=36 ] - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + number: 0 + skip: True # [py < 38] + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps --use-pep517 -vvv + run_exports: + - {{ pin_subpackage('pcst-fast', max_pin="x") }} requirements: build: @@ -21,7 +23,7 @@ requirements: - pip - pybind11 >=2.4 - python - - setuptools + - setuptools_scm run: - pybind11 >=2.4 - python @@ -34,7 +36,8 @@ about: home: https://github.com/fraenkel-lab/pcst_fast license: MIT license_family: MIT - summary: Implementation for PCST + license_file: LICENSE.txt + summary: "A fast implementation of the Goemans-Williamson scheme for the PCST (prize-collecting Steiner tree/forest) problem." extra: recipe-maintainers: From fafcf3772b74ada067e4c3e1c3d2b2eac911d8fb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 14:31:46 -0500 Subject: [PATCH 0632/1813] Update pybiolib to 1.1.1755 (#46023) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 1b55ef019fc9c..8d80ba7513048 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1749" %} +{% set version = "1.1.1755" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: ec24fc1418b84918ffa85a9bf7a251e102e3dd025eb9460745ba19ba32600bf3 + sha256: 1bc65e6a214cf103a453b5119178e6e0db26757d1d7f3fc62d65a2ce188caf95 build: noarch: python From f7d861c5af6e51243ceb4e8d6acd3764f21a81db Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 15:28:12 -0500 Subject: [PATCH 0633/1813] Update magus-msa to 0.1.3 (#46022) * Update magus-msa to 0.1.3 * "host:" should only list build-time requirements * Update meta.yaml --------- Co-authored-by: Marcel Martin --- recipes/magus-msa/meta.yaml | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/recipes/magus-msa/meta.yaml b/recipes/magus-msa/meta.yaml index 1693c9e79db90..feb4112d6441e 100644 --- a/recipes/magus-msa/meta.yaml +++ b/recipes/magus-msa/meta.yaml @@ -1,13 +1,12 @@ {% set name = "magus-msa" %} -{% set version = "0.1.2" %} -{% set sha256 = "9ee1156921dba68b55d6d737aab75e68f6f3b29d76ce31a9a30cb3dcb69b2eb8" %} +{% set version = "0.1.3" %} +{% set sha256 = "de96170bd768a15d07e03724fc4f32b6c7cb8992e2cd259a45f1371363b6a7c1" %} package: name: {{ name }} version: {{ version }} source: - # url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz url: https://github.com/vlasmirnov/MAGUS/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} @@ -23,11 +22,6 @@ requirements: - python >=3.6 - pip - setuptools - - mafft - - mcl - - fasttree - - clustalo - - hmmer run: - python >=3.6 - dendropy >=4.5.2 From e3c8221bed6e3e2c4a4d09b76a5869d9356e2429 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 15:33:24 -0500 Subject: [PATCH 0634/1813] Update agat to 1.3.0 (#45979) * Update agat to 1.3.0 * add run_exports for AGAT --------- Co-authored-by: worku005 --- recipes/agat/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/agat/meta.yaml b/recipes/agat/meta.yaml index 99c23db5c7482..bae51d9129cd0 100755 --- a/recipes/agat/meta.yaml +++ b/recipes/agat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "AGAT" %} -{% set version = "1.2.0" %} -{% set sha256 = "c812e4b4ca1d27b5b8804025fa5a33f56e9b542948b44885662b2cbb98d06055" %} +{% set version = "1.3.0" %} +{% set sha256 = "4898f83fa214b07f7946c2a8592c11efcbda0db4137a577d2b95206c253981a3" %} package: name: "{{ name|lower }}" @@ -13,6 +13,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage("agat", max_pin="x") }} requirements: host: From 7a304b9e1c6414a4143868efac135c2a0edda9b9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 15:35:46 -0500 Subject: [PATCH 0635/1813] Update hmftools-sage to 3.4.1 (#46031) --- recipes/hmftools-sage/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hmftools-sage/meta.yaml b/recipes/hmftools-sage/meta.yaml index 36e0eef3e635a..46046d1908e61 100644 --- a/recipes/hmftools-sage/meta.yaml +++ b/recipes/hmftools-sage/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.4" %} -{% set sha256 = "f4fa9788cd3492a612fafaeb8ea1748c549a644fa4e45b98e6cb19f316793467" %} +{% set version = "3.4.1" %} +{% set sha256 = "c81c97fc40aae7b312324e8412daaf2ecf0ee42eb68784ccc642f45a3d46346c" %} package: name: hmftools-sage @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage('hmftools-sage', max_pin="x") }} From 163e4c80eafde1935aef0875b136bfc5616f4fcf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 15:35:57 -0500 Subject: [PATCH 0636/1813] Update annonars to 0.36.0 (#46025) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 7cfa355bc6dbb..b4c87b30ceb5b 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.35.0" %} +{% set version = "0.36.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: cdea1de0bdcc1d223093fcf8d629af5c24bc788900a0cc47256e42fba587c2c8 + sha256: 8e28087350d225bc749e285d4e3ac17b8ceb4819e0aaf3459a457e23c01f45ae requirements: build: From 4101cac4c4c29b351c385255786cc791a51b1164 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 15:36:32 -0500 Subject: [PATCH 0637/1813] Update dxpy to 0.370.2 (#46018) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index e2bc358122061..163150722513c 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.369.1" %} +{% set version = "0.370.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 6e83d6c0756ff2b6691c9b789298ef5fdbe3f3df67b8fd90beb8420782219d41 + sha256: 7cb494300e8ae195ff0551708838a2fdaf5f5f68e4575e9014e9749e7186fbc6 build: number: 0 From f7fa397fdf1ae235b6f8b636b7db3cd8a9819ae7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 15:37:20 -0500 Subject: [PATCH 0638/1813] Update egglib to 3.3.2 (#46012) --- recipes/egglib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/egglib/meta.yaml b/recipes/egglib/meta.yaml index 00a8af2197238..db7cc9d666615 100644 --- a/recipes/egglib/meta.yaml +++ b/recipes/egglib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "egglib" %} -{% set version = "3.3.1" %} +{% set version = "3.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/EggLib-{{ version }}.zip - sha256: ef918149243b7a6c3007629b3bb8df59a49af53910300bc3a07c698ac84bec55 + sha256: 596838f6504c5a0f7ae9da9fbe41a595c3113e27d764e1a09a9e8795ef79d056 build: number: 0 From 26e2a238442e586a9aa069a59b6eab46e78d2cfb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 15:38:43 -0500 Subject: [PATCH 0639/1813] Update quatradis to 1.2.0 (#46005) --- recipes/quatradis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/quatradis/meta.yaml b/recipes/quatradis/meta.yaml index 3696f0501a2d7..995cf25751c82 100644 --- a/recipes/quatradis/meta.yaml +++ b/recipes/quatradis/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.1.0" %} +{% set version="1.2.0" %} package: name: quatradis @@ -6,7 +6,7 @@ package: source: url: https://github.com/quadram-institute-bioscience/QuaTradis/archive/refs/tags/{{ version }}.tar.gz - sha256: 10a49ec364f8ca9d86fd882f6186679fc9ce5932b4552381cc6d5a8a9b525be2 + sha256: f6595d8f69f98a99818fcc3c7797533e663271cfe477c8c3c9c961416c21deb5 build: number: 0 From fde2a340577c81e97ddbd8d7c9144f75fb6220a8 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Mon, 26 Feb 2024 21:41:55 +0100 Subject: [PATCH 0640/1813] Update hictk to v0.0.9 (#46004) * Add hictk v0.0.9 * Update URL and sha256 --- recipes/hictk/conanfile.txt.patch | 17 +++++++++-------- recipes/hictk/meta.yaml | 4 ++-- 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/recipes/hictk/conanfile.txt.patch b/recipes/hictk/conanfile.txt.patch index 7925b911e0e70..3e89ed9ffc3b1 100644 --- a/recipes/hictk/conanfile.txt.patch +++ b/recipes/hictk/conanfile.txt.patch @@ -1,25 +1,25 @@ diff --git a/conanfile.txt b/conanfile.txt -index c3cfb89..163ff31 100644 +index 0fc36a2..5577407 100644 --- a/conanfile.txt +++ b/conanfile.txt -@@ -3,74 +3,11 @@ +@@ -3,75 +3,11 @@ # SPDX-License-Identifier: MIT [requires] --boost/1.83.0#39551a6ba03b4fe2c7a86b9a6d80cd67 - bshoshany-thread-pool/3.5.0#5aaea7ccf37107d3c1ba9ca9ab246e42 +-boost/1.84.0#774abb4a1b3702b2f7171ac6b6de777a + bshoshany-thread-pool/4.0.1#b7ce99198b3a54e403393961480085c7 -catch2/3.5.2#9554dc3c4ffcab50daf8f2cac4b79308 --cli11/2.3.2#1424b9b1d9e3682a7122f415b078b4d7 +-cli11/2.4.1#afacffd31f631bbb8b7c7d6425fe7a66 concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502 -eigen/3.4.0#2e192482a8acff96fe34766adca2b24c --fast_float/6.0.0#6c8a953c57879453982a6ce69c0ba87c +-fast_float/6.1.0#85dc5bf9d3d6e605abf536818397baf3 -fmt/10.2.1#9199a7a0611866dea5c8849a77467b25 -hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1 --highfive/2.8.0#b1de99f678ff5699cce6fb5fcac44d2d +-highfive/2.9.0#c57477beed8b0110fadeb6da8f48bcc5 -libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602 parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7 readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83 - span-lite/0.10.3#1967d71abb32b314387c2ab9c558dd22 + span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422 -spdlog/1.13.0#2775cc949e26b339029a852785b6b276 -zstd/1.5.5#b87dc3b185caa4b122979ac4ae8ef7e8 @@ -77,3 +77,4 @@ index c3cfb89..163ff31 100644 -highfive*:with_opencv=False -highfive*:with_xtensor=False -spdlog*:header_only=True +-zstd*:build_programs=False diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index 8045e185b4dd9..2f0e1d7330f04 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.8" %} -{% set sha256 = "4bdadf49cb053731ea31f50312c9e4fcbcdcbaf94c39715f7b325641629bed4b" %} +{% set version = "0.0.9" %} +{% set sha256 = "c64cb07a057863baa199b9d344b27b8f15a1db458390ccf7b5cac0627308d8c8" %} package: name: {{ name|lower }} From 4e074996551d9ed575332b63b6ff40e6a19a29a2 Mon Sep 17 00:00:00 2001 From: Clemens Schmid Date: Mon, 26 Feb 2024 21:58:06 +0100 Subject: [PATCH 0641/1813] update poseidon-trident to v1.4.1.0 (#46021) --- recipes/poseidon-trident/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/poseidon-trident/meta.yaml b/recipes/poseidon-trident/meta.yaml index e800846aebcf0..16afdef296300 100644 --- a/recipes/poseidon-trident/meta.yaml +++ b/recipes/poseidon-trident/meta.yaml @@ -1,13 +1,13 @@ -{% set version = "1.3.0.4" %} +{% set version = "1.4.1.0" %} package: name: poseidon-trident version: {{ version }} source: - url: https://github.com/poseidon-framework/poseidon-hs/releases/download/v{{ version }}/trident-conda-linux # [linux] - md5: 1d1d64e3cf84c3b8d51f5e84401006fa # [linux] + md5: 32399ef0bb0f0e0539b8e5de8da7909e # [linux] - url: https://github.com/poseidon-framework/poseidon-hs/releases/download/v{{ version }}/trident-macOS # [osx] - md5: e81fd58708cf617955e16b398a245303 # [osx] + md5: 8e84912883ee531c478a5e34158cfb05 # [osx] build: number: 0 From dd0fcca3b852e6be3e2d70e29a6a8c5e1872ff71 Mon Sep 17 00:00:00 2001 From: Jesse Connell Date: Mon, 26 Feb 2024 16:58:21 -0500 Subject: [PATCH 0642/1813] Update igblast to 1.22.0 (#45161) * bump igblast version from 1.21.0 to 1.22.0 * igblast: update shared_vdb.patch for latest src They just line-wrapped one thing in Makefile.igblastn.app in this latest igblast version, so I made a new .patch file to match. * igblast: define run_exports as per lint msg I believe igblast output should be backwards-compatible for minor and patch version number changes, just not major, so I set max_pin to "x" in run_exports. * Simplify configure --------- Co-authored-by: Marcel Martin --- recipes/igblast/build.sh | 32 ++++++-------------------------- recipes/igblast/meta.yaml | 11 +++++++---- recipes/igblast/shared_vdb.patch | 13 ++++++------- 3 files changed, 19 insertions(+), 37 deletions(-) diff --git a/recipes/igblast/build.sh b/recipes/igblast/build.sh index 8a7cbeb95c655..131eeeb29c598 100644 --- a/recipes/igblast/build.sh +++ b/recipes/igblast/build.sh @@ -13,37 +13,17 @@ mkdir -p $PREFIX/bin mkdir -p $SHARE_DIR/bin if [[ $(uname) == Linux ]]; then - export CPPFLAGS="$CPPFLAGS -I$PREFIX/include/ncbi-vdb" - export CC_FOR_BUILD=$CC export AR="$AR rcs" cd c++ - # IgBLAST is based on the BLAST source code and building it produces - # a similar set of shared libraries if --with-dll is used. To avoid - # conflicts when installing IgBLAST and BLAST simultaneously, - # we link IgBLAST statically. - ./configure.orig \ - --with-static-exe \ - --with-mt \ - --with-openmp \ - --without-autodep \ - --without-makefile-auto-update \ - --with-flat-makefile \ - --with-caution \ - --without-lzo \ - --without-debug \ - --with-strip \ - --with-z=$PREFIX \ - --with-bz2=$PREFIX \ - --with-vdb=$PREFIX \ - --without-krb5 \ - --without-openssl \ - --without-gnutls \ - --without-gcrypt \ - --with-build-root=ReleaseMT \ - --prefix=$PREFIX + ./configure \ + --with-z=$PREFIX \ + --with-bz2=$PREFIX \ + --with-vdb=$PREFIX + make -j2 + # Move one up so it looks like the binary release mv ReleaseMT/bin . mv src/app/igblast/{internal_data,optional_file} $SHARE_DIR diff --git a/recipes/igblast/meta.yaml b/recipes/igblast/meta.yaml index 92909eef6c732..b3d81839b3f4b 100644 --- a/recipes/igblast/meta.yaml +++ b/recipes/igblast/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.21.0" %} +{% set version = "1.22.0" %} package: name: igblast @@ -20,14 +20,16 @@ about: source: url: ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/{{ version }}/ncbi-igblast-{{ version }}-src.tar.gz # [linux] - sha256: f679a417b170e96103c088a9d1e82bfd40571526080da00fdf62de74aee82d16 # [linux] + sha256: a04eb195087447cf42e673401ae2d9f6ef8414b34f1534724a6953f41224df68 # [linux] url: ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/{{ version }}/ncbi-igblast-{{ version }}-x64-macosx.tar.gz # [osx] - sha256: 9d8f13a7ab3b2ab42df3565cdf3b480bd9c04fb0ffb1d54834e67fa37d4fc09b # [osx] + sha256: b8a0034642b5dbef7f41c7fcfbb4bc035d2c5877d3e987af43605ea8e3d55c40 # [osx] patches: - shared_vdb.patch # [linux] build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('igblast', max_pin="x") }} requirements: build: @@ -41,6 +43,7 @@ requirements: - gnutls # [osx] - libidn11 - lzo # [osx] + - libsqlite >=3 - ncbi-vdb >=2.9.6 run: - ncbi-vdb >=2.9.6 diff --git a/recipes/igblast/shared_vdb.patch b/recipes/igblast/shared_vdb.patch index 8e099e4a7c5a1..1ee0a5e8c12a9 100644 --- a/recipes/igblast/shared_vdb.patch +++ b/recipes/igblast/shared_vdb.patch @@ -1,12 +1,11 @@ -diff -u -ru ncbi-igblast-1.15.0-src/c++/src/app/igblast/Makefile.igblastn.app ncbi-igblast-1.15.0-src-patched/c++/src/app/igblast/Makefile.igblastn.app ---- ncbi-igblast-1.15.0-src/c++/src/app/igblast/Makefile.igblastn.app 2019-08-04 23:12:21.000000000 +0200 -+++ ncbi-igblast-1.15.0-src-patched/c++/src/app/igblast/Makefile.igblastn.app 2020-02-19 14:30:43.571473876 +0100 -@@ -11,7 +11,7 @@ - CXXFLAGS = $(FAST_CXXFLAGS:ppc=i386) +--- ncbi-igblast-1.22.0-src/c++/src/app/igblast/Makefile.igblastn.app 2023-10-06 15:33:05.000000000 -0400 ++++ ncbi-igblast-1.22.0-src-patched/c++/src/app/igblast/Makefile.igblastn.app 2024-01-10 11:35:41.231820985 -0500 +@@ -12,7 +12,7 @@ LDFLAGS = $(FAST_LDFLAGS:ppc=i386) --LIBS = $(GENBANK_THIRD_PARTY_LIBS) $(VDB_STATIC_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS) -+LIBS = $(GENBANK_THIRD_PARTY_LIBS) $(VDB_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS) + LIBS = $(BLAST_THIRD_PARTY_LIBS) $(GENBANK_THIRD_PARTY_LIBS) \ +- $(VDB_STATIC_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) ++ $(VDB_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) REQUIRES = VDB objects -Cygwin From f04bcef23a32178e631603446c30459d0ab55775 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 17:01:26 -0500 Subject: [PATCH 0643/1813] Update cobra-meta to 1.2.3 (#46029) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cobra-meta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cobra-meta/meta.yaml b/recipes/cobra-meta/meta.yaml index 509ff1273ccc4..75e252817b53c 100644 --- a/recipes/cobra-meta/meta.yaml +++ b/recipes/cobra-meta/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cobra-meta" %} -{% set version = "1.2.2" %} +{% set version = "1.2.3" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/linxingchen/cobra/archive/refs/tags/v{{ version }}.tar.gz - sha256: 26f3cab513f8bb78d0aeb5ccfa3aed57bafb62f42bee1ac814e74e43c330a390 + sha256: 877813cd705cb5a8b3611f3fca705bb6576ba82a8283552bed73c34bec880375 build: entry_points: From e8dd1d1c39a201b6fd8cd1909ced7aede1cc4e46 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 17:15:38 -0500 Subject: [PATCH 0644/1813] Update piscem-infer to 0.6.0 (#46036) --- recipes/piscem-infer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/piscem-infer/meta.yaml b/recipes/piscem-infer/meta.yaml index 01b9ea8560cea..885cbc257f927 100644 --- a/recipes/piscem-infer/meta.yaml +++ b/recipes/piscem-infer/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.2" %} +{% set version = "0.6.0" %} package: name: piscem-infer @@ -11,7 +11,7 @@ build: source: url: https://github.com/COMBINE-lab/piscem-infer/archive/v{{ version }}.tar.gz - sha256: 95bdab6724428ebb05dc7459ea717857e2c90fb3fe1065d131858a70273a16c5 + sha256: 6ffaaf9d101f42a983d715857504c99ef60c3449ff14505e4c6b6c521e00d928 requirements: build: From cd630cfed1a4b58802a6af8a0282b1194618598e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 18:31:27 -0500 Subject: [PATCH 0645/1813] Update r-conos to 1.5.2 (#46038) --- recipes/r-conos/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-conos/meta.yaml b/recipes/r-conos/meta.yaml index d7c122620cdaf..764a6f992dd1a 100644 --- a/recipes/r-conos/meta.yaml +++ b/recipes/r-conos/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.5.1' %} +{% set version = '1.5.2' %} package: name: r-conos @@ -8,7 +8,7 @@ source: url: - {{ cran_mirror }}/src/contrib/conos_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/conos/conos_{{ version }}.tar.gz - sha256: bb479d63a2836bfa163b6abc9f8f2bac9e081cdcc5b781f1bee201e7b99da205 + sha256: 736a00a2574fd39d063d70038ae1ff738cfcb6de61827aaf765f7004c67ac65c build: number: 0 From fd5b71ee07f49216b03316abac67c7b3611a5ee9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 18:32:01 -0500 Subject: [PATCH 0646/1813] Update galaxy-files to 23.2.1 (#45946) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning Co-authored-by: Ryan Dale --- recipes/galaxy-files/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml index ffe4ded18d97d..e62f7e1bcf271 100644 --- a/recipes/galaxy-files/meta.yaml +++ b/recipes/galaxy-files/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.1.4" %} -{% set sha256 = "9d36250e580a29c8982904e90b1ad89b1712de0743750e72bea3f740960a6524" %} +{% set version = "23.2.1" %} +{% set sha256 = "aa658c52eac6e7a7aa9eca7b132714d0887bf2649d5de472f90776d1c2ca7838" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From 3df8487af9579308164c78c018cd15481de6f34e Mon Sep 17 00:00:00 2001 From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com> Date: Mon, 26 Feb 2024 15:35:50 -0800 Subject: [PATCH 0647/1813] Update/fix kb (remove kallisto and bustools dependencies) (#45846) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * kb python compatibility kb build fails due to obscure pysam incompatibilities on python 3.9. * Update meta.yaml * Update meta.yaml Kallisto and bustools are not required for kb, and are in fact incompatible with kb. * Update meta.yaml * Removed short-circuit patch --------- Co-authored-by: Björn Grüning --- recipes/kb-python/config.py.patch | 19 ------------------- recipes/kb-python/meta.yaml | 7 ++----- 2 files changed, 2 insertions(+), 24 deletions(-) delete mode 100644 recipes/kb-python/config.py.patch diff --git a/recipes/kb-python/config.py.patch b/recipes/kb-python/config.py.patch deleted file mode 100644 index d1bf314ad1f56..0000000000000 --- a/recipes/kb-python/config.py.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- a/kb_python/config.py -+++ b/kb_python/config.py -@@ -19,6 +19,7 @@ def get_provided_kallisto_path(): - :return: path to the binary, `None` if not found - :rtype: str - """ -+ return "kallisto" - bin_filename = 'kallisto.exe' if PLATFORM == 'windows' else 'kallisto' - path = os.path.join( - PACKAGE_PATH, BINS_DIR, PLATFORM, 'kallisto', bin_filename -@@ -34,6 +35,7 @@ def get_provided_bustools_path(): - :return: path to the binary, `None` if not found - :rtype: str - """ -+ return "bustools" - bin_filename = 'bustools.exe' if PLATFORM == 'windows' else 'bustools' - path = os.path.join( - PACKAGE_PATH, BINS_DIR, PLATFORM, 'bustools', bin_filename - diff --git a/recipes/kb-python/meta.yaml b/recipes/kb-python/meta.yaml index 840469c6ff8be..f7bd0adb17bd0 100644 --- a/recipes/kb-python/meta.yaml +++ b/recipes/kb-python/meta.yaml @@ -8,10 +8,9 @@ package: source: url: https://github.com/pachterlab/kb_python/archive/v{{ version }}.tar.gz sha256: e8c910865fd5196b1b3163e18a565ef96c8518b2cf34f87f288dfdc85b339078 - patches: config.py.patch build: - number: 1 + number: 2 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" entry_points: @@ -33,13 +32,11 @@ requirements: - nbformat >=4.4.0 - ngs-tools >=1.5.11 - numpy >=1.17.2 - - pandas >=1.0.0 + - pandas >=1.0.0, <2 - plotly >=4.5.0 - scanpy >=1.4.4.post1 - scikit-learn >=0.21.3 - tqdm >=4.39.0 - - kallisto >=0.46.2 - - bustools >=0.40.0 - requests >=2.22.0 - typing-extensions >=3.7.4 From 86655cc7898912979faf2fbd0584fc87864e7bc0 Mon Sep 17 00:00:00 2001 From: Mateusz Warowny Date: Tue, 27 Feb 2024 00:40:55 +0100 Subject: [PATCH 0648/1813] Add AACon 1.1 recipe (#46015) --- recipes/aacon/aacon.sh | 11 +++++++++ recipes/aacon/build.sh | 11 +++++++++ recipes/aacon/meta.yaml | 49 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 71 insertions(+) create mode 100644 recipes/aacon/aacon.sh create mode 100644 recipes/aacon/build.sh create mode 100644 recipes/aacon/meta.yaml diff --git a/recipes/aacon/aacon.sh b/recipes/aacon/aacon.sh new file mode 100644 index 0000000000000..e69d47183a5e0 --- /dev/null +++ b/recipes/aacon/aacon.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -e + +JAR_NAME="compbio-conservation.jar" + +if [ -x "$JAVA_HOME/bin/java" ]; then + JAVA=$JAVA_HOME/bin/java +else + JAVA=$(which java) +fi +$JAVA -jar "$(dirname $(readlink -f "$0"))/$JAR_NAME" "$@" diff --git a/recipes/aacon/build.sh b/recipes/aacon/build.sh new file mode 100644 index 0000000000000..df55624091e03 --- /dev/null +++ b/recipes/aacon/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -eu + +OUTDIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $OUTDIR +mkdir -p $PREFIX/bin + +cp $SRC_DIR/compbio-conservation-$PKG_VERSION.jar $OUTDIR/compbio-conservation.jar +cp $RECIPE_DIR/aacon.sh $OUTDIR/aacon +ln -s $OUTDIR/aacon $PREFIX/bin/aacon +chmod +x $PREFIX/bin/aacon diff --git a/recipes/aacon/meta.yaml b/recipes/aacon/meta.yaml new file mode 100644 index 0000000000000..ab2a510cd4664 --- /dev/null +++ b/recipes/aacon/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.1" %} +{% set sha256sum = "8dd97c70d46d0f8cf6ca79f0cc7641e629db2ab3fec30bd6dbbf9de8c0607145" %} + +package: + name: aacon + version: {{ version }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('aacon', max_pin="x") }} + +source: + url: https://github.com/bartongroup/aacon/releases/download/v{{ version }}/compbio-conservation-{{ version }}.jar + sha256: {{ sha256sum }} + +requirements: + run: + - openjdk >=8 + +test: + commands: + - aacon --help + +about: + home: https://www.compbio.dundee.ac.uk/aacon/ + dev_url: https://github.com/bartongroup/aacon + license: Apache-2.0 + summary: "AACon: A Fast Amino Acid Conservation Calculation Service" + description: + AACon is a set of tools implementing 17 different conservation scores + reviewed by Valdar as well as the more complex SMERFS algorithm for + predicting protein functional sites. AACon has been written with efficiency + in mind and takes less than a second to calculate conservation by all 18 + methods for an alignment of 500 sequences 350 residues long on a single CPU. + AACon exploits parallelism for the more demanding methods and to allow + multiple methods to run simultaneously. The parallel code gives close to + linear speedup with the number of processors, thus making it suitable for + server applications or other demanding environments. + +extra: + notes: + AACon is a Java program that comes with a custom wrapper shell script. + The shell wrapper is called "aacon" and is present on $PATH by default. + The Java program is executed with java specified by the $JAVA_HOME + variable. Otherwise, a "java" program from the current environment is used. + identifiers: + - biotools:aacon From 3a97ac0ef7a47c4796c2ce9029cac597e1735398 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 18:46:38 -0500 Subject: [PATCH 0649/1813] Update ncbi-datasets-pylib to 16.6.0 (#46041) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index ca968a0c85017..b2054dbde9eb1 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.5.0" %} -{% set sha256 = "df952921dac4244df9e40d467bd441169f95c2435846b1ab55f2ccfcce805acc" %} +{% set version = "16.6.0" %} +{% set sha256 = "5c5e0afef07ab5e28de96aff4f600316a82570fc0f233a0ba9daf531e92c475f" %} package: name: {{ name|lower }} From 9262fec558713139ab50e2215c273066ecba31cc Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Mon, 26 Feb 2024 18:49:47 -0500 Subject: [PATCH 0650/1813] Bump piscem to 0.8.0 (#46035) --- recipes/piscem/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/piscem/meta.yaml b/recipes/piscem/meta.yaml index d1158ff26aa29..2d201ea73f29e 100644 --- a/recipes/piscem/meta.yaml +++ b/recipes/piscem/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.1" %} -{% set git_commit = "db091893716b1709d97cdf4a8659607e99f5b534" %} +{% set version = "0.8.0" %} +{% set git_commit = "413dd69008519c5d8157b7985578e767b321109c" %} {% set sha256 = "a72af2ab728e95aa6766a3bb4520af6273a9ea3be44a6a8dc260cd97615877df" %} package: @@ -19,7 +19,7 @@ source: requirements: build: - - rust >=1.74.1 + - rust >=1.75 - cmake - autoconf - make From 201c03da8d5e64e3d73f27668f62791575d1c692 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 19:24:32 -0500 Subject: [PATCH 0651/1813] Update pastml to 1.9.43 (#46027) * Update pastml to 1.9.43 * add run_exports --------- Co-authored-by: mencian --- recipes/pastml/meta.yaml | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/recipes/pastml/meta.yaml b/recipes/pastml/meta.yaml index 6a2f5557e6daf..b2a90ab3529f6 100644 --- a/recipes/pastml/meta.yaml +++ b/recipes/pastml/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pastml" %} -{% set version = "1.9.40" %} +{% set version = "1.9.43" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 5334bc8de70a968117240b90d90878ac935be18de6e6e485fb1a8f90cd539fea + sha256: 04307d153b92b7b25b8ddda49ff388884b9e5fd394856b256a459b497af02f82 build: number: 0 @@ -16,12 +16,14 @@ build: - pastml = pastml.acr:main - geomap = pastml.visualisation.generate_geomap:main - transition_counter = pastml.utilities.transition_counter:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" + run_exports: + - {{ pin_subpackage('pastml', max_pin="x") }} requirements: host: - pip - - python >=3.8 + - python >=3.9 run: - biopython >=1.70 - ete3 >=3.1.1 @@ -29,7 +31,7 @@ requirements: - jinja2 >=2.11.0 - numpy >=1.22 - pandas >=1.0.0 - - python >=3.8 + - python >=3.9 - scipy >=1.5.0 test: @@ -53,8 +55,8 @@ about: node states based on the tip states, with a selection of maximum likelihood and parsimonious methods. The result is then visualised as a zoomable html map. - license: GPL-3.0 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE doc_url: https://pastml.pasteur.fr/help dev_url: https://github.com/evolbioinfo/pastml From 9ac55f6003c9b65a85771796725f337c75fcee9a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 19:32:49 -0500 Subject: [PATCH 0652/1813] Update segzoo to 1.0.12 (#46032) * Update segzoo to 1.0.12 * add run_exports --------- Co-authored-by: mencian --- recipes/segzoo/meta.yaml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/recipes/segzoo/meta.yaml b/recipes/segzoo/meta.yaml index 40c193fa5d709..8c86f829f6e04 100644 --- a/recipes/segzoo/meta.yaml +++ b/recipes/segzoo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "segzoo" %} -{% set version = "1.0.11" %} +{% set version = "1.0.12" %} package: name: "{{ name|lower }}" @@ -7,26 +7,29 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3422fc3e29320253e15bafef22d378470ed1d0d88b8364ecb553b756bb9a9d53 + sha256: 8e1001759aadd267ed2a92ca87089ce9725473a386d3713209f2a6d801d64e2a build: noarch: python number: 0 entry_points: - segzoo=segzoo.main:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" + run_exports: + - {{ pin_subpackage('segzoo', max_pin="x") }} requirements: host: - - python >=3.8 + - python >=3.7 - pip run: - - python >=3.8 + - python >=3.7 - seaborn - segtools - ggd - - snakemake + - snakemake-minimal - pybedtools + test: imports: - segzoo @@ -35,7 +38,7 @@ test: about: home: "https://github.com/hoffmangroup/segzoo" - license: "GNU General Public v2 (GPLv2)" + license: "GPL-2.0-or-later" license_family: GPL2 license_file: LICENSE.txt summary: "System for turnkey analysis of semi-automated genome annotations" From 30d79a963533fac94aad262fee6d19359666081e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 19:33:11 -0500 Subject: [PATCH 0653/1813] Update open-cravat to 2.5.0 (#46026) * Update open-cravat to 2.5.0 * pin python to <3.12 --------- Co-authored-by: mencian --- recipes/open-cravat/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/open-cravat/meta.yaml b/recipes/open-cravat/meta.yaml index 18237d9992629..b02c7491e9f12 100644 --- a/recipes/open-cravat/meta.yaml +++ b/recipes/open-cravat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "open-cravat" %} -{% set version = "2.4.2" %} +{% set version = "2.5.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: af069fb71cceb5d687b2dae24cb89c3fd69591a1df9f9aea29ec7c91c581f203 + sha256: 683ac5248f4bb6694cff8958f3da1289efc51637ede26412ef353e0b15aa42ec build: number: 0 @@ -21,7 +21,7 @@ build: requirements: host: - pip - - python >=3.8 + - python >=3.8,<3.12 run: - aiohttp - aiosqlite @@ -34,7 +34,7 @@ requirements: - oyaml - psutil - pyliftover - - python >=3.8 + - python >=3.8,<3.12 - pyyaml - requests - requests-toolbelt @@ -48,7 +48,7 @@ test: - cravat about: - home: "http://www.opencravat.org" + home: "https://www.opencravat.org" license: MIT license_family: MIT license_file: LICENSE From 8b6455bc6bb639114e7e1c5c3638d1774327edd5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 19:37:04 -0500 Subject: [PATCH 0654/1813] Update fgpyo to 0.2.0 (#46033) * Update fgpyo to 0.2.0 * Update meta.yaml --------- Co-authored-by: Nils Homer --- recipes/fgpyo/meta.yaml | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/recipes/fgpyo/meta.yaml b/recipes/fgpyo/meta.yaml index 2082d162ec3a6..a95a9fecfe949 100644 --- a/recipes/fgpyo/meta.yaml +++ b/recipes/fgpyo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fgpyo" %} -{% set version = "0.1.3" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/fulcrumgenomics/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: fbf58a5bb936a7b817c61cd3fb905f7daf48326b9b642a96e16310c14d236715 + sha256: 2555357c1c6d9ca02e1b2335221dcae5edd288d307ba617ab648ee7b10a25ea5 build: noarch: python @@ -19,14 +19,13 @@ build: requirements: host: - pip - - python >=3.7 + - python >=3.8 - poetry run: - - python >=3.7 - - typing_extensions >=3.7.4 # [py < 38] - - typing_inspect >=0.3.1 # [py < 38] + - python >=3.8 + - typing_extensions >=3.7.4 # [py > 311] - attrs >=19.3.0 - - pysam >=0.20.0 + - pysam >=0.22.0 - pytest >=7.4.0 run_constrained: - sphinx 4.3.1 From abaa8e7956a131023523f84cb95d3e78ca3cf9b5 Mon Sep 17 00:00:00 2001 From: Jim Shaw Date: Mon, 26 Feb 2024 20:24:42 -0500 Subject: [PATCH 0655/1813] added fairy recipe (#46040) --- recipes/fairy/build.sh | 8 ++++++++ recipes/fairy/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 recipes/fairy/build.sh create mode 100644 recipes/fairy/meta.yaml diff --git a/recipes/fairy/build.sh b/recipes/fairy/build.sh new file mode 100644 index 0000000000000..3662f6efb60db --- /dev/null +++ b/recipes/fairy/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX diff --git a/recipes/fairy/meta.yaml b/recipes/fairy/meta.yaml new file mode 100644 index 0000000000000..ec86bae4a9353 --- /dev/null +++ b/recipes/fairy/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "0.5.2" %} + +package: + name: fairy + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('fairy', max_pin='x.x') }} + +source: + url: https://github.com/bluenote-1577/fairy/archive/v{{ version }}.tar.gz + sha256: 61882e078b64da6d8f4f9ed64770f83776f8a9e2e2c9a2e3c759c285aa97d6cd + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.61 + - make + - cmake >=3.12 + +test: + commands: + - fairy --help + +about: + home: https://github.com/bluenote-1577/fairy + license: MIT + summary: fairy calculates all-to-all approximate coverage for multi-sample metagenomic binning > 100x faster than alignment. + license_file: LICENSE + +extra: + recipe-maintainers: + - bluenote-1577 + From 2676794b487360001df195516a09552ab09c06dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 20:35:19 -0500 Subject: [PATCH 0656/1813] Update toil to 6.1.0 (#45984) * Update toil to 6.1.0 * remove patch --------- Co-authored-by: mencian --- .../drop_ruamel_yaml_string_dependency.patch | 52 ------------------- recipes/toil/meta.yaml | 11 ++-- 2 files changed, 5 insertions(+), 58 deletions(-) delete mode 100644 recipes/toil/drop_ruamel_yaml_string_dependency.patch diff --git a/recipes/toil/drop_ruamel_yaml_string_dependency.patch b/recipes/toil/drop_ruamel_yaml_string_dependency.patch deleted file mode 100644 index e2121b54bca4b..0000000000000 --- a/recipes/toil/drop_ruamel_yaml_string_dependency.patch +++ /dev/null @@ -1,52 +0,0 @@ -commit 893aa9b3295400829a86054cab028635e9bd2dd2 -Author: Michael R. Crusoe -Date: Mon Jan 22 14:58:45 2024 +0100 - - remove ruamel.yaml.string dependency for a simpler solution - -diff --git a/requirements.txt b/requirements.txt -index c34aceb56..b0e85191d 100644 ---- a/requirements.txt -+++ b/requirements.txt -@@ -11,6 +11,5 @@ pytz>=2012 - enlighten>=1.5.2, <2 - configargparse>=1.7,<2 - ruamel.yaml>=0.15 --ruamel.yaml.string>=0.1.1 - pyyaml>=6,<7 - typing-extensions>=4.6.2, <5 -diff --git a/src/toil/common.py b/src/toil/common.py -index d2531d3aa..c8852c8ce 100644 ---- a/src/toil/common.py -+++ b/src/toil/common.py -@@ -23,6 +23,7 @@ import tempfile - import time - import uuid - import warnings -+from io import StringIO - - from ruamel.yaml import YAML - from ruamel.yaml.comments import CommentedMap -@@ -580,15 +581,16 @@ def generate_config(filepath: str) -> None: - with AtomicFileCreate(filepath) as temp_path: - with open(temp_path, "w") as f: - f.write("config_version: 1.0\n") -- yaml = YAML(typ=['rt', 'string']) -+ yaml = YAML(typ='rt') - for data in all_data: - if "config_version" in data: - del data["config_version"] -- for line in yaml.dump_to_string(data).split("\n"): # type: ignore[attr-defined] -- if line: -- f.write("#") -- f.write(line) -- f.write("\n") -+ with StringIO() as data_string: -+ yaml.dump(data, data_string) -+ for line in data_string.readline(): -+ if line: -+ f.write("#") -+ f.write(f"{line}\n") - - - def parser_with_common_options( diff --git a/recipes/toil/meta.yaml b/recipes/toil/meta.yaml index 0f3965135414e..7b8575a283ced 100644 --- a/recipes/toil/meta.yaml +++ b/recipes/toil/meta.yaml @@ -1,6 +1,6 @@ {% set name = "toil" %} -{% set version = "6.0.0" %} -{% set sha256 = "6cf772b744b886a53eaaf700e51ea2fd03bac15d384c34ee9e53455cbe00b33b" %} +{% set version = "6.1.0" %} +{% set sha256 = "0a92ab1b4af9ab379b9218cd4b4d59997a6bf8db2fc6e134e0dd69662d8c8a43" %} package: name: {{ name|lower }} @@ -9,13 +9,11 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz sha256: {{ sha256 }} - patches: - - drop_ruamel_yaml_string_dependency.patch # https://github.com/DataBiosphere/toil/pull/4760 build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv run_exports: - {{ pin_subpackage(name, max_pin="x") }} entry_points: @@ -109,9 +107,10 @@ test: - toil-cwl-runner --help about: - home: 'http://toil.ucsc-cgl.org/' + home: 'https://toil.ucsc-cgl.org/' summary: 'A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python' dev_url: 'https://github.com/DataBiosphere/toil' doc_url: 'https://toil.readthedocs.io/en/latest/' license: Apache-2.0 + license_family: APACHE license_file: LICENSE From 2ccac8de09242b0d925de4a248786d736329532a Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 26 Feb 2024 20:15:56 -0600 Subject: [PATCH 0657/1813] Update gmap to 2024.02.22 (#46034) * Update gmap to 2024.02.22 * edit build.sh * revert to skipping OSX --- recipes/gmap/build.sh | 12 ++++-------- recipes/gmap/meta.yaml | 4 ++-- 2 files changed, 6 insertions(+), 10 deletions(-) diff --git a/recipes/gmap/build.sh b/recipes/gmap/build.sh index f7a0c51aced84..f8c4331734fc6 100644 --- a/recipes/gmap/build.sh +++ b/recipes/gmap/build.sh @@ -1,7 +1,7 @@ -#!/bin/bash +#!/bin/bash -euo -export INCLUDE_PATH=${PREFIX}/include -export LIBRARY_PATH=${PREFIX}/lib +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3" export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" @@ -12,11 +12,7 @@ if [ "$(uname)" == "Darwin" ]; then export CFLAGS="${CFLAGS} -m64" fi -export LANGUAGE=en_US.UTF-8 -export LANG=en_US.UTF-8 -export LC_ALL=en_US.UTF-8 - -autoreconf -i +autoreconf -if ./configure CC="${CC}" CFLAGS="${CFLAGS}" \ CPPFLAGS="${CPPFLAGS}" \ LDFLAGS="${LDFLAGS}" \ diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index cceb395e938e3..c4d1ffcb146e2 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GMAP" %} -{% set version = "2023.12.01" %} -{% set sha256 = "878193a4ec16539d4aa2594424e55a9670e2bdae607e63e088962c904ec6ef69" %} +{% set version = "2024.02.22" %} +{% set sha256 = "d528c2d9554cb5f98f805eebb412c58297125edb1e7164dba6bbc2f72ff2204c" %} package: name: {{ name|lower }} From 4f13e237280380f5c3cf3238cb3407ed26f6b407 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 26 Feb 2024 22:20:17 -0500 Subject: [PATCH 0658/1813] Update vg to 1.55.0 (#46044) --- recipes/vg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml index c67d295ba6970..7fa4d9974f826 100644 --- a/recipes/vg/meta.yaml +++ b/recipes/vg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vg" %} -{% set version = "1.54.0" %} +{% set version = "1.55.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg - sha256: 84bee2444b3714b5b8672ea4a4e28063c0eb41a22b8b7359641c10467fe8b247 + sha256: 2c602084b4eab7b50147fba31f51e126135d7ceaaf405632445bff96d68ba6c7 build: number: 0 From 74de28b80587b122f932db755b1db1b664d5f857 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 26 Feb 2024 21:47:47 -0600 Subject: [PATCH 0659/1813] Relax R dependencies (#46045) --- recipes/strainr2/build.sh | 17 +++++++++-------- recipes/strainr2/meta.yaml | 24 ++++++++++++------------ 2 files changed, 21 insertions(+), 20 deletions(-) diff --git a/recipes/strainr2/build.sh b/recipes/strainr2/build.sh index 9e30d76742542..7919ee79c22f1 100644 --- a/recipes/strainr2/build.sh +++ b/recipes/strainr2/build.sh @@ -1,7 +1,8 @@ -#! /bin/bash -mkdir -p ${PREFIX}/bin +#!/bin/bash -euo -$CC $SRC_DIR/subcontig.c -o subcontig +mkdir -p "${PREFIX}/bin" + +${CC} ${SRC_DIR}/subcontig.c -o subcontig chmod +x $SRC_DIR/PreProcessR chmod +x $SRC_DIR/subcontig @@ -9,8 +10,8 @@ chmod +x $SRC_DIR/hashcounter.py chmod +x $SRC_DIR/Plot.R chmod +x $SRC_DIR/StrainR -cp $SRC_DIR/PreProcessR ${PREFIX}/bin/ -cp $SRC_DIR/subcontig ${PREFIX}/bin/ -cp $SRC_DIR/hashcounter.py ${PREFIX}/bin/ -cp $SRC_DIR/Plot.R ${PREFIX}/bin/ -cp $SRC_DIR/StrainR ${PREFIX}/bin/ +cp $SRC_DIR/PreProcessR ${PREFIX}/bin/ +cp $SRC_DIR/subcontig ${PREFIX}/bin/ +cp $SRC_DIR/hashcounter.py ${PREFIX}/bin/ +cp $SRC_DIR/Plot.R ${PREFIX}/bin/ +cp $SRC_DIR/StrainR ${PREFIX}/bin/ diff --git a/recipes/strainr2/meta.yaml b/recipes/strainr2/meta.yaml index d0e50a9dcfb66..48ea5f5ae72aa 100644 --- a/recipes/strainr2/meta.yaml +++ b/recipes/strainr2/meta.yaml @@ -9,25 +9,25 @@ source: sha256: 6ed9671c875ec6388960dbac02a73629d58ad20adad1fe297d905d8969ec0489 build: - number: 0 + number: 1 run_exports: - - {{ pin_subpackage("strainr2", max_pin="x.x") }} + - {{ pin_subpackage("strainr2", max_pin="x") }} requirements: build: - {{ compiler('c') }} host: - - python >=3.12.0 - - r-base >=4.3.2 + - python + - r-base >=4.2.0 run: - - bbmap >=39.01 - - fastp >=0.23.4 - - python >=3.12.0 - - samtools >=1.18 - - sourmash >=4.8.4 - - r-base >=4.3.2 - - r-optparse >=1.7.3 - - r-tidyverse >=2.0.0 + - python + - bbmap + - fastp + - samtools + - sourmash >=4.0.0 + - r-base >=4.2.0 + - r-optparse + - r-tidyverse test: commands: From 7ce232dcd8edfde5f178cf67faf6e4cdf43b245b Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 26 Feb 2024 22:26:12 -0600 Subject: [PATCH 0660/1813] Remove LICENSE from monopogen recipe (#46046) * Remove LICENSE from monopogen recipe * add build.sh --- recipes/monopogen/LICENSE | 674 ------------------------------------ recipes/monopogen/build.sh | 8 + recipes/monopogen/meta.yaml | 3 +- 3 files changed, 9 insertions(+), 676 deletions(-) delete mode 100644 recipes/monopogen/LICENSE create mode 100644 recipes/monopogen/build.sh diff --git a/recipes/monopogen/LICENSE b/recipes/monopogen/LICENSE deleted file mode 100644 index f288702d2fa16..0000000000000 --- a/recipes/monopogen/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/recipes/monopogen/build.sh b/recipes/monopogen/build.sh new file mode 100644 index 0000000000000..77db429cd8ee9 --- /dev/null +++ b/recipes/monopogen/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -euo + +mkdir -p ${PREFIX}/bin + +${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation + +chmod +rx ${SP_DIR}/Monopogen.py +cp ${SP_DIR}/Monopogen.py ${PREFIX}/bin diff --git a/recipes/monopogen/meta.yaml b/recipes/monopogen/meta.yaml index 21136e395ad53..9470742aac938 100644 --- a/recipes/monopogen/meta.yaml +++ b/recipes/monopogen/meta.yaml @@ -11,9 +11,8 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: python - script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation run_exports: - {{ pin_subpackage('monopogen', max_pin="x") }} From 99025fc4a6f393fa44f94fd93926667e9a544d2f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 27 Feb 2024 02:13:08 -0500 Subject: [PATCH 0661/1813] Update gxf2bed to 0.2.1 (#46047) --- recipes/gxf2bed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gxf2bed/meta.yaml b/recipes/gxf2bed/meta.yaml index b95b9777d8ddb..914c92ba00eb3 100644 --- a/recipes/gxf2bed/meta.yaml +++ b/recipes/gxf2bed/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gxf2bed" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: gxf2bed @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5bd42033a2b72fe8e4a6dd467fb97ca3cd4ebd71d2f4466467cec384c5acbf9c + sha256: 139efd9c4294d92a27f058db2bc58dfbcaaab8be45ca1022794a4f3780cd962f build: number: 0 From 45ed1ec47b411fb44f3a476c93b8a3ff6d80cd93 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 27 Feb 2024 02:47:32 -0500 Subject: [PATCH 0662/1813] Update hmftools-mark-dups to 1.1.2 (#46048) --- recipes/hmftools-mark-dups/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-mark-dups/meta.yaml b/recipes/hmftools-mark-dups/meta.yaml index e85200d715b60..535227f7b06c6 100644 --- a/recipes/hmftools-mark-dups/meta.yaml +++ b/recipes/hmftools-mark-dups/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.1" %} -{% set sha256 = "053440f3aac22a6bd627795bd5968180c0e6b7dcce43e45dab1a5536e1220abd" %} +{% set version = "1.1.2" %} +{% set sha256 = "e1a8e5ea860627a9cb04eb7fd1ad501b22d4676092dfbb6f42077c34d6bf98fd" %} package: name: hmftools-mark-dups From 86629b8d91df47bde00fa3f6d715297d1be61a37 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 27 Feb 2024 10:48:04 -0500 Subject: [PATCH 0663/1813] Update cramino to 0.14.5 (#46051) --- recipes/cramino/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cramino/meta.yaml b/recipes/cramino/meta.yaml index dedfeb0ffcfa5..ae53c0a7a5a9d 100644 --- a/recipes/cramino/meta.yaml +++ b/recipes/cramino/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.4" %} +{% set version = "0.14.5" %} package: name: cramino @@ -12,7 +12,7 @@ build: source: url: https://github.com/wdecoster/cramino/archive/v{{ version }}.tar.gz - sha256: b07a40180dae4d413ba1cb3ea1307bcf5208634cab38ede352e70e8edd84e6ba + sha256: d3b31ab76808ca76171e2539cfe30e66fe24cbd4af4ff9a941c282a0bc438032 requirements: build: From bb4474dcbf8e26011a08b2f515ed9b6b8b358de8 Mon Sep 17 00:00:00 2001 From: mwaldl Date: Tue, 27 Feb 2024 17:08:14 +0100 Subject: [PATCH 0664/1813] Update to new RRIkinDP release (#46017) * remove LDFlags from make call * update to new release RRIkinDP v0.0.2 with pybind11 wrapper fro core c++ class * Reset build number * Add pybind11 dependency --------- Co-authored-by: Sebastian Will --- recipes/rrikindp/build.sh | 2 +- recipes/rrikindp/meta.yaml | 13 ++++--------- 2 files changed, 5 insertions(+), 10 deletions(-) diff --git a/recipes/rrikindp/build.sh b/recipes/rrikindp/build.sh index 0f8e3cfde1a94..f76fe49b36083 100644 --- a/recipes/rrikindp/build.sh +++ b/recipes/rrikindp/build.sh @@ -4,5 +4,5 @@ $PYTHON -m pip install . --no-deps --ignore-installed -vv cd src/rrikindp -make -j ${CPU_COUNT} CXXFLAGS+="-I${CONDA_PREFIX}/include" LDFLAGS+="-L${CONDA_PREFIX}/lib" +make -j ${CPU_COUNT} CXXFLAGS+="-I${CONDA_PREFIX}/include" install RRIkinDP "${PREFIX}/bin" diff --git a/recipes/rrikindp/meta.yaml b/recipes/rrikindp/meta.yaml index 18246c4e9a938..3e89245d087da 100644 --- a/recipes/rrikindp/meta.yaml +++ b/recipes/rrikindp/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RRIkinDP" %} -{% set version = "0.0.1" %} +{% set version = "0.0.2" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: source: url: https://github.com/mwaldl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 75f6f0dd0c993796423ca812ab4926225c44d718ab3bbe90c0be856aa5d83d2f + sha256: 3bdaa7657224b90945d864d0238010cf3337975f58c41106ab60427dd52bc93f build: number: 0 @@ -20,8 +20,10 @@ requirements: - python - pip - make + - pybind11 - {{ compiler('cxx') }} host: + - pybind11 - python - boost-cpp - viennarna >=2.6.0 @@ -37,13 +39,6 @@ requirements: - seaborn >=0.12.0 - pandas >=2.0.0 - -output: - files: - - src/RRIkinDP/RRIkinDP - py_modules: - - rrikindp - test: commands: - RRIkinDP --version From 1337cc2ee8ab440d9baaca8a168a67870b7a35ce Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 27 Feb 2024 11:57:21 -0500 Subject: [PATCH 0665/1813] Update pybiolib to 1.1.1774 (#46049) * Update pybiolib to 1.1.1769 * Update pybiolib to 1.1.1774 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 8d80ba7513048..3196c4e0be67c 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1755" %} +{% set version = "1.1.1774" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 1bc65e6a214cf103a453b5119178e6e0db26757d1d7f3fc62d65a2ce188caf95 + sha256: d7983af921fef2e208105c864bf6076343e6c877c3ab5e95aa5c407252a27729 build: noarch: python From af35e6937f31732ef2365b5c103deece9fb5094b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 03:35:59 -0500 Subject: [PATCH 0666/1813] Update wgd to 2.0.26 (#46066) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index aabbc58070e0f..106a69c3b0845 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.25" %} +{% set version = "2.0.26" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: d43295772471abbade56b343f8e2152682594ed16fc8ca779a2a0ec642a784f5 + sha256: eca2e580095b1857868a31fb58b02eb886e0de500569afa44930e8469bb1c12d build: number: 0 From ff0fb2bf9fa4e422956a52ee72e7b334c0a9b4b2 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 28 Feb 2024 16:02:26 +0100 Subject: [PATCH 0667/1813] Bump Multiqc (#46075) Bump MultiQC and update source URL --- recipes/multiqc/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 2f3097c7e9847..822b056cb2126 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -1,15 +1,15 @@ -{% set version = "1.20" %} +{% set version = "1.21" %} package: name: multiqc version: {{ version }} source: - url: https://github.com/ewels/MultiQC/archive/v{{ version }}.tar.gz - sha256: 46e01394ee4c213eee3c14fde01afcb0da3e87a29b09a119e5aaeabf2817313d + url: https://github.com/MultiQC/MultiQC/archive/v{{ version }}.tar.gz + sha256: c0e4887598628567b8fb1539445cf7b34a7ac6a8db2e52e10cc42cfa8e2202e2 build: - number: 2 + number: 0 entry_points: - multiqc=multiqc.__main__:run_multiqc noarch: python From 408cd3d864db05e1ff91af91c3c662b9378c3e69 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 10:56:03 -0500 Subject: [PATCH 0668/1813] Update sdrf-pipelines to 0.0.25 (#46076) --- recipes/sdrf-pipelines/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sdrf-pipelines/meta.yaml b/recipes/sdrf-pipelines/meta.yaml index 781f33c8be3ae..1fd34b609a64e 100644 --- a/recipes/sdrf-pipelines/meta.yaml +++ b/recipes/sdrf-pipelines/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sdrf-pipelines" %} -{% set version = "0.0.24" %} +{% set version = "0.0.25" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a52441d8b4be0b597c64973d45a4ad2dc2b91560cf7fbee956080efd9a306dbd + sha256: a390a61a5fc696a60f7e27c221e078b2e8d1f7e81625cec05e5486c5554d9ebc build: number: 0 From 0cc0b91a8f03ff21ead6c339ae784ec9fd473ff6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 11:29:51 -0500 Subject: [PATCH 0669/1813] Update pyfastx to 2.1.0 (#46074) --- recipes/pyfastx/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyfastx/meta.yaml b/recipes/pyfastx/meta.yaml index 9006bae819474..e3e7a117d395f 100644 --- a/recipes/pyfastx/meta.yaml +++ b/recipes/pyfastx/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pyfastx" %} -{% set version = "2.0.2" %} -{% set sha256 = "763bb59f58d7884cad8a15ff8b0f0bbc5e29f867a4260d1e5ed9ecb2035ac70b" %} +{% set version = "2.1.0" %} +{% set sha256 = "a3458bba4fa19a637d9ec8bdf9bfdd6e7321a916aeca674d02aa0fe5aeee1c95" %} package: name: {{ name|lower }} From a84eb087d66354a1d5115bf6a908497106f3a226 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 11:30:07 -0500 Subject: [PATCH 0670/1813] Update ont-fast5-api to 4.1.3 (#46072) --- recipes/ont-fast5-api/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ont-fast5-api/meta.yaml b/recipes/ont-fast5-api/meta.yaml index f860d6263889c..61dcfc3873f45 100644 --- a/recipes/ont-fast5-api/meta.yaml +++ b/recipes/ont-fast5-api/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ont-fast5-api" %} -{% set version = "4.1.2" %} +{% set version = "4.1.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c7c59c6100e992ef8bc239cdf91f7a8ab46abf57ecd689f94b2b98e72a9e9472 + sha256: 302d10ed87b439f8f22c2c06d45d68d017e47dd8df9bd48f155cad041f464b68 build: number: 0 From 4c3d5e1bd2dea50fb26425f0a0df8f98507cea40 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 11:31:06 -0500 Subject: [PATCH 0671/1813] Update phykit to 1.14.0 (#46065) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index 5199781fe01be..df44afb0cd1f8 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.13.1" %} +{% set version = "1.14.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: bd8076262d7f25f6780deed903af3d16abeb268975420e8f2fd2a3e5379e40cd + sha256: 796a849e9a3dff3c93a7d6e0f3d8145a549340bdc9db7b616190c16e9b7e4f08 build: noarch: python From 0f57bf5a6fd8efdcd09607ad8f1d73cf8134a0d5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 11:31:31 -0500 Subject: [PATCH 0672/1813] Update pyensembl to 2.3.11 (#46063) --- recipes/pyensembl/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index cb30778055db9..0a9814354ab74 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PyEnsembl" %} -{% set version = "2.3.9" %} -{% set sha256 = "444c4f489818fd639c34a631a9527cd6bb6586bf20b58daffe1b79d1d1ef86f4" %} +{% set version = "2.3.11" %} +{% set sha256 = "e3283514218b93b0626165ad3aa34b6487198b715555394e026a48aed7ff0901" %} package: name: {{ name|lower }} From 87bf4fafefa7d1dadf3d47e8d38e17a290c0cb4e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 12:14:25 -0500 Subject: [PATCH 0673/1813] Update fairy to 0.5.3 (#46067) --- recipes/fairy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fairy/meta.yaml b/recipes/fairy/meta.yaml index ec86bae4a9353..068a0072ee13f 100644 --- a/recipes/fairy/meta.yaml +++ b/recipes/fairy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.2" %} +{% set version = "0.5.3" %} package: name: fairy @@ -11,7 +11,7 @@ build: source: url: https://github.com/bluenote-1577/fairy/archive/v{{ version }}.tar.gz - sha256: 61882e078b64da6d8f4f9ed64770f83776f8a9e2e2c9a2e3c759c285aa97d6cd + sha256: 8a949dde81a89b8c6f7bea74e793d90df923b34addd360448263a129977771e8 requirements: build: From 8ef019e23610df03bab91d39c89db4d2bfdc6811 Mon Sep 17 00:00:00 2001 From: Patrick Blumenkamp Date: Wed, 28 Feb 2024 19:57:51 +0100 Subject: [PATCH 0674/1813] update Curare to 0.6.0 (#46062) * update Curare to 0.6.0 * modify sha256 --------- Co-authored-by: Patrick Blumenkamp --- recipes/curare/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/curare/meta.yaml b/recipes/curare/meta.yaml index 961edaf9848d9..0458d942c20e0 100644 --- a/recipes/curare/meta.yaml +++ b/recipes/curare/meta.yaml @@ -1,5 +1,5 @@ {% set name = "curare" %} -{% set version = "0.5.1" %} +{% set version = "0.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/pblumenkamp/Curare/archive/refs/tags/{{ version }}.tar.gz - sha256: bf1d47c889b90bb33b5b5353b87d8486a23321394a928e863510c6ac2e8eb0c7 + sha256: e98935fce614bf0b8b3db4e9c65c9fbba999fab84e69e4158209b6319f59a0da build: number: 0 @@ -29,6 +29,8 @@ requirements: - python =3.10 - pyyaml =6.0 - docopt =0.6.2 + - progressbar2 =4.3.2 + - biopython =1.83 test: imports: From f8f7634e790df78e809af47ca1985b4ec4010981 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 13:59:41 -0500 Subject: [PATCH 0675/1813] Update pyopal to 0.5.2 (#46068) --- recipes/pyopal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyopal/meta.yaml b/recipes/pyopal/meta.yaml index fe7ef5a8f3e0e..12f3680ab55a1 100644 --- a/recipes/pyopal/meta.yaml +++ b/recipes/pyopal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyopal" %} -{% set version = "0.5.1" %} +{% set version = "0.5.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: debc526d00f605f1a9f75ece2bb124b6b370f8649857bc33ec7bdc264e8cc6cb + sha256: c58b573890a13197caea03d25b7db1de6fd8f8ece91b1337ab96c7b1668616c9 build: number: 0 From d0d88d32db4de1c04736a10d7ee9fb568e7f1f22 Mon Sep 17 00:00:00 2001 From: Catherine Chahrour <74187550+CChahrour@users.noreply.github.com> Date: Wed, 28 Feb 2024 19:03:14 +0000 Subject: [PATCH 0676/1813] update recipe for seqnado (#46059) * update recipe for seqando * update hashes * update release number * edit version number --- recipes/seqnado/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/seqnado/meta.yaml b/recipes/seqnado/meta.yaml index c9914ff336c16..8442d89bc166a 100644 --- a/recipes/seqnado/meta.yaml +++ b/recipes/seqnado/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqnado" %} -{% set version = "0.4.1" %} +{% set version = "0.4.3" %} package: name: {{ name|lower }} @@ -7,7 +7,8 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqnado-{{ version }}.tar.gz - sha256: 171d551baf6eb3e6b7402510826688804f9fab0d3dba0db9907da92a1059dc47 + sha256: 21a943093411bc81e82a23ab64a59945d9c5c142159abd5ddbcd75a0ca63fb85 + build: number: 0 @@ -41,7 +42,7 @@ requirements: - seaborn - setuptools-scm - singularity - - snakemake <=7.3.2 + - snakemake >=7.32.4, <8.0.0 - snakemake-wrapper-utils - tracknado - wget From 270d472c46f826ed0d2f7763ef49305ac25bc381 Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 28 Feb 2024 19:04:03 +0000 Subject: [PATCH 0677/1813] Add recipe for ebi-eva-common-pyutils (#46050) * add recipe for eva-common-pyutils * add run_exports * add noarch: python --- recipes/ebi-eva-common-pyutils/meta.yaml | 47 ++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/ebi-eva-common-pyutils/meta.yaml diff --git a/recipes/ebi-eva-common-pyutils/meta.yaml b/recipes/ebi-eva-common-pyutils/meta.yaml new file mode 100644 index 0000000000000..2cb79f2171346 --- /dev/null +++ b/recipes/ebi-eva-common-pyutils/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "ebi-eva-common-pyutils" %} +{% set version = "0.6.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ebi_eva_common_pyutils-{{ version }}.tar.gz + sha256: 6e5480b12b11fad97412c95a2d6687c0022f4f3f753fd0cb0c6d6c928a064728 + +build: + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python + - pip + run: + - python + - requests + - lxml + - pyyaml + - cached-property + - retry + +test: + imports: + - ebi_eva_common_pyutils + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/EBIVariation/eva-common-pyutils + summary: EBI EVA - Common Python Utilities + license: Apache-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - apriltuesday From 615ad8f0149c7b89764a8fff8e59979523c1a7fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 14:04:49 -0500 Subject: [PATCH 0678/1813] Update parascopy to 1.15.0 (#46053) * Update parascopy to 1.15.0 * added zlib --------- Co-authored-by: Thanh Lee --- recipes/parascopy/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/parascopy/meta.yaml b/recipes/parascopy/meta.yaml index f83ef261d7f2e..5f8fbfe538d8a 100644 --- a/recipes/parascopy/meta.yaml +++ b/recipes/parascopy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "parascopy" %} -{% set version = "1.14.1" %} +{% set version = "1.15.0" %} package: name: {{ name|lower }} @@ -15,7 +15,7 @@ build: source: url: https://github.com/tprodanov/{{ name }}/archive/v{{ version }}.tar.gz - sha256: a475086faeea706448db866ca8c504b3c17f3988a67fd8c174f1a334bd4bb4f1 + sha256: 4e588ccefb63694f0cc434d92ad45999425dc4dfd168c37155d14d9cf249c4d4 requirements: build: @@ -28,10 +28,12 @@ requirements: - python - pip - bzip2 + - zlib - htslib - tabixpp run: - python + - zlib - numpy >=1.15 - scipy >=1.5 - pysam >=0.17 From 626b0fe853d270620ee4b2cdb306712b20738ee5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 14:05:00 -0500 Subject: [PATCH 0679/1813] Update pybiolib to 1.1.1780 (#46057) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 3196c4e0be67c..12823302525bb 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1774" %} +{% set version = "1.1.1780" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: d7983af921fef2e208105c864bf6076343e6c877c3ab5e95aa5c407252a27729 + sha256: 02373e8364507796f416175d0eb1d2970c1980b4c81f628047f0163b77418bd4 build: noarch: python From 567b059a3334957bc9c408873f9fe902dc312407 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 14:05:21 -0500 Subject: [PATCH 0680/1813] Update dimet to 0.2.2 (#46064) --- recipes/dimet/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dimet/meta.yaml b/recipes/dimet/meta.yaml index 8a230316e2d32..601dacf485321 100644 --- a/recipes/dimet/meta.yaml +++ b/recipes/dimet/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dimet" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dimet-{{ version }}.tar.gz - sha256: e5ad617a5f45072bfd4257cc09b965cf27341a252de979864462c3a8e0ba94dc + sha256: f5d601a43994705d6bc0cd3948b57756b89dfbd8784266549929a0c8ac3368db build: noarch: python From 0c34317ee7753abff338d93604c38604aa2d1254 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 14:06:03 -0500 Subject: [PATCH 0681/1813] Update pydeseq2 to 0.4.6 (#46071) --- recipes/pydeseq2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml index c66af03900ccf..47fda48bd6c9f 100644 --- a/recipes/pydeseq2/meta.yaml +++ b/recipes/pydeseq2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydeseq2" %} -{% set version = "0.4.5" %} +{% set version = "0.4.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz - sha256: 51b32980f1959bb14c8830b151f60493fff7d8c5e0a1774889ef09de5aa194f1 + sha256: 952fff95213f66dd4c1c9a2d86d863b4ba062f84192e80caefe3620484271fda build: noarch: python From e9f0deff85b96764d2c37a19e4e3947d073f685e Mon Sep 17 00:00:00 2001 From: Martin Larralde Date: Wed, 28 Feb 2024 20:20:06 +0100 Subject: [PATCH 0682/1813] Update GECCO to `v0.9.10` (#46055) * Update GECCO to `v0.9.10` * Add missing `run_exports` to GECCO recipe --- recipes/gecco/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/gecco/meta.yaml b/recipes/gecco/meta.yaml index 6dec56a044f8e..34a6b65a20e38 100644 --- a/recipes/gecco/meta.yaml +++ b/recipes/gecco/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GECCO" %} {% set name_pypi = "gecco-tool" %} -{% set version = "0.9.8" %} +{% set version = "0.9.10" %} package: name: "{{ name|lower }}" @@ -8,12 +8,14 @@ package: source: url: https://pypi.org/packages/source/g/{{ name_pypi }}/{{ name_pypi }}-{{ version }}.tar.gz - sha256: 4d67a654e84258c574ec1e3506ea1411c2ffa2d8b1abac41c198bb276edd4626 + sha256: 6ab405587824228a2a2baa08ccb9e6df1f6df214fe6c1a531b778a613fb1e90d build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + run_exports: + - {{ pin_subpackage("gecco", max_pin="x.x") }} requirements: host: @@ -34,8 +36,8 @@ requirements: - numpy >=1.16 - polars >=0.16.1 - psutil >=5.8 - - pyhmmer >=0.8.0 - - pyrodigal >=2.1.0 + - pyhmmer >=0.10.0 + - pyrodigal >=3.0 - rich >=12.4.0 - scikit-learn >=1.0 - scipy >=1.4 From a875c49389bdc203e8d99ebc29fa5813f948c4d2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 14:43:08 -0500 Subject: [PATCH 0683/1813] Update snakemake-storage-plugin-fs to 1.0.0 (#46069) * Update snakemake-storage-plugin-fs to 1.0.0 * add run_exports --------- Co-authored-by: mencian --- recipes/snakemake-storage-plugin-fs/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/snakemake-storage-plugin-fs/meta.yaml b/recipes/snakemake-storage-plugin-fs/meta.yaml index 996d529132ccb..1ee27eb1bf8c4 100644 --- a/recipes/snakemake-storage-plugin-fs/meta.yaml +++ b/recipes/snakemake-storage-plugin-fs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-fs" %} -{% set version = "0.2.0" %} +{% set version = "1.0.0" %} package: name: {{ name|lower }} @@ -7,14 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_fs-{{ version }}.tar.gz - sha256: cad1859036cbf429ea6fdb97f242567ec54a36d0b6ff900ce0d3ecfb6a824ae7 + sha256: de4ed37232173b604fadbf93cd84b05a8c28fa3e1d3167426bef181c7256e22c build: noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation number: 0 run_exports: - - {{ pin_subpackage(name, max_pin="x.x") }} + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: @@ -23,9 +23,10 @@ requirements: - pip run: - python >=3.11.0,<4.0.0 - - snakemake-interface-common >=1.14.2,<2.0.0 - - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 + - snakemake-interface-common >=1.17.0,<2.0.0 + - snakemake-interface-storage-plugins >=3.1.0,<4.0.0 - sysrsync >=1.1.1,<2.0.0 + - reretry >=0.11.8,<0.12.0 test: # We do not test the import as the plugin needs snakemake for importing, but adding @@ -39,6 +40,7 @@ about: home: https://github.com/snakemake/snakemake-storage-plugin-fs summary: 'A Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync' license: MIT + license_family: MIT license_file: LICENSE extra: From 34181294d5db8ac01be0a9e0a93d92d8c818607c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Wed, 28 Feb 2024 22:48:19 +0100 Subject: [PATCH 0684/1813] Add nanoinsight (#46079) * Add nanoinsight * Add license file --- recipes/nanoinsight/LICENSE.txt | 674 ++++++++++++++++++++++++++++++++ recipes/nanoinsight/meta.yaml | 44 +++ 2 files changed, 718 insertions(+) create mode 100644 recipes/nanoinsight/LICENSE.txt create mode 100644 recipes/nanoinsight/meta.yaml diff --git a/recipes/nanoinsight/LICENSE.txt b/recipes/nanoinsight/LICENSE.txt new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/nanoinsight/LICENSE.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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But first, please read +. diff --git a/recipes/nanoinsight/meta.yaml b/recipes/nanoinsight/meta.yaml new file mode 100644 index 0000000000000..881ab16d68a82 --- /dev/null +++ b/recipes/nanoinsight/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "nanoinsight" %} +{% set version = "0.0.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanoinsight-{{ version }}.tar.gz + sha256: a0ca0076fc6cbf11f6460d48ba3a07a97fea01f77282e70da2e992df97afc3c9 + +build: + entry_points: + - nanoinsight=nanoinsight.nanoinsight:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('nanoinsight', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - biopython >=1.82 + - scikit-allel >=1.3.7 + - pandas >=1.5.3 + - mafft + - repeatmasker + +test: + imports: + - nanoinsight + commands: + - nanoinsight --help + +about: + home: https://github.com/AsmaaSamyMohamedMahmoud/nanoinsight + summary: Repeat annotation tool for insertions called by NanoVar + license: GPL-3.0-or-later + license_file: LICENSE.txt + From f63af41805257982dbda09911c046e8a206ab24a Mon Sep 17 00:00:00 2001 From: Nezar Abdennur Date: Wed, 28 Feb 2024 19:14:21 -0500 Subject: [PATCH 0685/1813] Update pybigtools to v0.1.2 (#46052) * Update pybigtools to v0.1.1 * Include run_exports * Update meta.yaml * Fix target dir * clean up recipe * bump to 0.1.2 * edit license_file line --------- Co-authored-by: mencian --- recipes/pybigtools/build.sh | 12 +++++++++--- recipes/pybigtools/meta.yaml | 16 ++++++++++------ 2 files changed, 19 insertions(+), 9 deletions(-) diff --git a/recipes/pybigtools/build.sh b/recipes/pybigtools/build.sh index d9c921719d1d8..c42f164e8f033 100644 --- a/recipes/pybigtools/build.sh +++ b/recipes/pybigtools/build.sh @@ -4,14 +4,20 @@ # -x = print every executed command set -ex +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + # Use a custom temporary directory as home on macOS. # (not sure why this is useful, but people use it in bioconda recipes) if [ `uname` == Darwin ]; then - export HOME=`mktemp -d` + export HOME=`mktemp -d` fi +# build statically linked binary with Rust +RUST_BACKTRACE=1 # Build the package using maturin - should produce *.whl files. -maturin build -m pybigtools/Cargo.toml --interpreter $PYTHON --release +maturin build -b pyo3 --interpreter "${PYTHON}" --release --strip # Install *.whl files using pip -$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv +${PYTHON} -m pip install . --no-deps --no-build-isolation -vvv diff --git a/recipes/pybigtools/meta.yaml b/recipes/pybigtools/meta.yaml index fb3f24390e236..0660d73d9a205 100644 --- a/recipes/pybigtools/meta.yaml +++ b/recipes/pybigtools/meta.yaml @@ -1,24 +1,27 @@ -{% set version = "0.1.0" %} +{% set name = "pybigtools" %} +{% set version = "0.1.2" %} package: - name: pybigtools + name: {{ name }} version: {{ version }} source: - url: https://github.com/jackh726/bigtools/archive/refs/tags/pybigtools@v{{ version }}.tar.gz - sha256: "bb1a1f1d1f39ce0b73eafb40e291b1ded26fbb283898371ade3414c008b80cdf" + url: "https://pypi.io/packages/source/p/pybigtools/{{ name }}-{{ version }}.tar.gz" + sha256: "0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58" build: number: 0 + run_exports: + - {{ pin_subpackage('pybigtools', max_pin="x.x") }} requirements: build: - {{ compiler('c') }} - {{ compiler('rust') }} - - maturin host: - pip - python + - maturin run: - python - numpy @@ -32,8 +35,9 @@ about: license: MIT summary: 'pybigtools: Python bindings to the Bigtools Rust library for high-performance BigWig and BigBed I/O' license_family: MIT - license_file: LICENSE + license_file: pybigtools/LICENSE doc_url: https://bigtools.readthedocs.io + dev_url: https://github.com/jackh726/bigtools/ extra: identifiers: From f3905d8320101f1366e3257e40e310b20f13af9c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 19:14:50 -0500 Subject: [PATCH 0686/1813] Update pgenlib to 0.90.2 (#46070) * Update pgenlib to 0.90.2 * add run_exports --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pgenlib/meta.yaml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/pgenlib/meta.yaml b/recipes/pgenlib/meta.yaml index e90bef1332072..b573cc847787c 100644 --- a/recipes/pgenlib/meta.yaml +++ b/recipes/pgenlib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pgenlib" %} -{% set version = "0.90.1" %} +{% set version = "0.90.2" %} package: name: "{{ name|lower }}" @@ -7,11 +7,13 @@ package: source: url: "https://pypi.io/packages/source/P/Pgenlib/Pgenlib-{{ version }}.tar.gz" - sha256: 069db673c1cc5baffcb9b20c2e6e26cc9fdaadd0095f55a188b41502d0511cb9 + sha256: 09825be43ffb25bc68b6e243b98989a5bc35a8aa22cd749fd9f602d778dd6bd0 build: number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" + run_exports: + - {{ pin_subpackage('pgenlib', max_pin="x.x") }} requirements: build: @@ -21,12 +23,10 @@ requirements: - pip - cython - numpy - - setuptools - zlib run: - python - - numpy - - zlib + - {{ pin_compatible('numpy') }} test: imports: @@ -34,7 +34,7 @@ test: about: home: "https://github.com/chrchang/plink-ng" - license: "GNU Lesser General Public v3 (LGPLv3)" + license: "LGPL-3.0-or-later" license_family: LGPL license_file: LICENSE summary: "Python wrapper for pgenlib's basic reader and writer." From 6c593936636744f5f622502e4de15fc8ed39f0aa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 19:55:41 -0500 Subject: [PATCH 0687/1813] Update plassembler to 1.6.0 (#46080) --- recipes/plassembler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/plassembler/meta.yaml b/recipes/plassembler/meta.yaml index 6eeca0a86bd9e..faae83bd295c0 100644 --- a/recipes/plassembler/meta.yaml +++ b/recipes/plassembler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "plassembler" %} -{% set version = "1.5.1" %} +{% set version = "1.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: ab3a4f7b3b0cb391df9e8189bbf5af4ea6fbdd919da65467053f70ad0a7f9c12 + sha256: 5c913edb384c04bc0cc68e886a71940d2405510d570afc25b37487b1390bb5c7 build: number: 0 From 662b521be74e7eef03f753465d6c602d3fec325c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 28 Feb 2024 20:05:51 -0500 Subject: [PATCH 0688/1813] Update fibertools-rs to 0.3.9 (#46081) --- recipes/fibertools-rs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fibertools-rs/meta.yaml b/recipes/fibertools-rs/meta.yaml index 112fffa6d7bc4..7186c17f62c4d 100644 --- a/recipes/fibertools-rs/meta.yaml +++ b/recipes/fibertools-rs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.8" %} +{% set version = "0.3.9" %} {% set name = "fibertools-rs" %} {% set build_number = "0" %} @@ -9,7 +9,7 @@ package: source: url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz - sha256: 7e244ceafa5371d21de45a9e6ea5dd66e4922283142bc9a332c1114d5118fa02 + sha256: 9ba952338f60108d957caa0b89fbe38263e1d3df08351cbf09f4c1acb1acc73b build: From d7d6d67ee1258273ea168826179f7f09ecfc632f Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 29 Feb 2024 08:06:34 +0100 Subject: [PATCH 0689/1813] add magic-impute (#46078) * add magic-impute * cleanup the run requirements --- recipes/magic-impute/LICENSE | 339 +++++++++++++++++++++++++++++++++ recipes/magic-impute/meta.yaml | 47 +++++ 2 files changed, 386 insertions(+) create mode 100644 recipes/magic-impute/LICENSE create mode 100644 recipes/magic-impute/meta.yaml diff --git a/recipes/magic-impute/LICENSE b/recipes/magic-impute/LICENSE new file mode 100644 index 0000000000000..23cb790338e19 --- /dev/null +++ b/recipes/magic-impute/LICENSE @@ -0,0 +1,339 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. 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It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + {description} + Copyright (C) {year} {fullname} + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + {signature of Ty Coon}, 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. diff --git a/recipes/magic-impute/meta.yaml b/recipes/magic-impute/meta.yaml new file mode 100644 index 0000000000000..af8166a8e5aaa --- /dev/null +++ b/recipes/magic-impute/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "magic-impute" %} +{% set version = "3.0.0" %} +{% set sha256 = "0c3f6d17baf586c412c174709a19164f04e693fd1933a8c0399ae5c5bf1cfd7a" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/magic-impute-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + script: {{ PYTHON }} -m pip install . --no-deps -vvv + run_exports: + - {{ pin_subpackage('magic-impute', max_pin="x.x") }} + noarch: python + +requirements: + host: + - python + - pip + run: + - python + - matplotlib-base + - pandas + - numpy + - scprep + - graphtools + +test: + imports: + - magic + +about: + home: https://github.com/KrishnaswamyLab/MAGIC + summary: "Markov Affinity-based Graph Imputation of Cells" + license: GPL-2.0 + license_family: GPL + license_file: LICENSE + doc_url: https://magic.readthedocs.io/en/stable/ + dev_url: https://github.com/KrishnaswamyLab/MAGIC + +extra: + identifiers: + - doi:10.1016/j.cell.2018.05.061 From a15c325449adb075778d6b5f0bd81c0628b854e4 Mon Sep 17 00:00:00 2001 From: Young Date: Thu, 29 Feb 2024 00:08:59 -0700 Subject: [PATCH 0690/1813] Add CirculoCov (#45921) * Create circulocov meta.yml * Added pycirclize * Rename meta.yml to meta.yaml * fix minimap2 version * Downgraded python * update release version to match pypi --------- Co-authored-by: Robert A. Petit III --- recipes/circulocov/meta.yaml | 51 ++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 recipes/circulocov/meta.yaml diff --git a/recipes/circulocov/meta.yaml b/recipes/circulocov/meta.yaml new file mode 100644 index 0000000000000..ac4cd3556ab77 --- /dev/null +++ b/recipes/circulocov/meta.yaml @@ -0,0 +1,51 @@ +{% set name = "circulocov" %} +{% set version = "0.1.20240104" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 6c585c90e63ff5ce4028157cb7f943f4abb679234daadb0349778bfb8141cd87 + +build: + number: 0 + noarch: python + entry_points: + - circulocov=circulocov.circulocov:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('circulocov', max_pin='x') }} + +requirements: + host: + - python >=3.8,<4.0 + - pip + run: + - python >=3.8,<4.0 + - matplotlib-base >=3.8.2 + - biopython >=1.58 + - numpy >=1.26.2 + - pandas >=2.1.4 + - pysam >=0.22.0 + - pycirclize >=1.3.0 + - minimap2 >=2.25 + +test: + imports: + - circulocov + commands: + - circulocov --help + +about: + home: https://github.com/erinyoung/CirculoCov + license: GPL-3.0 + license_family: GPL + license_file: LICENSE + summary: CirculoCov is a Python tool designed for circular-aware coverage analysis of draft genomes + doc_url: https://github.com/erinyoung/CirculoCov/blob/main/README.md + +extra: + recipe-maintainers: + - erinyoung From 917aec85947bc548d08432b1240e2efcfd6a1c79 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Thu, 29 Feb 2024 10:04:22 +0100 Subject: [PATCH 0691/1813] Add IPK recipe (#40369) * add ipk * osx compilation patch * removed last run test (>15 minutes on Azure) following bioconda's team demand --------- Co-authored-by: Jacques Dainat Co-authored-by: Benjamin Linard <22132778+blinard-BIOINFO@users.noreply.github.com> Co-authored-by: Benjamin Linard --- ...to_expect_binaries_in_same_directory.patch | 20 ++++++ ..._1_to_avoid_raxmlng_oversubscription.patch | 13 ++++ ..._sstream_for_std-basic_istringstream.patch | 11 +++ recipes/ipk/build.sh | 28 ++++++++ recipes/ipk/meta.yaml | 56 ++++++++++++++++ recipes/ipk/run_test.sh | 67 +++++++++++++++++++ 6 files changed, 195 insertions(+) create mode 100644 recipes/ipk/0001_makes_python_wrapper_to_expect_binaries_in_same_directory.patch create mode 100644 recipes/ipk/0002_default_threads_to_1_to_avoid_raxmlng_oversubscription.patch create mode 100644 recipes/ipk/0003_osx_compilation_requires_sstream_for_std-basic_istringstream.patch create mode 100644 recipes/ipk/build.sh create mode 100644 recipes/ipk/meta.yaml create mode 100644 recipes/ipk/run_test.sh diff --git a/recipes/ipk/0001_makes_python_wrapper_to_expect_binaries_in_same_directory.patch b/recipes/ipk/0001_makes_python_wrapper_to_expect_binaries_in_same_directory.patch new file mode 100644 index 0000000000000..09fbddb9e465f --- /dev/null +++ b/recipes/ipk/0001_makes_python_wrapper_to_expect_binaries_in_same_directory.patch @@ -0,0 +1,20 @@ +diff --git a/ipk.py b/ipk.py +index fb884f3..71bf356 100755 +--- a/ipk.py ++++ b/ipk.py +@@ -268,12 +268,12 @@ def build_database(ar, + if keep_positions: + raise RuntimeError("--keep-positions is not supported for DNA.") + else: +- bin = f"{current_dir}/bin/ipk/ipk-dna" ++ bin = f"{current_dir}/ipk-dna" + else: + if keep_positions: +- bin = f"{current_dir}/bin/ipk/ipk-aa-pos" ++ bin = f"{current_dir}/ipk-aa-pos" + else: +- bin = f"{current_dir}/bin/ipk/ipk-aa" ++ bin = f"{current_dir}/ipk-aa" + + + command = [ diff --git a/recipes/ipk/0002_default_threads_to_1_to_avoid_raxmlng_oversubscription.patch b/recipes/ipk/0002_default_threads_to_1_to_avoid_raxmlng_oversubscription.patch new file mode 100644 index 0000000000000..a8ca9c821a683 --- /dev/null +++ b/recipes/ipk/0002_default_threads_to_1_to_avoid_raxmlng_oversubscription.patch @@ -0,0 +1,13 @@ +diff --git a/ipk.py b/ipk.py +index fb884f3..1310237 100755 +--- a/ipk.py ++++ b/ipk.py +@@ -191,7 +191,7 @@ def validate_model(ctx, param, value): + Saves time during database load and save, but requires more disk space.""") + @click.option('--threads', + type=int, +- default=4, ++ default=1, + show_default=True, + help="Number of threads used to compute phylo-k-mers.") + def build(ar, diff --git a/recipes/ipk/0003_osx_compilation_requires_sstream_for_std-basic_istringstream.patch b/recipes/ipk/0003_osx_compilation_requires_sstream_for_std-basic_istringstream.patch new file mode 100644 index 0000000000000..3e26523c379f4 --- /dev/null +++ b/recipes/ipk/0003_osx_compilation_requires_sstream_for_std-basic_istringstream.patch @@ -0,0 +1,11 @@ +diff --git a/ipk/src/ar.cpp b/ipk/src/ar.cpp +index 2ea4eed..cebe283 100644 +--- a/ipk/src/ar.cpp ++++ b/ipk/src/ar.cpp +@@ -1,5 +1,6 @@ + #include + #include ++#include + #include + #include + #include diff --git a/recipes/ipk/build.sh b/recipes/ipk/build.sh new file mode 100644 index 0000000000000..7bc80e3d09470 --- /dev/null +++ b/recipes/ipk/build.sh @@ -0,0 +1,28 @@ +#!/bin/bash +set -ex + +export CPLUS_INCLUDE_PATH=${PREFIX}/include +export CPP_INCLUDE_PATH=${PREFIX}/include +export CXX_INCLUDE_PATH=${PREFIX}/include + +#to ensure zlib location +export CFLAGS="$CFLAGS -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" + +mkdir -p $PREFIX/bin +mkdir -p $PREFIX/lib + +cmake -B build -DHASH_MAP=USE_TSL_ROBIN_MAP -DCMAKE_CXX_FLAGS="-O3" -DBUILD_SHARED_LIBS=ON --install-prefix=$PREFIX +cmake --build build --target all +cmake --install build + +ls build/ipk + +cp build/ipk/ipk-aa $PREFIX/bin +cp build/ipk/ipk-aa-pos $PREFIX/bin +cp build/ipk/ipk-dna $PREFIX/bin + +chmod +x $PREFIX/bin/ipk-aa +chmod +x $PREFIX/bin/ipk-dna +chmod +x $PREFIX/bin/ipk-aa-pos +chmod +x $PREFIX/bin/ipk.py diff --git a/recipes/ipk/meta.yaml b/recipes/ipk/meta.yaml new file mode 100644 index 0000000000000..a44263c3004b3 --- /dev/null +++ b/recipes/ipk/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "IPK" %} +{% set version = "0.5.0" %} +{% set sha256 = "7d073583d0f9891a30ec6865fee33818b526086a1f0de04028409496b279004c" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/phylo42/{{ name|lower }}/releases/download/v{{ version }}/IPK-v{{ version }}_src_for_bioconda.tar.gz + sha256: {{ sha256 }} + patches: + - 0001_makes_python_wrapper_to_expect_binaries_in_same_directory.patch + - 0002_default_threads_to_1_to_avoid_raxmlng_oversubscription.patch + - 0003_osx_compilation_requires_sstream_for_std-basic_istringstream.patch + +build: + number: 0 + run_exports: + - {{ pin_subpackage('ipk', max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + - cmake + host: + - boost-cpp >=1.67 + - zlib + run: + - boost-cpp >=1.67 + - raxml-ng + - phyml + - python + - click + +# git-lfs is absent from the docker image, so test files are not cloned +# unstable workaround it to set wget as a test dependancy +# and download them from github in the run_tests.sh script +test: + requires: + - wget + # because they are not cloned, we cannot copy them from source in the test environment + #source_files: + # - tests/data/neotrop/reference.fasta + # - tests/data/neotrop/tree.rooted.newick + + +about: + home: https://github.com/phylo42/ipk + license: MIT + license_family: MIT + license_file: LICENSE + summary: "IPK is a tool for computing phylo-k-mers for a fixed phylogeny." + description: "IPK is a tool for computing phylo-k-mers for a fixed phylogeny. Please cite: doi.org/10.1093/bioinformatics/btad692" + diff --git a/recipes/ipk/run_test.sh b/recipes/ipk/run_test.sh new file mode 100644 index 0000000000000..64be368cb924b --- /dev/null +++ b/recipes/ipk/run_test.sh @@ -0,0 +1,67 @@ +#!/usr/bin/env bash + +PASS=true + +# A +echo "test A" +command -v ipk-dna +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + +# B +echo "test B" +command -v ipk-aa +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + +# C +echo "test C" +ipk-dna 2>&1 | grep "the option '--ar-binary' is required" +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + +# D +echo "test D" +ipk.py build --help +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + +# E +# test files cannot be retrieved via meta.yaml (field test:source) +# because git-lfs is not available in the github tarball release +# we need to download them manually +#echo "test E" + +#wget -O reference.fasta https://github.com/phylo42/IPK/raw/main/tests/data/neotrop/reference.fasta +#wget -O tree.rooted.newick https://github.com/phylo42/IPK/raw/main/tests/data/neotrop/tree.rooted.newick +#test -s reference.fasta +#test -s tree.rooted.newick +#mkdir -p tests_output +#ipk.py build -r reference.fasta -t tree.rooted.newick -m GTR -k 7 --omega 2.0 -u 1.0 -b $(which raxml-ng) -w tests_output +#if [ $? -ne 0 ]; then +# echo "failed" +# PASS=false +#fi + +#ls tests_output +#echo $PASS + +# F +#echo "test F" +#if [ ! -s tests_output/DB_k7_o2.0.rps ]; then +# echo "failed" +# PASS=false +#fi + +if [ "$PASS" = false ]; then + echo "At least 1 test failed !" + exit 1 +fi From b4b865f508a5d2973a1a7cf18aa853f669620dd5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 29 Feb 2024 07:49:30 -0500 Subject: [PATCH 0692/1813] Update sansa to 0.1.1 (#46088) * Update sansa to 0.1.1 * exports * license --------- Co-authored-by: Tobias Rausch --- recipes/sansa/build.sh | 4 +--- recipes/sansa/meta.yaml | 21 +++++++++++++++++---- 2 files changed, 18 insertions(+), 7 deletions(-) diff --git a/recipes/sansa/build.sh b/recipes/sansa/build.sh index a3f3b721a6495..dc2400afabae2 100644 --- a/recipes/sansa/build.sh +++ b/recipes/sansa/build.sh @@ -1,5 +1,3 @@ #!/bin/sh -make all CXX=$CXX CXXFLAGS="-D__STDC_FORMAT_MACROS -I${PREFIX}/include -L${PREFIX}/lib" -mkdir -p $PREFIX/bin -cp src/sansa $PREFIX/bin +CXXFLAGS="${CXXFLAGS} -D__STDC_FORMAT_MACROS" make CXX="${CXX}" prefix="${PREFIX}" install diff --git a/recipes/sansa/meta.yaml b/recipes/sansa/meta.yaml index 0cab341eedf48..e22272e18b320 100644 --- a/recipes/sansa/meta.yaml +++ b/recipes/sansa/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.0.8" %} -{% set sha256 = "124abc76cd65d13dbc3f1bc701af266d55e3d58be618f01b772d6d9dd6b185ee" %} +{% set version = "0.1.1" %} +{% set sha256 = "ab477696eca25d3aa84145ba9734f519ea84bea902267836019c3e08aa8b2669" %} package: name: sansa @@ -10,18 +10,31 @@ source: sha256: '{{ sha256 }}' build: - number: 6 + number: 0 + run_exports: + - {{ pin_subpackage('sansa', max_pin="x.x") }} requirements: build: - make - {{ compiler('cxx') }} + - autoconf + - automake + - pkg-config + - clangdev + - llvm-openmp host: - boost-cpp - htslib + - zlib + - bzip2 + - clangdev + - llvm-openmp run: - boost-cpp - htslib + - zlib + - bzip2 test: commands: @@ -29,7 +42,7 @@ test: about: home: https://github.com/dellytools/sansa - license: BSD License + license: BSD-3-Clause license_family: BSD license_file: LICENSE summary: Structural variant annotation From 5c0961db3ef9c2a8b3557b920b083b0639c17cc3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gen=C3=ADs=20Bayarri?= Date: Thu, 29 Feb 2024 15:52:28 +0100 Subject: [PATCH 0693/1813] [biobb_cmip] update 4.1.1 (#46092) --- recipes/biobb_cmip/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biobb_cmip/meta.yaml b/recipes/biobb_cmip/meta.yaml index a8a334ea71e12..14d69afc54704 100644 --- a/recipes/biobb_cmip/meta.yaml +++ b/recipes/biobb_cmip/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_cmip" %} -{% set version = "4.1.0" %} +{% set version = "4.1.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b25c9376e3091740e326911e3cb5006dfe03a092b98dae2ff525087fb2e77bed + sha256: 4d6fc4d8f4410c84e09cde21de645d40fd003bdff493b6bf9bb2bfaaa2b380a2 build: number: 0 From bf349f78e0627b6d495bbc7500f34e30ba077c85 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 29 Feb 2024 14:29:08 -0500 Subject: [PATCH 0694/1813] Update nf-core to 2.13.1 (#46098) --- recipes/nf-core/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index af43d2adb35cf..ac60d3bce94fb 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nf-core" %} -{% set version = "2.13" %} -{% set sha256 = "7e0eb09bd56b2dd2861ea162204c6c0b2c966be29cacde2bb758831423ce7c81" %} +{% set version = "2.13.1" %} +{% set sha256 = "297bb52144a0651b3b718325726b10a14bef0b1b3a1d65a0eadb4badb47c8a6f" %} package: name: {{ name|lower }} From 0720c87a9611d0726d5c2fae1fffb9285e7c9354 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 29 Feb 2024 22:47:15 -0500 Subject: [PATCH 0695/1813] Update synapseclient to 4.1.1 (#46082) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/synapseclient/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/synapseclient/meta.yaml b/recipes/synapseclient/meta.yaml index fa49bf12a5f38..9ecb6a51c0cd7 100644 --- a/recipes/synapseclient/meta.yaml +++ b/recipes/synapseclient/meta.yaml @@ -1,5 +1,5 @@ {% set name = "synapseclient" %} -{% set version = "4.1.0" %} +{% set version = "4.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/synapseclient-{{ version }}.tar.gz - sha256: a3a3bb581a5424d4d57408a6c81505b0c50907b7b88ad1cea59f62bf9ee8919e + sha256: c5e0ac45faed1aa618cd66a0f50bf1a8149a2902a71d07487a0e470250955083 build: noarch: python From ac9ba4e499d13044b0eda2962e87f744fbd4d402 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 29 Feb 2024 22:47:22 -0500 Subject: [PATCH 0696/1813] Update pybiolib to 1.1.1794 (#46086) * Update pybiolib to 1.1.1782 * Update pybiolib to 1.1.1786 * Update pybiolib to 1.1.1794 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 12823302525bb..8023c89646edd 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1780" %} +{% set version = "1.1.1794" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 02373e8364507796f416175d0eb1d2970c1980b4c81f628047f0163b77418bd4 + sha256: 403bd74ed356430d5c28747289d17f99692b04b5917e3908300c2d061496f98a build: noarch: python From 032555e9243c626703f12822e81ab93ed3b63fcd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 29 Feb 2024 22:48:32 -0500 Subject: [PATCH 0697/1813] Update phanotate to 1.6.5 (#46101) --- recipes/phanotate/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phanotate/meta.yaml b/recipes/phanotate/meta.yaml index 7965786cd5199..5c4db157f9366 100644 --- a/recipes/phanotate/meta.yaml +++ b/recipes/phanotate/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phanotate" %} -{% set version = "1.6.4" %} +{% set version = "1.6.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "315524223515c88a00b13104c91c1b85f8187e8eec5459bdf66046c30ff1e23f" + sha256: "4be12306eeace16d018538499299b1e01f3fc5a904af5836ed0172eacdda3483" build: number: 0 From 912b1c2999ab07453d6dc48cd644dca3a7b00299 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 29 Feb 2024 22:49:13 -0500 Subject: [PATCH 0698/1813] Update gseapy to 1.1.2 (#46099) --- recipes/gseapy/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 2f28298f064f6..00d552a8a7b8f 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -1,10 +1,10 @@ package: name: gseapy - version: "1.1.1" + version: "1.1.2" source: - url: https://files.pythonhosted.org/packages/c9/1b/b8bba54953a7ba433b73d701343557103bd96dfd76652698544b75fe5439/gseapy-1.1.1.tar.gz - sha256: 5062fc8d625037beb3d41762cb0cd7cad25653bb3a0c71b8f188ba458da77d4a + url: https://files.pythonhosted.org/packages/bc/54/4e09f7d74d0d1778b081fff8853a3ca6d03a951032424691be6d2df6fbea/gseapy-1.1.2.tar.gz + sha256: fd861b9e75a5103bd4a6bd67925f8f4a3c5b48d51e0ae068f56fb01aa9201e9e build: entry_points: From b8cc3a75eecbc6313885d5254d42cad9805cb1b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 29 Feb 2024 22:49:24 -0500 Subject: [PATCH 0699/1813] Update harpy to 0.7.0 (#46097) --- recipes/harpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index 8ceac942c5b01..a76365e42b1df 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.1" %} -{% set sha256 = "82841865d78362b084f76031329b30ff82521160d7ebdfb64386bfd32dac131c" %} +{% set version = "0.7.0" %} +{% set sha256 = "cf1f3189de98c301d3efa9bf12abefb3988390b06866e9a6e39c28bb1abe23dd" %} package: name: harpy From 30a7af2e1c56785bdc570a064eb06a7576bbafb8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 00:34:31 -0500 Subject: [PATCH 0700/1813] Update influx_si to 7.0.2 (#46094) * Update influx_si to 7.0.2 * Update meta.yaml of influx_si v7.0.2 (#46095) * Update meta.yaml * Update meta.yaml of influx_si --------- Co-authored-by: Serguei Sokol --- recipes/influx_si/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/influx_si/meta.yaml b/recipes/influx_si/meta.yaml index 2604d723ff941..e8a9540f95912 100644 --- a/recipes/influx_si/meta.yaml +++ b/recipes/influx_si/meta.yaml @@ -1,5 +1,5 @@ {% set name = "influx_si" %} -{% set version = "7.0.1" %} +{% set version = "7.0.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "24756a8c4ae1882244ffb2fd1faf83fe51e0cb6bb0d81756ce2c97c816764f3d" + sha256: "c76482e538363b1d158da78f26b21ead699e2e5d0cea3391173463eef76329c9" build: number: 0 @@ -21,8 +21,8 @@ build: - ftbl2netan = influx_si.cli:cli - ftbl2optR = influx_si.cli:cli - ftbl2xgmml = influx_si.cli:cli - - influx_s = influx_si.cli:cli - - influx_i = influx_si.cli:cli + - influx_s = influx_si.influx_s:main + - influx_i = influx_si.influx_i:main - res2ftbl_meas = influx_si.cli:cli - txt2ftbl = influx_si.txt2ftbl:main - ftbl2mtf = influx_si.ftbl2mtf:main From 9fd39e7a46d86deb6c7865cec00a456da28806c3 Mon Sep 17 00:00:00 2001 From: daylin <47667941+daylinmorgan@users.noreply.github.com> Date: Thu, 29 Feb 2024 23:35:40 -0600 Subject: [PATCH 0701/1813] anndata2ri: fix rpy2 dependency for v1.3.1 (#46096) * anndata2ri: fix rpy2 dependency for v1.3.1 * anndata2ri: satsify linting with run_export --- recipes/anndata2ri/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/anndata2ri/meta.yaml b/recipes/anndata2ri/meta.yaml index ef5463b85c2d8..b9c15422687c7 100644 --- a/recipes/anndata2ri/meta.yaml +++ b/recipes/anndata2ri/meta.yaml @@ -6,9 +6,11 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps -vvv" + run_exports: + - {{ pin_subpackage('anndata2ri', max_pin="x") }} source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz @@ -20,14 +22,14 @@ requirements: - flit - pip - get_version - - rpy2 >=3.4.3 + - rpy2 >=3.5.2 - hatchling - hatch-vcs run: - python >=3.6 - anndata - get_version - - rpy2 >=3.4.3 + - rpy2 >=3.5.2 - tzlocal test: From 251d735065ab90628e7fbcc0e46e493360bb30be Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 00:43:14 -0500 Subject: [PATCH 0702/1813] Update snakemake-executor-plugin-slurm to 0.4.1 (#46087) * Update snakemake-executor-plugin-slurm to 0.4.0 * Update snakemake-executor-plugin-slurm to 0.4.1 --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 0e3d1706f16d2..ed2edf2bc4eb0 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.3.2" %} +{% set version = "0.4.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 3912f2895eab1270d7a42959a2e221ce53428dfffb847e03ec6bc4eead88e30b + sha256: bd05fd3908530cb3d542090ee4123de8d7515082f48b37bded6339f1967e43d6 build: noarch: python From 03ec0d9dcafded6367d789873a8df3c5703cacb4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 01:30:07 -0500 Subject: [PATCH 0703/1813] Update exomiser-rest-prioritiser to 14.0.0 (#46091) * Update exomiser-rest-prioritiser to 14.0.0 * bump openjdk requirement * edit meta.yaml --------- Co-authored-by: mencian --- recipes/exomiser-rest-prioritiser/meta.yaml | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/recipes/exomiser-rest-prioritiser/meta.yaml b/recipes/exomiser-rest-prioritiser/meta.yaml index 03395c15f4f0a..5f67ff79744ad 100644 --- a/recipes/exomiser-rest-prioritiser/meta.yaml +++ b/recipes/exomiser-rest-prioritiser/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "13.3.0" %} -{% set sha256 = "bff2399f63d26f11169e4b2de5e397bcd3c61f74022703a5d8eff20b2ac4926c" %} +{% set version = "14.0.0" %} +{% set sha256 = "6817537b1e602f533219089fc89d6c1d154e26e61efb05a5de382a56eeba4094" %} package: name: exomiser-rest-prioritiser @@ -17,7 +17,7 @@ build: requirements: run: - - openjdk >=8 + - openjdk >=17 - zlib test: @@ -27,4 +27,11 @@ test: about: home: https://github.com/exomiser/Exomiser summary: Exomiser prioritiser REST API - license: AGPL3 + license: AGPL-3.0-or-later + license_family: AGPL + doc_url: https://exomiser.readthedocs.io/en/latest/ + dev_url: https://github.com/exomiser/Exomiser + +extra: + identifiers: + - biotools:exomiser From 07df1b699994736005fd335e5f11c2cbbed9229f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 02:02:23 -0500 Subject: [PATCH 0704/1813] Update metacache to 2.3.2 (#46090) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update metacache to 2.3.2 * Update meta.yaml Add run_exports * Update meta.yaml --------- Co-authored-by: Andreas Sjödin --- recipes/metacache/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/metacache/meta.yaml b/recipes/metacache/meta.yaml index 4712e702cb10f..b56fab267d2cd 100644 --- a/recipes/metacache/meta.yaml +++ b/recipes/metacache/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.3.1" %} +{% set version = "2.3.2" %} package: name: metacache @@ -6,11 +6,13 @@ package: source: url: https://github.com/muellan/metacache/archive/refs/tags/v{{ version }}.tar.gz - sha256: bd31f9ab2a1251c0264480ff16b711c2c548648ac3c15fc142309c12aa8e5e7f + sha256: 3d5bb4e49a0fd3e59a4c60ba1100c162912a52e15e9a8aea4316a2e5d01d4b66 build: - number: 2 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('metacache', max_pin="x") }} requirements: build: From 836e7497b9adb68729a05547352e8fc3f17054b0 Mon Sep 17 00:00:00 2001 From: lspindler2509 <83402447+lspindler2509@users.noreply.github.com> Date: Fri, 1 Mar 2024 12:58:40 +0100 Subject: [PATCH 0705/1813] update bio digest recipe (#45954) * add setup step as script * updated version * correct version * updated build number * restrict python version * for debugging purposes * adjusted script * test different import * added all needed dependencies * updated imports * add channel * added channels * deleted invalid import * adjustment of skript * add post lonk skript * added bash * add prints to messages * correct rights * add logs * adjust recipe * add pathon again * setup step in build * keep files * delete unnecessary files section * try suggested build.sh * added test * adjusted test * deleted not working test * different test * test as command * make test faster * added channels for testing * added dependency * log for debugging * delete dependencies * Update meta.yaml * Update meta.yaml * Update meta.yaml * Try graph-tool-base * go back to post-link * delete unnecessary import * added pip install --------- Co-authored-by: Marcel Martin --- recipes/biodigest/meta.yaml | 12 ++++++------ recipes/biodigest/post-link.sh | 5 +++++ 2 files changed, 11 insertions(+), 6 deletions(-) create mode 100644 recipes/biodigest/post-link.sh diff --git a/recipes/biodigest/meta.yaml b/recipes/biodigest/meta.yaml index 1f5455223cb84..b9f74d92d4a32 100644 --- a/recipes/biodigest/meta.yaml +++ b/recipes/biodigest/meta.yaml @@ -10,16 +10,17 @@ source: sha256: 7618cedf40fedd6dd60aa2fbf8635fb4af0a2c0ae16c01ef9741d30729b6e8bc build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" noarch: python run_exports: - {{ pin_subpackage('biodigest', max_pin="x.x") }} + requirements: host: - pip - - python >=3.7 + - python >=3.7, <=3.9 run: - biothings_client ==0.2.6 - gseapy ==0.10.5 @@ -28,11 +29,10 @@ requirements: - pandas ==1.5.2 - psutil ==5.9.0 - pycairo >=1.21.0 - - python >=3.7 - - requests ==2.28.2 + - python >=3.7, <=3.9 + - requests >=2.28.2 - scipy ==1.8.0 - - seaborn ==0.12.2 - + - seaborn >=0.12.2 test: imports: diff --git a/recipes/biodigest/post-link.sh b/recipes/biodigest/post-link.sh new file mode 100644 index 0000000000000..75d67231bbb28 --- /dev/null +++ b/recipes/biodigest/post-link.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +echo "Running setup script..." >> "$PREFIX/.messages.txt" +python -c "from biodigest import setup; setup.main(setup_type='api')" >> "$PREFIX/.messages.txt" +echo "Setup script finished." >> "$PREFIX/.messages.txt" \ No newline at end of file From 731d50eebfd03c3b9d5cf6db47162eda3b430474 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 09:04:36 -0500 Subject: [PATCH 0706/1813] Update taxmyphage to 0.2.8 (#46117) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index 379c12a36a2bd..9681cef1fff14 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.2.7" %} +{% set version = "0.2.8" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: 8208758ca9814435a72ffd11ba76538a829c355c73b276f567962c2334b149ec + sha256: 30e0194b4df6e8df8a3593729a0a6f19dd074e3d81d23c86f831f85356c8fd79 build: entry_points: From d0e1b2dc212a49a80b914846b76f649c562a2aad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 09:13:21 -0500 Subject: [PATCH 0707/1813] Update annonars to 0.36.1 (#46116) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index b4c87b30ceb5b..5d652eb89c8e3 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.36.0" %} +{% set version = "0.36.1" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8e28087350d225bc749e285d4e3ac17b8ceb4819e0aaf3459a457e23c01f45ae + sha256: 7aee8b87780956171a922b8fead5201c1506d5ec9cadc7ea33c009ce2f0b3816 requirements: build: From e3832311a7d6727b2cc9bad6dcbc2fac533331f6 Mon Sep 17 00:00:00 2001 From: Oliver Schwengers Date: Fri, 1 Mar 2024 19:55:24 +0100 Subject: [PATCH 0708/1813] pin Diamond to 2.1.8 (#46111) * pin Diamond to 2.1.8 Temporarily pin Diamond to v2.1.8 due to a known upstream bug https://github.com/bbuchfink/diamond/issues/785. * bump build number --- recipes/bakta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml index f33a11054a52e..cddd0f93850a0 100644 --- a/recipes/bakta/meta.yaml +++ b/recipes/bakta/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 script: python -m pip install --no-deps --ignore-installed . entry_points: - bakta = bakta.main:main @@ -37,7 +37,7 @@ requirements: - infernal >=1.1.4 - piler-cr - pyhmmer >=0.10.4 - - diamond >=2.1.8 + - diamond ==2.1.8 - blast >=2.14.0 - ncbi-amrfinderplus >=3.11.26 - circos >=0.69.8 From 39e130c5add77d05bba18872db6a2823c839fcc9 Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Fri, 1 Mar 2024 10:55:55 -0800 Subject: [PATCH 0709/1813] hybran: limit biopython dependency to <1.82 due to breaking change (#46109) * hybran: limit biopython dependency to < 1.82 due to breaking change A deprecation snuck up: https://github.com/biopython/biopython/blob/master/DEPRECATED.rst#bioseqfeature > The `location_operator` argument was removed from the SeqFeature initializer in Release 1.82. * hybran: add run_exports --- recipes/hybran/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/hybran/meta.yaml b/recipes/hybran/meta.yaml index 5b4b6abd05446..12695806c6bfb 100644 --- a/recipes/hybran/meta.yaml +++ b/recipes/hybran/meta.yaml @@ -10,15 +10,17 @@ source: build: noarch: python - number: 0 + number: 1 script: python -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage('hybran', max_pin=None) }} requirements: host: - python >=3.9 - pip run: - - biopython >=1.80 + - biopython >=1.80, <1.82 - blast - cd-hit - diamond From bce460ac0131c7bd92041d41b4c25e3fe5a7d590 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 13:56:43 -0500 Subject: [PATCH 0710/1813] Update drep to 3.5.0 (#46103) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update drep to 3.5.0 * Update meta.yaml Update dependencies to reflect new version. * checkm -> checkm-genome --------- Co-authored-by: Andreas Sjödin Co-authored-by: mencian --- recipes/drep/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/drep/meta.yaml b/recipes/drep/meta.yaml index 8e0c4025e8f64..b85c516641122 100644 --- a/recipes/drep/meta.yaml +++ b/recipes/drep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "drep" %} -{% set version = "3.4.5" %} +{% set version = "3.5.0" %} package: name: drep @@ -7,12 +7,12 @@ package: source: url: https://pypi.io/packages/source/d/drep/drep-{{ version }}.tar.gz - sha256: 147ddbb775c8f81e8cf4c4d79dc0378039628bd375ea135b8052b8a1d07180c3 + sha256: 4bd2fe9021fdcbcdf646ef5c558d4ea5d9440b290c0a42454037008997a9cfc6 build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed --no-cache-dir -vvv . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir -vvv . run_exports: - {{ pin_subpackage('drep', max_pin="x") }} @@ -22,16 +22,18 @@ requirements: - pip run: - python >3 + - tqdm - numpy - pandas - seaborn - matplotlib-base - - biopython - scikit-learn - mummer4 - mash - prodigal - fastani + - checkm-genome + - skani test: imports: From fec029d8abd3240f80c838271b9751753ef2cf38 Mon Sep 17 00:00:00 2001 From: Mateusz Warowny Date: Fri, 1 Mar 2024 19:59:07 +0100 Subject: [PATCH 0711/1813] Add JRONN recipe (#46093) --- recipes/jronn/build.gradle | 26 ++++++++++++++++++ recipes/jronn/build.sh | 12 +++++++++ recipes/jronn/jronn.sh | 11 ++++++++ recipes/jronn/meta.yaml | 54 ++++++++++++++++++++++++++++++++++++++ 4 files changed, 103 insertions(+) create mode 100644 recipes/jronn/build.gradle create mode 100644 recipes/jronn/build.sh create mode 100644 recipes/jronn/jronn.sh create mode 100644 recipes/jronn/meta.yaml diff --git a/recipes/jronn/build.gradle b/recipes/jronn/build.gradle new file mode 100644 index 0000000000000..a205cea7dbc3d --- /dev/null +++ b/recipes/jronn/build.gradle @@ -0,0 +1,26 @@ +plugins { + id "java" +} + +version = "$System.env.PKG_VERSION" +sourceCompatibility = 11 + +repositories { + mavenCentral() +} + +dependencies { + implementation "org.biojava:biojava-protein-disorder:$System.env.PKG_VERSION" +} + +jar { + manifest { + attributes "Main-Class": "org.biojava.nbio.ronn.ORonn" + } + + archiveBaseName = "jronn" + duplicatesStrategy = DuplicatesStrategy.EXCLUDE + from { + configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) } + } +} diff --git a/recipes/jronn/build.sh b/recipes/jronn/build.sh new file mode 100644 index 0000000000000..e91ffbeb416a5 --- /dev/null +++ b/recipes/jronn/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu + +OUTDIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $OUTDIR +mkdir -p $PREFIX/bin + +PKG_VERSION="$PKG_VERSION" gradle jar +cp build/libs/jronn-$PKG_VERSION.jar $OUTDIR/ +sed "s/{{PKG_VERSION}}/$PKG_VERSION/" $RECIPE_DIR/jronn.sh > $OUTDIR/jronn +ln -s $OUTDIR/jronn $PREFIX/bin/jronn +chmod +x $PREFIX/bin/jronn diff --git a/recipes/jronn/jronn.sh b/recipes/jronn/jronn.sh new file mode 100644 index 0000000000000..e0be794a48630 --- /dev/null +++ b/recipes/jronn/jronn.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -e + +JAR_NAME="jronn-{{PKG_VERSION}}.jar" + +if [ -x "$JAVA_HOME/bin/java" ]; then + JAVA=$JAVA_HOME/bin/java +else + JAVA=$(which java) +fi +$JAVA -jar "$(dirname $(readlink -f "$0"))/$JAR_NAME" "$@" diff --git a/recipes/jronn/meta.yaml b/recipes/jronn/meta.yaml new file mode 100644 index 0000000000000..120929dc1c9b2 --- /dev/null +++ b/recipes/jronn/meta.yaml @@ -0,0 +1,54 @@ +# no need to update version anywhere else +{% set version="7.1.0" %} + +package: + name: jronn + version: {{ version }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('jronn', max_pin="x.x") }} + +source: + path: "./build.gradle" + sha256: b554e160a0f7b40a528d2c85c2d9a2e943d42150381ea9290a1df4a2ef0efc91 + +requirements: + build: + - gradle =7.4 + host: + - openjdk >=11,<18 + run: + - openjdk >=11 + +test: + commands: + - jronn 2>&1 | grep "JRONN version 3.1" + +about: + home: https://biojava.org/ + dev_url: https://github.com/biojava/biojava/tree/master/biojava-protein-disorder + license: Apache-2.0 + summary: "JRONN is based on the C implementation of RONN algorithm." + description: >- + JRONN is a Java implementation of RONN. JRONN is based on RONN and uses the + same model data, therefore gives the same predictions. Main motivation + behind JRONN development was providing an implementation of RONN more + suitable to use by the automated analysis pipelines and web services. + + Original version of RONN is described in Yang,Z.R., Thomson,R., + McMeil,P. and Esnouf,R.M. (2005) RONN: the bio-basis function neural network + technique applied to the detection of natively disordered regions in proteins + Bioinformatics 21: 3369-3376 + See also http://www.strubi.ox.ac.uk/RONN + +extra: + notes: + JRONN is a Java program that comes with a custom wrapper shell script. + The shell wrapper is called "jronn" and is present on $PATH by default. + The Java program is executed by jvm pointed to by the $JAVA_HOME variable. + Otherwise, a "java" program from the current environment is used. + identifiers: + - biotools:protein-disorder From b38932ee7670bec3d96d11a300e3ef32085eaebe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 14:03:10 -0500 Subject: [PATCH 0712/1813] Update marti to 0.9.16 (#46123) --- recipes/marti/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/marti/meta.yaml b/recipes/marti/meta.yaml index 53848307a0c89..e86203beedb7e 100644 --- a/recipes/marti/meta.yaml +++ b/recipes/marti/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MARTi" %} -{% set version = "0.9.15" %} +{% set version = "0.9.16" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/richardmleggett/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8bb5851d382ce91bda51602d6af46ace995b25520635836dcddf1e5de069e6f6 + sha256: 85b06a61df8860d17c6de5282a820a8bd1b66bbb3d1f2351dbf5b54522aa1cb6 build: noarch: generic From e97ea8f689fdbf0728a56aceb7d8a927c27c2c4b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 14:03:38 -0500 Subject: [PATCH 0713/1813] Update pydeseq2 to 0.4.7 (#46121) --- recipes/pydeseq2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml index 47fda48bd6c9f..b2931dd3b81b1 100644 --- a/recipes/pydeseq2/meta.yaml +++ b/recipes/pydeseq2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydeseq2" %} -{% set version = "0.4.6" %} +{% set version = "0.4.7" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz - sha256: 952fff95213f66dd4c1c9a2d86d863b4ba062f84192e80caefe3620484271fda + sha256: acdd7911d47128c1d58203cbd161a8c1c5bec8062ebd4724d5dbc63bd2f4f78c build: noarch: python From 05d8ac416cdb80b409dbebdb20ca1941cc2389e8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 14:03:50 -0500 Subject: [PATCH 0714/1813] Update harpy to 0.7.3 (#46120) * Update harpy to 0.7.2 * Update harpy to 0.7.3 --- recipes/harpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index a76365e42b1df..811932262d836 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.0" %} -{% set sha256 = "cf1f3189de98c301d3efa9bf12abefb3988390b06866e9a6e39c28bb1abe23dd" %} +{% set version = "0.7.3" %} +{% set sha256 = "0ed76b2be37bbb6529f3cefbd3b8587f33ddb90afdd53931d99230b8af642668" %} package: name: harpy From a5bfcaf7739495923991d91c8245feb113e4ca0d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 14:04:05 -0500 Subject: [PATCH 0715/1813] Update micom to 0.33.2 (#46118) --- recipes/micom/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/micom/meta.yaml b/recipes/micom/meta.yaml index cd53b1a6dd737..103288784536f 100644 --- a/recipes/micom/meta.yaml +++ b/recipes/micom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "micom" %} -{% set version = "0.33.1" %} +{% set version = "0.33.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 75e8a1fe8f1535d12a466a028cd4e3caa7c199788b02c18d1bff9f03ae1d92ec + sha256: 0fd335b178badcd9a1d96d1b6f2568b15da922be2fa57e8a6004971510f3708b build: number: 0 From eaed7690b3d1464d5e7673c1daf0c22bb801d0e9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 14:04:45 -0500 Subject: [PATCH 0716/1813] Update gtfsort to 0.2.2 (#46122) --- recipes/gtfsort/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gtfsort/meta.yaml b/recipes/gtfsort/meta.yaml index 33e2dc96045a2..b04cc6fac6f30 100644 --- a/recipes/gtfsort/meta.yaml +++ b/recipes/gtfsort/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gtfsort" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz - sha256: 0fdaa15e22bd34193e2b16b53697b413af0fcf485401f45d48ac48054f1d70f4 + sha256: d22a8ef32e30111ad2dd08d1da0e0914ac62a728483b8e39a4ef8ea4e6133b4f build: number: 0 From 174fa6dcfa840c4711f06ddeaba645d8e0af7cbf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Mar 2024 14:05:11 -0500 Subject: [PATCH 0717/1813] Update squigulator to 0.3.0 (#46110) --- recipes/squigulator/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/squigulator/meta.yaml b/recipes/squigulator/meta.yaml index cdb6c3d60102f..e55f517d8a142 100644 --- a/recipes/squigulator/meta.yaml +++ b/recipes/squigulator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "squigulator" %} -{% set version = "0.2.2" %} +{% set version = "0.3.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/hasindu2008/squigulator/releases/download/v{{ version }}/squigulator-v{{ version }}-release.tar.gz - sha256: c1159c71ab04623e678c265081a2b0fc6b790b5cc86260deac1646d87c180e35 + sha256: fca1427fe609c20125e679459c1f509b320acf8a44887fa265649607d8a47789 build: number: 0 From 820c78793b0c16c9bfd853dc4d9bbddc0f32ba1c Mon Sep 17 00:00:00 2001 From: y4nnick8 <151630397+y4nnick8@users.noreply.github.com> Date: Fri, 1 Mar 2024 20:55:56 +0100 Subject: [PATCH 0718/1813] Add macs3 recipe (#45886) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * added macs3 recipe * update recipe * update macs3 recipe * fix lint * fix test * remove noarch * add run_exports * fix run_exports * move run_exports under build * Update meta.yaml try again with specific versions of dependencies * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * update sha256 * Update meta.yaml * trial * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Pavankumar Videm Co-authored-by: Björn Grüning Co-authored-by: Bjoern Gruening --- recipes/macs3/meta.yaml | 62 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 recipes/macs3/meta.yaml diff --git a/recipes/macs3/meta.yaml b/recipes/macs3/meta.yaml new file mode 100644 index 0000000000000..760b2845607d9 --- /dev/null +++ b/recipes/macs3/meta.yaml @@ -0,0 +1,62 @@ +{% set name = "MACS3" %} +{% set version = "3.0.1" %} +{% set sha256 = "9e1a63685629852e6128a3270d264f990790538f48610aac7fd2fd139ef8fe12" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + git_url: https://github.com/macs3-project/MACS.git + git_rev: 34f9a81398ec2af78317cd0b128f3a1e52a68f17 + +build: + number: 0 + script: python3 -m pip install . --no-deps --ignore-installed -vvv + run_exports: + - {{ pin_subpackage('macs3', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - python >=3.9 + - zlib + - pip + - numpy >=1.25 + - scipy >=1.12 + - cython >=3.0 + - hmmlearn 0.3 + - scikit-learn >=1.3 + - cykhash >=2.0,<3.0 + run: + - python >=3.9 + - numpy >=1.25 + - scipy >=1.12 + - hmmlearn 0.3 + - scikit-learn >=1.3 + - cykhash >=2.0,<3.0 + +test: + imports: + - MACS3 + commands: + - macs3 -h + +about: + dev_url: https://github.com/macs3-project/MACS/ + doc_url: https://macs3-project.github.io/MACS/ + home: https://pypi.org/project/MACS3/ + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE + summary: Model Based Analysis for ChIP-Seq data + +extra: + identifiers: + - biotools:macs + - doi:10.1186/gb-2008-9-9-r137 + - usegalaxy-eu:peakcalling_macs + skip-lints: + - uses_vcs_url + - missing_hash From 28e8e91de0a8a160cd5a7b7d67d99819ca4eaca9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Mar 2024 00:06:18 -0500 Subject: [PATCH 0719/1813] Update oarfish to 0.3.0 (#46127) --- recipes/oarfish/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oarfish/meta.yaml b/recipes/oarfish/meta.yaml index d571d3d5e4b3f..9082eefbb46f0 100644 --- a/recipes/oarfish/meta.yaml +++ b/recipes/oarfish/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: oarfish @@ -11,7 +11,7 @@ build: source: url: https://github.com/COMBINE-lab/oarfish/archive/v{{ version }}.tar.gz - sha256: 47e9ad6ae8af5f96eac16f294052319948a25892a9554c36ac5fe73646f20c2e + sha256: a523fec730f1f98b2fbce62d9a1a63fbec4dc400efad80af871265f60252e8d6 requirements: build: From e8b2291bae51b062af4fa68f9f1984bae80865dd Mon Sep 17 00:00:00 2001 From: Reid Wagner <74672860+reid-wagner@users.noreply.github.com> Date: Sat, 2 Mar 2024 13:28:24 -0600 Subject: [PATCH 0720/1813] - Fix jarfile path (#46124) - Fix automated test - Remove zip from installation --- recipes/ionquant/build.sh | 1 + recipes/ionquant/ionquant.py | 2 +- recipes/ionquant/meta.yaml | 4 ++-- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/ionquant/build.sh b/recipes/ionquant/build.sh index 9a487d861c802..2d90fc8dea952 100644 --- a/recipes/ionquant/build.sh +++ b/recipes/ionquant/build.sh @@ -31,3 +31,4 @@ fi cd "$TARGET" unzip "IonQuant-$PKG_VERSION.zip" ln -s "IonQuant-$PKG_VERSION/IonQuant-$PKG_VERSION.jar" "IonQuant.jar" +rm "IonQuant-$PKG_VERSION.zip" diff --git a/recipes/ionquant/ionquant.py b/recipes/ionquant/ionquant.py index b9de0803001e1..a56491cf08d33 100755 --- a/recipes/ionquant/ionquant.py +++ b/recipes/ionquant/ionquant.py @@ -9,7 +9,7 @@ import subprocess from os import access, getenv, X_OK -jar_file = os.path.join(os.path.dirname(__file__), "IonQuant.jar") +jar_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "IonQuant.jar") default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] diff --git a/recipes/ionquant/meta.yaml b/recipes/ionquant/meta.yaml index 3b87b49eeac8c..aa9cf7e1b9ded 100644 --- a/recipes/ionquant/meta.yaml +++ b/recipes/ionquant/meta.yaml @@ -10,7 +10,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('ionquant', max_pin="x.x") }} @@ -27,7 +27,7 @@ requirements: test: commands: - - ionquant --key {{ academic_use_only_key }} -Xms512m -Xmx1g --help 2>&1 | grep 'IonQuant' + - ionquant --key {{ academic_use_only_key }} -Xms512m -Xmx1g --help | grep 'License key verified' about: home: https://github.com/Nesvilab/IonQuant From 8fde61cff82834925f5eca3ceb2d280e6f997cfb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Mar 2024 23:58:25 -0500 Subject: [PATCH 0721/1813] Update oarfish to 0.3.1 (#46131) --- recipes/oarfish/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oarfish/meta.yaml b/recipes/oarfish/meta.yaml index 9082eefbb46f0..b712795b7de42 100644 --- a/recipes/oarfish/meta.yaml +++ b/recipes/oarfish/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: oarfish @@ -11,7 +11,7 @@ build: source: url: https://github.com/COMBINE-lab/oarfish/archive/v{{ version }}.tar.gz - sha256: a523fec730f1f98b2fbce62d9a1a63fbec4dc400efad80af871265f60252e8d6 + sha256: 242b524f2b1bd877df3c30b71283598f7386b1627b6a8534d943643089b63c16 requirements: build: From 9ad8055f6294c2b69afce53471a8cd9922fa93aa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 3 Mar 2024 08:39:55 -0500 Subject: [PATCH 0722/1813] Update captus to 1.0.1 (#46128) --- recipes/captus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/captus/meta.yaml b/recipes/captus/meta.yaml index 44207123a1eea..48bc3a204b6d2 100644 --- a/recipes/captus/meta.yaml +++ b/recipes/captus/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.0.0" %} -{% set sha256 = "2ecdab60cc0ce9b422e66e325a4746a04f2700c8b477790458217f0c9d0b8adb" %} +{% set version = "1.0.1" %} +{% set sha256 = "a9331d4a3d8d967e4b679c14e5af6fd98539659de3b740da876b1fa5c8dd0ba3" %} package: name: captus From 346f36a6219e11e219e85a758c05e45db6f099a7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 3 Mar 2024 20:11:18 -0500 Subject: [PATCH 0723/1813] Update plassembler to 1.6.1 (#46130) --- recipes/plassembler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/plassembler/meta.yaml b/recipes/plassembler/meta.yaml index faae83bd295c0..96d18ed21a39f 100644 --- a/recipes/plassembler/meta.yaml +++ b/recipes/plassembler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "plassembler" %} -{% set version = "1.6.0" %} +{% set version = "1.6.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 5c913edb384c04bc0cc68e886a71940d2405510d570afc25b37487b1390bb5c7 + sha256: b66b61fda366c80b50eefbd68b93d8fdbc0cdefb0441093ed1ed9e571a549817 build: number: 0 From 0e61bf424f8f9468d70a5a20747d748d110bf5b2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 02:09:28 -0500 Subject: [PATCH 0724/1813] Update genomad to 1.7.5 (#46135) --- recipes/genomad/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genomad/meta.yaml b/recipes/genomad/meta.yaml index e52a7e786a2c5..21506ba0e10de 100644 --- a/recipes/genomad/meta.yaml +++ b/recipes/genomad/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genomad" %} -{% set version = "1.7.4" %} +{% set version = "1.7.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3f7395ef18652c8f4ef1809d7bc97d7c3a7ae59fc86012cbf1ed35b7986ecad2 + sha256: 9f981c56d2c59774fb17fae144800a09db809a957b547073b54f6bbf72cec2ae build: number: 0 From 13c38e991175da255bce4662495b51393439839f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 03:46:00 -0500 Subject: [PATCH 0725/1813] Update kaiju to 1.10.1 (#46134) --- recipes/kaiju/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kaiju/meta.yaml b/recipes/kaiju/meta.yaml index a12694188896f..f93353ab203e3 100644 --- a/recipes/kaiju/meta.yaml +++ b/recipes/kaiju/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.10.0" %} +{% set version = "1.10.1" %} package: name: kaiju @@ -6,7 +6,7 @@ package: source: url: https://github.com/bioinformatics-centre/kaiju/archive/v{{ version }}.tar.gz - sha256: 328c85ee1d5e4eafb18b8dd0bcf26b6ba88ba15ab4f14443ac643cd7e6675267 + sha256: 3cc05533bf6007ffeff2d755c935354952b09a6b903c5e538dff14285b3c86e8 build: number: 0 From a0720016539c5d36ed3138fd78a512989b5791c5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 09:35:25 -0500 Subject: [PATCH 0726/1813] Update kseqpp to 1.1.2 (#46145) * Update kseqpp to 1.1.2 * Add missing run_exports (#46146) --------- Co-authored-by: Ali Ghaffaari --- recipes/kseqpp/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/kseqpp/meta.yaml b/recipes/kseqpp/meta.yaml index 97cc6aefc36aa..595e642475766 100644 --- a/recipes/kseqpp/meta.yaml +++ b/recipes/kseqpp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kseqpp" %} -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} package: name: {{ name|lower }} @@ -7,10 +7,12 @@ package: source: url: https://github.com/cartoonist/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 7bad18d7b00b74f15503f1961c71455d5dcf751e539287aa8fc74c31a63a513f + sha256: 80d5da09f725517fe27c13bbc3efea55735ef426ffe086fd0544e18e670190be build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: From eddc83028cc36c774502f01eb222ba92a972133d Mon Sep 17 00:00:00 2001 From: Mateusz Warowny Date: Mon, 4 Mar 2024 15:36:13 +0100 Subject: [PATCH 0727/1813] Change incorrect license to LGPL-2.1 form Apache-2.0 (#46147) * Change incorrect license to LGPL-2.1 form Apache-2.0 * Update meta.yaml --------- Co-authored-by: Marcel Martin --- recipes/jronn/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jronn/meta.yaml b/recipes/jronn/meta.yaml index 120929dc1c9b2..3e5f84db816be 100644 --- a/recipes/jronn/meta.yaml +++ b/recipes/jronn/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('jronn', max_pin="x.x") }} @@ -30,7 +30,7 @@ test: about: home: https://biojava.org/ dev_url: https://github.com/biojava/biojava/tree/master/biojava-protein-disorder - license: Apache-2.0 + license: LGPL-2.1 summary: "JRONN is based on the C implementation of RONN algorithm." description: >- JRONN is a Java implementation of RONN. JRONN is based on RONN and uses the From 23adc4a82bac52111513467ea30e2c65eacecc32 Mon Sep 17 00:00:00 2001 From: Ali Ghaffaari Date: Mon, 4 Mar 2024 16:51:34 +0100 Subject: [PATCH 0728/1813] Update gum to v2.0.2 (#46148) * Update gum to v2.0.2 * Update SHA256 for gum --- recipes/gum/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/gum/meta.yaml b/recipes/gum/meta.yaml index b8292930c1f83..80d205fd59d79 100644 --- a/recipes/gum/meta.yaml +++ b/recipes/gum/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gum" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: - url: https://github.com/cartoonist/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 70f314ec89d8dc767eaf7184c43fdb793948dbdf6bec63a88ba3e8a539e465aa + sha256: 3afd2bed67cdc053d5afacdb1b951a15dce36738874f92cc74a9fafbf7bb65c0 patches: - 00-fix-ext-cmake.patch - url: https://github.com/cartoonist/sdsl-lite/archive/af1820fa3c25d2eb64bbab37a1a94938af862ec8.tar.gz @@ -16,8 +16,8 @@ source: - url: https://github.com/greg7mdp/parallel-hashmap/archive/d2bed96d2947c13b8fc90337198c315b2200e058.tar.gz sha256: 387ce116c8568f2d2be43658024a233ed807f420cc9152b4723a780472b97c04 folder: ext/parallel-hashmap - - url: https://github.com/cartoonist/gfakluge/archive/e4cd7b02317d65b321385cac5415a3cab0a1d0cc.tar.gz - sha256: 1303152ea59cade4f21528c414da6fba073b86299c11f259ad8a3d50a450b5ab + - url: https://github.com/cartoonist/gfakluge/archive/9f635f2e49dc42443160d30368e07864ab221efd.tar.gz + sha256: 85504b0e9c0a0d68361d65984be9168f728eb0b3faad1ca42fc6e08156d57850 folder: ext/gfakluge - url: https://github.com/cartoonist/tinyFA/archive/bfe1eea6bc5dbd2c87b7b3d48d99e05dafce7073.tar.gz sha256: 92d00462cd770c421a2d30f99aef0de997c732714defead8e05da390e3528755 From 7444bb98926ab1e6449579b05c4eee9e4683439d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 13:53:51 -0500 Subject: [PATCH 0729/1813] Update strobealign to 0.13.0 (#46154) --- recipes/strobealign/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/strobealign/meta.yaml b/recipes/strobealign/meta.yaml index 11fa5f4b70fe5..f2b28b7497ef1 100644 --- a/recipes/strobealign/meta.yaml +++ b/recipes/strobealign/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.12.0" %} +{% set version = "0.13.0" %} package: name: strobealign @@ -11,7 +11,7 @@ build: source: url: https://github.com/ksahlin/strobealign/archive/refs/tags/v{{ version }}.tar.gz - sha256: 1ea8d081ee172b5444578bcbf261d130ea6744d9cbfc76154121e17f405ea975 + sha256: 50f1585a8b3b733680067aa7ae20146a7d94d064d9fa234df0715bfcc5289c41 requirements: build: From 3dc4d7e18aa9482fceb6eb28e674abd016bb813f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:35:57 -0500 Subject: [PATCH 0730/1813] Update pybiolib to 1.1.1815 (#46143) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 8023c89646edd..05e1f5613035c 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1794" %} +{% set version = "1.1.1815" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 403bd74ed356430d5c28747289d17f99692b04b5917e3908300c2d061496f98a + sha256: 53be318613e0eb135d4634fa89841c9b4cd1e085e07fc5ccd2351b82ff2bb5fe build: noarch: python From c0783c000f4cf636066c0207683d905e889fe202 Mon Sep 17 00:00:00 2001 From: Martin Larralde Date: Mon, 4 Mar 2024 20:40:49 +0100 Subject: [PATCH 0731/1813] Update `pyhmmer` recipe to `v0.10.7` and run integrated unit tests (#45910) * Run integrated unit tests in `pyhmmer` recipe * Update build number in `pyhmmer` recipe * Add missing `importlib-resources` test dependency to `pyhmmer` * Update `pyhmmer` to `v0.10.6` * Fix `max_pin` in `pyhmmer` * Reset build number of `pyhmmer` to `0` * Bump `pyhmmer` recipe to `v0.10.7` --- recipes/pyhmmer/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 38c369f3a8ce2..bd6805e585491 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.6" %} +{% set version = "0.10.7" %} package: name: "{{ name|lower }}" @@ -7,14 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 47e017ccc523046400312afc937d4d68306f6ca0ed82e313deb3697d4fd8ccff + sha256: 5f738644c413bba5df69aaf6eee8c847bacd34fd58dd69e9ca63cfaa326c19a9 build: number: 0 skip: True #[py2k or win] script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" run_exports: - - {{ pin_subpackage('pyhmmer', max_pin="x") }} + - {{ pin_subpackage('pyhmmer', max_pin="x.x") }} requirements: build: @@ -30,8 +30,12 @@ requirements: - psutil >=5.8 test: + requires: + - importlib_resources #[py36 or py37 or py38] imports: - {{ name }} + commands: + - python -m unittest -vv {{ name }}.tests about: home: https://github.com/althonos/pyhmmer From fbb6853b31cd35ac6a471543750fd330dee81963 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:42:26 -0500 Subject: [PATCH 0732/1813] Update hybracter to 0.7.0 (#46138) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index aca31cdfc5401..cee091ee7a396 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.6.0" %} +{% set version = "0.7.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 2d7d79818f6b896e47c0ad4c4e4583d2028019a2d43c5aa502762c4a22cbacd1 + sha256: ae2ea5fcfc525b1b4d71975d56ead81015afed342e54f1cc3e232f7671033278 build: number: 0 From 37ade67cd1a00d4666c09cc766c326a0447f3448 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:43:25 -0500 Subject: [PATCH 0733/1813] Update oakvar to 2.9.90 (#46133) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index a8f76bc238221..a653eae0f46a1 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.89" %} -{% set sha256 = "1c55c4d0bf7b849c14deaaa213591ca825ff33f8cb5d4b17b787e49bb60f11a3" %} +{% set version = "2.9.90" %} +{% set sha256 = "5f9a118f57f3bf4477a59d0c3fc2b1c9fdb3aa5a273ba8e7fda463be39da65d4" %} package: name: {{ name|lower }} From 2a4a4de4a85950c4cf9bb481babe543fbac96177 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:44:06 -0500 Subject: [PATCH 0734/1813] Update seqerakit to 0.4.6 (#46141) --- recipes/seqerakit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqerakit/meta.yaml b/recipes/seqerakit/meta.yaml index 4ee5c9b1f6cd7..992daf113f85d 100644 --- a/recipes/seqerakit/meta.yaml +++ b/recipes/seqerakit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqerakit" %} -{% set version = "0.4.5" %} +{% set version = "0.4.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqerakit-{{ version }}.tar.gz - sha256: 792bd4fa53de4b3959929413d1ad8f39e20587971c9c5451419da1ff68cf3f49 + sha256: 286a9f7174f7ee242f90a3526dd018b67370a0f8cc9c66c220731b7a741433dd build: entry_points: From fb71e3384942ecedad37a4bd45812be2e97c26d9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:44:20 -0500 Subject: [PATCH 0735/1813] Update psm-utils to 0.7.3 (#46144) --- recipes/psm-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index e2767e8637fc8..f6fc17d1acfe2 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.7.2" %} -{% set sha256 = "a6b892f3ca6dfb8c2b298e0788c79965d754e84e7049c560b52263b096b82a17" %} +{% set version = "0.7.3" %} +{% set sha256 = "d97b197276c7ebfa14aa74119e0f576466f1c87949ad00ce60ce1bba2fdc43b2" %} package: name: {{ name|lower }} From f846cc9787bb5f90b4a1c7d4a6c5e801980a32e3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:44:47 -0500 Subject: [PATCH 0736/1813] Update cptac to 1.5.13 (#46150) --- recipes/cptac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cptac/meta.yaml b/recipes/cptac/meta.yaml index bab54c17e1958..650ccc357ca33 100644 --- a/recipes/cptac/meta.yaml +++ b/recipes/cptac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cptac" %} -{% set version = "1.5.11" %} +{% set version = "1.5.13" %} package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: f890f69e78193a61f0017f1f2585d1d4bca0a4af5221baeb624b08177f9d0b5b + sha256: be96ee2ed931625aa80d9e876163a4343afed2e2f82e7851231176058cc393c5 build: number: 0 From b66fd61c9356e4f1b074ff6e2d33e40be3f815bb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:45:03 -0500 Subject: [PATCH 0737/1813] Update mehari to 0.24.2 (#46153) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 1f8536fe1df30..76b6889cf2e0a 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.24.1" %} -{% set sha256 = "bf130073533d279ca31e51871e3cc4126c9799f2cf08024a18ef7483e719e68f" %} +{% set version = "0.24.2" %} +{% set sha256 = "079d86302bcd9a631acff934ffcacd9042f1f3a750c3b87efcc60786923883d8" %} package: name: mehari From 96a935459331b8d8b31d55042037afb46bd81771 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:46:05 -0500 Subject: [PATCH 0738/1813] Update mercat2 to 1.4.0 (#46129) --- recipes/mercat2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mercat2/meta.yaml b/recipes/mercat2/meta.yaml index 1808493425f7d..e9ea1d303868d 100644 --- a/recipes/mercat2/meta.yaml +++ b/recipes/mercat2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mercat2" %} -{% set version = "1.3" %} +{% set version = "1.4.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: edcee22e339bdf15ce4709c3192f85c32f576f07eedfd044bad8d3a396cbe0a9 + sha256: e100287a9772832df1f51295b5f80969aff1010942ecabf24f566083aa31d22c build: number: 0 From e31b6ce6f079f69aba75e6ce1344d7f6816b3e00 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:46:20 -0500 Subject: [PATCH 0739/1813] Update pbsim3 to 3.0.4 (#46132) --- recipes/pbsim3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbsim3/meta.yaml b/recipes/pbsim3/meta.yaml index 8b4d4a835b177..c9902c70eb6ef 100644 --- a/recipes/pbsim3/meta.yaml +++ b/recipes/pbsim3/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbsim3" %} -{% set version = "3.0.2" %} -{% set sha256 = "db938d58bbe3003f36b0b6f9fdc5a190816ff1c30e1d7da53b87e0fb6aee4795" %} +{% set version = "3.0.4" %} +{% set sha256 = "d9dd51d7522d9f2f21d3cab6f5f7ff0131702cba73dd1baa0b7d13f813d3854e" %} package: name: {{ name }} From a6d2d897af4c3b271e47e31f63a1fe35a7566fcb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Mar 2024 16:06:51 -0500 Subject: [PATCH 0740/1813] Update pymzml to 2.5.6 (#46119) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pymzml/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pymzml/meta.yaml b/recipes/pymzml/meta.yaml index 5ac2c87b095ef..c5512c2bef155 100644 --- a/recipes/pymzml/meta.yaml +++ b/recipes/pymzml/meta.yaml @@ -1,10 +1,10 @@ package: name: pymzml - version: "2.5.5" + version: "2.5.6" source: - url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.5.tar.gz - sha256: ffe96ccad5bd1eb7214b4afbc8c42c07d3a1a9f8cb41bcc0bad422c71af625c4 + url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.6.tar.gz + sha256: 82f7c36c11f4c7e868faf97f5f7a18585fe198142309bfe6a6820b4c764d9e0c build: number: 0 From 36731b7342b95580db38cf396026e4a8593cb22b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 4 Mar 2024 22:42:35 +0100 Subject: [PATCH 0741/1813] feat: add initial support for arm builds (#40550) --- .circleci/check-for-additional-platforms.sh | 44 ++++ .circleci/config.yml | 260 ++++++++++++++++++++ recipes/abra2/meta.yaml | 13 +- 3 files changed, 315 insertions(+), 2 deletions(-) create mode 100755 .circleci/check-for-additional-platforms.sh create mode 100644 .circleci/config.yml diff --git a/.circleci/check-for-additional-platforms.sh b/.circleci/check-for-additional-platforms.sh new file mode 100755 index 0000000000000..a05da11215509 --- /dev/null +++ b/.circleci/check-for-additional-platforms.sh @@ -0,0 +1,44 @@ +#!/bin/bash + +# Check to see if any changed recipes have specified the key +# extra:additional-platforms, and if so, if they match the platform of the +# currently-running machine. + +# arguments +git_range=$1 +job_name=$2 + +# Download ARM version of yq +yq_platform=$(uname) +yq_arch=$(uname -m) +[[ $yq_arch = "aarch64" ]] && yq_arch="arm64" +wget https://github.com/mikefarah/yq/releases/latest/download/yq_${yq_platform}_${yq_arch} -O /usr/local/bin/yq + +# Find recipes changed from this merge +files=`git diff --name-only --diff-filter AMR ${git_range} | grep -E 'meta.yaml$' ` +build=0 + +for file in $files; do + echo $file + # To create a properly-formatted yaml that yq can parse, comment out jinja2 + # variable setting with {% %} and remove variable use with {{ }}. + additional_platforms=$(cat $file \ + | sed -E 's/(.*)\{%(.*)%\}(.*)/# \1\2\3/g' \ + | sed -E 's/(.*)\{\{(.*)\}\}(.*)/\1\2\3/g' \ + | yq '.extra.additional-platforms[]') + # Check if any additional platforms match this job + for additional_platform in $additional_platforms; do + if [ "${CIRCLE_JOB}" = "${job_name}-${additional_platform}" ] + then + build=1 + break + fi + done +done + +# If no changed recipes apply to this platform, skip remaining steps +if [[ build -lt 1 ]] +then + echo "No recipes using this platform, skipping rest of job." + circleci-agent step halt +fi diff --git a/.circleci/config.yml b/.circleci/config.yml new file mode 100644 index 0000000000000..7020f97145379 --- /dev/null +++ b/.circleci/config.yml @@ -0,0 +1,260 @@ +# .circleci/config.yml +version: 2.1 + +executors: + # osx-arm64: + # macos: + # xcode: 14.2.0 # indicate your selected version of Xcode + # resource_class: macos.m1.large.gen1 + linux-aarch64: + machine: + image: ubuntu-2204:current + resource_class: arm.medium + +jobs: # a basic unit of work in a run + build_and_test: + parameters: + os: + type: executor + executor: << parameters.os >> + steps: + - checkout + + - run: + name: Check for Additional Platforms + command: ./.circleci/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" + + - run: + name: Fetch bioconda install script + command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh + + - run: + name: Install bioconda-utils + command: | + sudo mkdir -p /opt/ + sudo chmod o+rwx /opt + bash install-and-set-up-conda.sh + + - run: + name: Setup PATH + command: + echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV" + + # We reconfigure conda to use the right channel setup. + # This has to be done after the cache is restored, because + # the channel setup is not cached as it resides in the home directory. + # We could use a system-wide (and therefore cached) channel setup, + # but mamba does not support that at the time of implementation + # (it ignores settings made by --system). + - run: + name: Configure conda + command: bash configure-conda.sh + + - run: + name: Build and test + command: | + source /opt/mambaforge/etc/profile.d/conda.sh + source /opt/mambaforge/etc/profile.d/mamba.sh + mamba activate bioconda + bioconda-utils build recipes config.yml \ + --lint --docker --mulled-test \ + --docker-base-image quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch) \ + --git-range origin/master HEAD + + - run: + name: Prepare artifacts + command: | + ( + mkdir -p /tmp/artifacts/packages + cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 + find -name .cache | xargs rm -rf || true + for n in index.html channeldata.json linux-aarch64 linux-64 osx-64 noarch; do + cp -rv $n /tmp/artifacts/packages || true + done + if command -V docker >/dev/null; then + mkdir -p /tmp/artifacts/images + cd /tmp/artifacts/images + docker image ls --format='{{.Repository}}:{{.Tag}}' | \ + { grep biocontainers || true ; } | \ + xargs -n1 -P4 bash -c ' + test -n "${1+x}" || exit 0 + echo "Start compressing docker image ${1} ..." + docker save "${1}" | gzip -c > "${1##*/}.tar.gz" + echo "Finished compressing docker image ${1} ." + ' -- + fi + ) || true + + - store_artifacts: + path: /tmp/artifacts + + build_and_upload: + parameters: + os: + type: executor + executor: << parameters.os >> + steps: + - checkout + + - run: + name: Check for Additional Platforms + command: ./.circleci/check-for-additional-platforms.sh "${CIRCLE_SHA1}~1 ${CIRCLE_SHA1}" "build_and_upload" + + - run: + name: Fetch bioconda install script + command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh + + - run: + name: Install bioconda-utils + command: | + sudo mkdir -p /opt + sudo chmod o+rwx /opt + bash install-and-set-up-conda.sh + + - run: + name: Setup PATH + command: + echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV" + + # We reconfigure conda to use the right channel setup. + # This has to be done after the cache is restored, because + # the channel setup is not cached as it resides in the home directory. + # We could use a system-wide (and therefore cached) channel setup, + # but mamba does not support that at the time of implementation + # (it ignores settings made by --system). + - run: + name: Configure conda + command: bash configure-conda.sh + + - run: + name: Build and push + command: | + source /opt/mambaforge/etc/profile.d/conda.sh + source /opt/mambaforge/etc/profile.d/mamba.sh + mamba activate bioconda + bioconda-utils handle-merged-pr recipes config.yml \ + --repo bioconda/bioconda-recipes \ + --git-range ${CIRCLE_SHA1}~1 ${CIRCLE_SHA1} \ + --fallback build \ + --artifact-source circleci + + bulk_build: + parameters: + os: + type: executor + runner: + type: integer + executor: << parameters.os >> + steps: + - add_ssh_keys: + fingerprints: + - 1e:85:74:42:35:5f:c5:a2:35:c2:ec:b7:80:c0:7c:40 + + - checkout + + - run: + name: Check for [ci run] + command: | + commit_message="$(git log --format=oneline -n 1 $CIRCLE_SHA1)" + if [[ $commit_message =~ "[ci run]" ]]; then + echo "[ci run] found, continuing." + else + echo "[ci run] not found, exiting." + circleci-agent step halt + fi + + - run: + name: set git user + command: | + git config user.name BiocondaBot + git config user.email biocondabot@users.noreply.github.com + git branch --set-upstream-to=origin/$CIRCLE_BRANCH $CIRCLE_BRANCH + + - run: + name: Fetch bioconda install script + command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh + + - run: + name: Install bioconda-utils + command: | + sudo mkdir -p /opt/ + sudo chmod o+rwx /opt + bash install-and-set-up-conda.sh + + - run: + name: Setup PATH + command: + echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV" + + # We reconfigure conda to use the right channel setup. + # This has to be done after the cache is restored, because + # the channel setup is not cached as it resides in the home directory. + # We could use a system-wide (and therefore cached) channel setup, + # but mamba does not support that at the time of implementation + # (it ignores settings made by --system). + - run: + name: Configure conda + command: bash configure-conda.sh + + # For now, do not upload ARM images to biocontainers: --mulled-upload-target biocontainers + - run: + name: Build and upload + command: | + set -e + source /opt/mambaforge/etc/profile.d/conda.sh + source /opt/mambaforge/etc/profile.d/mamba.sh + mamba activate bioconda + echo '============' + conda info --all + conda config --show-sources + python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' + echo '============' + bioconda-utils build recipes config.yml \ + --worker-offset << parameters.runner >> --n-workers 6 \ + --docker --mulled-test --docker-base-image quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch) \ + --anaconda-upload \ + --mulled-upload-target biocontainers \ + --record-build-failures \ + --skiplist-leafs + conda clean -y --all + + +workflows: + build and test (ARM): + jobs: + - build_and_test: + filters: + branches: + ignore: + - master + - bulk + matrix: + parameters: + os: + #- osx-arm64 + - linux-aarch64 + + build and upload (ARM): + jobs: + - build_and_upload: + filters: + branches: + only: master + matrix: + parameters: + os: + #- osx-arm64 + - linux-aarch64 + + Bulk branch (ARM): + jobs: + - bulk_build: + filters: + branches: + only: bulk + matrix: + parameters: + os: + #- osx-arm64 + - linux-aarch64 + runner: [0, 1, 2, 3, 4, 5] diff --git a/recipes/abra2/meta.yaml b/recipes/abra2/meta.yaml index 1d5adf33ab6ae..342af9bad048e 100644 --- a/recipes/abra2/meta.yaml +++ b/recipes/abra2/meta.yaml @@ -10,21 +10,30 @@ source: sha256: edb35fb6ff318239353a573d1abad148073b8ac0bb2cd44a18e561abe08aef32 build: - number: 2 + number: 3 skip: true # [osx] + run_exports: + - pin_subpackage(name, max_pin="x") requirements: build: - maven - make - {{ compiler('cxx') }} + host: + - zlib run: - openjdk >=8,<10 - coreutils + - zlib test: commands: - - 'abra2 2>&1 | grep "Abra version"' + - 'abra2 2>&1 | grep "Abra version" || (abra2 && exit 1)' + +extra: + additional-platforms: + - linux-aarch64 about: home: https://github.com/mozack/abra2 From 0fc33c0cf9df9989c474bc4f73957635f46105f6 Mon Sep 17 00:00:00 2001 From: "Edgardo M. Ortiz" Date: Tue, 5 Mar 2024 02:03:59 +0100 Subject: [PATCH 0742/1813] Add version restriction for pandas (#46157) - Due to recent breaking changes in `pandas` we need to restrict it to versions >=2.1.0 --- recipes/captus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/captus/meta.yaml b/recipes/captus/meta.yaml index 48bc3a204b6d2..dfabb039bb92b 100644 --- a/recipes/captus/meta.yaml +++ b/recipes/captus/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --ignore-installed -vv" run_exports: @@ -35,7 +35,7 @@ requirements: - megahit =1.2.9=hfbae3c0_0 # [osx] - mmseqs2 - muscle >=5 - - pandas + - pandas >=2.1.0 - perl-bioperl-core - perl-yaml - pigz From e7e95986120fbe6f58f2af5c006c886d653254b4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 00:20:38 -0500 Subject: [PATCH 0743/1813] Update somalier to 0.2.19 (#43167) * Update somalier to 0.2.19 * Small bump to trigger CI * Pin nim to an older version See https://github.com/brentp/mosdepth/issues/209 --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Liang-Bo Wang --- recipes/somalier/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/somalier/meta.yaml b/recipes/somalier/meta.yaml index 84fc5a4dd9425..32d5d2be59eec 100644 --- a/recipes/somalier/meta.yaml +++ b/recipes/somalier/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.18" %} +{% set version = "0.2.19" %} package: name: somalier @@ -6,7 +6,7 @@ package: source: url: https://github.com/brentp/somalier/archive/refs/tags/v{{ version }}.tar.gz - sha256: e95ba09a1ec0bd352643ea1907a1c3d23a43801b176e10fdbee198c0bec02af4 + sha256: d93b34d15deb12d75ce4637857d4c74eb94572e0aac6303df539a345e3485fa8 # Skip OSX following https://github.com/bioconda/bioconda-recipes/blob/73a14544ca8ef7926797b39259cb58b83732b7da/recipes/slivar/meta.yaml build: @@ -19,7 +19,7 @@ requirements: build: - {{ compiler('c') }} - curl - - nim + - nim <2 host: - openblas - htslib @@ -38,6 +38,7 @@ about: license: MIT summary: 'fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs.' + extra: identifiers: - doi:10.1186/s13073-020-00761-2 From 646390d074a1ec09fceb73171941ed6ab0b66048 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 5 Mar 2024 17:42:01 +1030 Subject: [PATCH 0744/1813] Add phynder (#46107) * Add phynder * Fix file name * Update recipes/phynder/build.sh * Update recipes/phynder/meta.yaml * Update recipes/phynder/meta.yaml --- recipes/phynder/build.sh | 37 +++++++++++++++++++++++++++++ recipes/phynder/meta.yaml | 50 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 recipes/phynder/build.sh create mode 100644 recipes/phynder/meta.yaml diff --git a/recipes/phynder/build.sh b/recipes/phynder/build.sh new file mode 100644 index 0000000000000..0c5bc4499456d --- /dev/null +++ b/recipes/phynder/build.sh @@ -0,0 +1,37 @@ +#!/bin/bash +set -x +set +e + +export CFLAGS="$CFLAGS -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" +export CPATH=${PREFIX}/include + +## Static lib required by phynder, thus following instructions +## rather than trying to take from a conda htslib +git clone https://github.com/samtools/htslib.git +cd htslib +git submodule update --init --recursive + +## from https://github.com/pachterlab/kallisto/issues/303#issuecomment-884612169 +sed '/AC_PROG_CC/a \ +AC_CANONICAL_HOST \ +AC_PROG_INSTALL \ +' configure.ac >configure.ac2 +mv configure.ac2 configure.ac +autoreconf -i +autoheader +autoconf + +./configure --prefix=${PREFIX} --enable-libcurl --with-libdeflate --enable-plugins --enable-gcs --enable-s3 +make lib-static htslib_static.mk +make CC=$CC install + +## Patch phynder Makefile to cloned htslib folder (original assumes alongside, not within) +cd ../ +sed -i 's#HTSDIR=../htslib#HTSDIR=./htslib#g' Makefile +sed -i -e 's#LDLIBS=$(HTSLIB) -lpthread $(HTSLIB_static_LIBS)#LDLIBS=$(HTSLIB) -lpthread $(HTSLIB_static_LIBS) $(LDFLAGS)#g' -e 's#cp phynder ~/bin##g' Makefile + +make CC=$CC CFLAGS="$CFLAGS" LDFLAGS="$LDFLAGS" +make install + +cp phynder $PREFIX/bin/ diff --git a/recipes/phynder/meta.yaml b/recipes/phynder/meta.yaml new file mode 100644 index 0000000000000..e8c861e84d27f --- /dev/null +++ b/recipes/phynder/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "phynder" %} +{% set version = "1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/richarddurbin/{{ name | lower }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 94d629d0c2e9085bfe9dbbe2c6302021ad81a00b3696696e103aa31db51d849f + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('phynder', max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - autoconf + - automake + host: + - libcurl + - bzip2 + - xz + - zlib + - libdeflate + - openssl # [not osx] + + +test: + commands: + - phynder -h +about: + home: https://github.com/richarddurbin/phynder + dev_url: https://github.com/richarddurbin/phynder + license: MIT + license_file: LICENSE + summary: Efficient likelihood calculations to place samples into a phylogenetic tree. + description: | + Efficient likelihood calculations to place samples into a phylogenetic tree. + In particular, phynder was originally designed for placing male ancient DNA + samples into the Y chromosome phylogeny, when there are arbitrarily high rates + of missing data. It has also been used for assigning ancient samples to whole + mitochondrial genome phylogenies. +extra: + maintainers: + - jfy133 \ No newline at end of file From 3906fc8f060c1494d316864bb58b25112b26cf55 Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Mon, 4 Mar 2024 23:12:33 -0800 Subject: [PATCH 0745/1813] Update nextclade to 3.3.0 (#46167) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index 174aad8dc0c36..11b326dcfadd5 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.2.1" %} +{% set version = "3.3.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 797d9dab371dad8fcd65d6fe8347f8e3caa21243a930b0b422cb0e68f2039b57 # [linux64] + sha256: 6d2566a510152378e7624104225c29cd765c0f2b8bb8c12bb2d6a161857f05bf # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: 9be0cca8dcf580bed2aa1746d8117a29711b72c96029ac960ca29e715f51abf3 # [osx and x86_64] + sha256: 330ad12cd1bb20429f49fd00bcd773c453b66662842913ec35bc9e288ab3db2a # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: e2dbf3d2fa624f8926068dee7a678d867bfbe607fa2efefe7ca0d2f478f8df1a # [arm64] + sha256: 1732681a651de65424f16b8fe5a2582183a4ab0098713e6aa39d63bd760009d3 # [arm64] build: number: 0 From 7835b8b91f421b418a2c5f227b485184a98367f1 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Tue, 5 Mar 2024 16:13:48 +0900 Subject: [PATCH 0746/1813] Update MMseqs2 build-number for arm build (#46164) --- recipes/mmseqs2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/mmseqs2/meta.yaml b/recipes/mmseqs2/meta.yaml index e7ecac44899cc..ff7ace052d96d 100644 --- a/recipes/mmseqs2/meta.yaml +++ b/recipes/mmseqs2/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('mmseqs2', max_pin=None) }} From cf63d5d5cb707db9a519ae9d470ff8bf58fef843 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 02:14:48 -0500 Subject: [PATCH 0747/1813] Update metaphor to 1.7.11 (#46163) --- recipes/metaphor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metaphor/meta.yaml b/recipes/metaphor/meta.yaml index a5d1801709fb8..5833df5021a2f 100644 --- a/recipes/metaphor/meta.yaml +++ b/recipes/metaphor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metaphor" %} -{% set version = "1.7.10" %} +{% set version = "1.7.11" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/vinisalazar/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: f8b49aac85fd16b78210cbacc34e615baeb8551e3aa11eed36748385333c9f49 + sha256: 45f01fc8a7c142f3ae26b4880488e77228103a670cffaa986e5377b7efcaff86 build: number: 0 From 3fa4341d07f57c23644c4553cb65cb9a74e80063 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 02:14:57 -0500 Subject: [PATCH 0748/1813] Update ont-modkit to 0.2.5 (#46161) --- recipes/ont-modkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml index 452de044fa9b1..8b366795bee15 100644 --- a/recipes/ont-modkit/meta.yaml +++ b/recipes/ont-modkit/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.4" %} -{% set sha256 = "fcf01e992a9a8fd1feccf8513370cbcdb630fd0b4c0d14ce76696bfef656fe79" %} +{% set version = "0.2.5" %} +{% set sha256 = "06bb7a0ad3de72c8b2865975bd793654bb9e88f4aa5db1ce46611c024fae5d6f" %} package: name: ont-modkit From e29cab9327fd0f4c688557aea7cb7b930551c10b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 02:15:50 -0500 Subject: [PATCH 0749/1813] Update hictk to 0.0.10 (#46155) --- recipes/hictk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index 2f0e1d7330f04..6ae4433671ca6 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.9" %} -{% set sha256 = "c64cb07a057863baa199b9d344b27b8f15a1db458390ccf7b5cac0627308d8c8" %} +{% set version = "0.0.10" %} +{% set sha256 = "0b2d60af73578b292317e5ab513f24965176f9852ceda29e8d02007a434588c3" %} package: name: {{ name|lower }} From f68af901bdf1110426387a36b5447bbda8db6baa Mon Sep 17 00:00:00 2001 From: George Bouras <84495559+gbouras13@users.noreply.github.com> Date: Tue, 5 Mar 2024 18:26:43 +1030 Subject: [PATCH 0750/1813] Add phold (#46159) * Add phold * change torch to pytorch * add poetry * add build.sh for cnn * merge scripts * take 2 * fix pypi release v0.1.1 * remove poetry --- recipes/phold/meta.yaml | 62 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 recipes/phold/meta.yaml diff --git a/recipes/phold/meta.yaml b/recipes/phold/meta.yaml new file mode 100644 index 0000000000000..a70b903485b75 --- /dev/null +++ b/recipes/phold/meta.yaml @@ -0,0 +1,62 @@ +{% set name = "phold" %} +{% set version = "0.1.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 73c4045cf7eb847eb43fa91ca79f7d6319d63122b3588279a1d8ea3ec53f7218 + +build: + number: 0 + noarch: python + entry_points: + - phold = phold:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('phold', max_pin='x') }} + +requirements: + host: + - python >=3.8,<3.12 + - pip + run: + - foldseek ==8.ef4e960 + - python >=3.8,<3.12 + - biopython >=1.76 + - alive-progress >=3.0.1 + - datasets >=2.15 + - requests >=2.25 + - pyarrow >=14.0.0 + - pandas >=1.4.2 + - loguru >=0.5.3 + - pyyaml >=6.0 + - click >=8.0.0 + - sentencepiece >=0.1.99 + - transformers >=4.34 + - pyrodigal-gv >=0.3.1 + - pytorch >=2.1.2 + - numpy >=1.20 + - pycirclize >=0.3.1 + + + +test: + imports: + - phold + commands: + - phold --help + +about: + home: https://github.com/gbouras13/phold + license: MIT + license_family: MIT + license_file: LICENSE + summary: Phage annotation using protein structures + doc_url: https://phold.readthedocs.io/en/latest/ + +extra: + recipe-maintainers: + - gbouras13 From b9c1e0bac8e3c6ba828e48bdb883cb4ebdc2a393 Mon Sep 17 00:00:00 2001 From: lspindler2509 <83402447+lspindler2509@users.noreply.github.com> Date: Tue, 5 Mar 2024 09:24:31 +0100 Subject: [PATCH 0751/1813] update biodigest (#46139) * update biodigest versions * spelling --- recipes/biodigest/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/biodigest/meta.yaml b/recipes/biodigest/meta.yaml index b9f74d92d4a32..8bb365dda3fca 100644 --- a/recipes/biodigest/meta.yaml +++ b/recipes/biodigest/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7618cedf40fedd6dd60aa2fbf8635fb4af0a2c0ae16c01ef9741d30729b6e8bc build: - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" noarch: python run_exports: @@ -20,16 +20,16 @@ build: requirements: host: - pip - - python >=3.7, <=3.9 + - python >=3.7 run: - biothings_client ==0.2.6 - gseapy ==0.10.5 - - graph-tool + - graph-tool >=2.58 - numpy ==1.24.3 - pandas ==1.5.2 - psutil ==5.9.0 - pycairo >=1.21.0 - - python >=3.7, <=3.9 + - python >=3.7 - requests >=2.28.2 - scipy ==1.8.0 - seaborn >=0.12.2 @@ -46,4 +46,4 @@ about: license: GPL-3.0-or-later license_family: GPL3 license_file: LICENSE - summary: "In silico Validation of Disease and Gene Sets, Clusterings or Subnetworks (DIGEST)" + summary: "In silico Validation of Disease and Gene sets, Clusterings or Subnetworks (DIGEST)" From 418435b56c64f33c7674756a5eb17cae90d32f1a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 05:41:31 -0500 Subject: [PATCH 0752/1813] Update hmftools-orange to 3.3.0 (#46179) --- recipes/hmftools-orange/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-orange/meta.yaml b/recipes/hmftools-orange/meta.yaml index afd2ba038d8f9..78bc9d85b10cc 100644 --- a/recipes/hmftools-orange/meta.yaml +++ b/recipes/hmftools-orange/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.0.0" %} -{% set sha256 = "ba3887c741501bd0d0815e701b68fe7a51dace01560ebd6e0f0647ff8c385e98" %} +{% set version = "3.3.0" %} +{% set sha256 = "6de088a73e354927fa782453d7fb7fc52a925a0fb9e8b14d54f83c238435cdb1" %} package: name: hmftools-orange From 069e444ef3197c03ac75260440b2f0ddea00efc0 Mon Sep 17 00:00:00 2001 From: Reid Wagner <74672860+reid-wagner@users.noreply.github.com> Date: Tue, 5 Mar 2024 07:58:04 -0700 Subject: [PATCH 0753/1813] Fixes to MSFragger recipe - Fix jarfile path - Fix automated test - Remove zip from installation --- recipes/msfragger/build.sh | 1 + recipes/msfragger/meta.yaml | 4 ++-- recipes/msfragger/msfragger.py | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/msfragger/build.sh b/recipes/msfragger/build.sh index f3d467463dbdd..c2f43d60481cf 100644 --- a/recipes/msfragger/build.sh +++ b/recipes/msfragger/build.sh @@ -31,3 +31,4 @@ fi cd "$TARGET" unzip "MSFragger-$PKG_VERSION.zip" ln -s "MSFragger-$PKG_VERSION/MSFragger-$PKG_VERSION.jar" "MSFragger.jar" +rm "MSFragger-$PKG_VERSION.zip" diff --git a/recipes/msfragger/meta.yaml b/recipes/msfragger/meta.yaml index 000aa4ee6fe93..5826d1d418714 100644 --- a/recipes/msfragger/meta.yaml +++ b/recipes/msfragger/meta.yaml @@ -10,7 +10,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('msfragger', max_pin="x.x") }} @@ -29,7 +29,7 @@ requirements: test: commands: - - msfragger --key {{ academic_use_only_key }} -Xms512m -Xmx1g --help 2>&1 | grep 'MSFragger' + - msfragger --key {{ academic_use_only_key }} -Xms512m -Xmx1g --help | grep 'License key verified' about: home: https://github.com/Nesvilab/MSFragger diff --git a/recipes/msfragger/msfragger.py b/recipes/msfragger/msfragger.py index 05d98f890af37..6484597f30a7e 100755 --- a/recipes/msfragger/msfragger.py +++ b/recipes/msfragger/msfragger.py @@ -9,7 +9,7 @@ import subprocess from os import access, getenv, X_OK -jar_file = os.path.join(os.path.dirname(__file__), "MSFragger.jar") +jar_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "MSFragger.jar") default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] From cf496f448aaad08bc62940b89b6c92b96f856c86 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 11:27:43 -0500 Subject: [PATCH 0754/1813] Update hyphy to 2.5.60 (#46183) --- recipes/hyphy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hyphy/meta.yaml b/recipes/hyphy/meta.yaml index 7e05e89fcba7a..580e79c6c74df 100644 --- a/recipes/hyphy/meta.yaml +++ b/recipes/hyphy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.5.59" %} -{% set sha256 = "18d7fc1569ca9fa5cbd7df0517ccb3e03de118fb42ab339073dbf3a7d82c8546" %} +{% set version = "2.5.60" %} +{% set sha256 = "bc3a5062ee3cee47de16c394189fb8a5feed48f9a8c12302432d6faa7f2ac301" %} package: name: hyphy From a8161fb213fbc7969262aa46119c30581093140f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 11:27:53 -0500 Subject: [PATCH 0755/1813] Update thapbi-pict to 1.0.11 (#46184) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index b2d52e5652b4e..234e1a3470a50 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.10" %} +{% set version = "1.0.11" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: 7ffd45fac9ede5fa635e08ff5c36d93918b62c287eff18dbd9b3bfbdf7980524 + sha256: d0f087d07b584a5a6e5aa9a6a077cfc60a339f3f37c43e09343adda41beadcc2 build: noarch: python From da9391c717373dfb4203fb22ff046c4b3a96d95b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 11:55:45 -0500 Subject: [PATCH 0756/1813] Update mehari to 0.25.0 (#46187) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 76b6889cf2e0a..3440fe3cce4b5 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.24.2" %} -{% set sha256 = "079d86302bcd9a631acff934ffcacd9042f1f3a750c3b87efcc60786923883d8" %} +{% set version = "0.25.0" %} +{% set sha256 = "62552913c0a338563e6011a40742f6aba682d6f2842e2af35ea40c3c817d5c5f" %} package: name: mehari From 9bfbb8eebfd506bbc62057e42b0fbe4b61450e4c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 12:03:23 -0500 Subject: [PATCH 0757/1813] Update pharokka to 1.7.0 (#46137) * Update pharokka to 1.7.0 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: George Bouras <84495559+gbouras13@users.noreply.github.com> --- recipes/pharokka/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pharokka/meta.yaml b/recipes/pharokka/meta.yaml index 21fb6adf06685..9463fd547e901 100644 --- a/recipes/pharokka/meta.yaml +++ b/recipes/pharokka/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.7.0" %} {% set name = "pharokka" %} -{% set sha256 = "b172d91d182bc0d25610bd6241c489e3efd947c2f4bdc4204cc5bf2b07a55afd" %} +{% set sha256 = "4637e70116c621872f6aea71548c8155312540d84ec8fc007f9729010287a948" %} {% set user = "gbouras13" %} package: @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 1 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-build-isolation --use-pep517 --no-deps -vvv" run_exports: @@ -25,7 +25,7 @@ requirements: run: - python >=3.5 - bcbio-gff >=0.7.0 - - biopython >=1.78,<1.82 + - biopython >=1.80,<1.82 - phanotate >=1.5.0,<1.6.4 - mmseqs2 ==13.45111 - trnascan-se >=2.0.9 From c2bccd4c0babb5b4dbdf903ee3df1c50d0c76c90 Mon Sep 17 00:00:00 2001 From: GuillaumeG Date: Tue, 5 Mar 2024 18:13:07 +0100 Subject: [PATCH 0758/1813] Update recipe for straindesign 3.2.3 (#46180) --- recipes/straindesign/meta.yaml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/recipes/straindesign/meta.yaml b/recipes/straindesign/meta.yaml index d7951054be15c..ead98afb52998 100644 --- a/recipes/straindesign/meta.yaml +++ b/recipes/straindesign/meta.yaml @@ -1,5 +1,5 @@ {% set name = "straindesign" %} -{% set version = "3.2.2" %} +{% set version = "3.2.3" %} package: name: {{ name }} @@ -7,23 +7,24 @@ package: source: url: https://github.com/brsynth/{{ name }}/archive/{{ version }}.tar.gz - sha256: 3574003d2034d2e417230990d751840ddef9c505e57ddcc60e243cc6980779e2 + sha256: 326d55fb45321a89a2f32b9a8e966dbe1a15e070e504366c5e0fa050b67baca8 build: number: 0 noarch: python script: {{ PYTHON }} -m pip install -vv . + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: - pip - - python + - python >=3.8 - pyyaml - setuptools run: - biopython - blessings - - click - cobra >=0.24 - escher - future @@ -32,14 +33,11 @@ requirements: - IProgress - lazy-object-proxy - plotly - - python - - markupsafe + - python >=3.8 - networkx - numexpr - - numpy <1.24 # Related to https://github.com/numpy/numpy/pull/22607 - openbabel - openpyxl - - optlang - ordered-set - palettable - pandas @@ -63,3 +61,4 @@ about: extra: recipe-maintainers: - guillaume-gricourt + - tduigou From 3d132ee65dfb55ba7ef8b6a8dc62ae452267e71c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 12:20:21 -0500 Subject: [PATCH 0759/1813] Update screadcounts to 1.4.0 (#46188) * Update screadcounts to 1.4.0 * Add run_exports to meta.yaml --------- Co-authored-by: Nathan Edwards --- recipes/screadcounts/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/screadcounts/meta.yaml b/recipes/screadcounts/meta.yaml index c9e32396235b3..3780536d73673 100644 --- a/recipes/screadcounts/meta.yaml +++ b/recipes/screadcounts/meta.yaml @@ -1,6 +1,6 @@ {% set name = "screadcounts" %} -{% set version = "1.3.2" %} -{% set sha256 = "d7dde05a80227ac5207b0495323fc9154202f2d4d082296964a1d5f16468870d" %} +{% set version = "1.4.0" %} +{% set sha256 = "61856534dc5c578e9d12bcb397dc696747685b33ef056c49d1ff766960676c30" %} package: name: {{ name }} @@ -13,6 +13,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('screadcounts', max_pin="x.x") }} extra: skip-lints: From 0d78770341a4987fda9b008d631fad09dbf654c1 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Wed, 6 Mar 2024 02:35:29 +0900 Subject: [PATCH 0760/1813] Update metaeuk for linux-aarch64 (#46172) * Update metaeuk for linux-aarch64 * Fix run exports --- recipes/metaeuk/build.sh | 16 +++++++++++++--- recipes/metaeuk/meta.yaml | 6 +++++- 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/recipes/metaeuk/build.sh b/recipes/metaeuk/build.sh index 0d987840efe4b..b06956020200b 100644 --- a/recipes/metaeuk/build.sh +++ b/recipes/metaeuk/build.sh @@ -1,8 +1,18 @@ -#!/bin/bash -e +#!/bin/bash + +ARCH_BUILD="" +case $(uname -m) in + x86_64) ARCH_BUILD="-DHAVE_SSE4_1=1" ;; + arm64|aarch64) ARCH_BUILD="-DHAVE_ARM8=1" ;; +esac + +if [ -z "${ARCH_BUILD}" ]; then + echo "Invalid architecture" + exit 1 +fi mkdir build cd build -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 -DHAVE_SSE4_1=1 -DVERSION_OVERRIDE="${PKG_VERSION}" .. +cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 ${ARCH_BUILD} -DVERSION_OVERRIDE="${PKG_VERSION}" .. make -j${CPU_COUNT} ${VERBOSE_CM} make install - diff --git a/recipes/metaeuk/meta.yaml b/recipes/metaeuk/meta.yaml index 1123976a0fc78..92bb339c597cb 100644 --- a/recipes/metaeuk/meta.yaml +++ b/recipes/metaeuk/meta.yaml @@ -7,7 +7,9 @@ package: version: {{ version|replace("-", ".") }} build: - number: 3 + number: 4 + run_exports: + - {{ pin_subpackage('metaeuk', max_pin="x") }} source: url: https://github.com/soedinglab/metaeuk/archive/{{ version }}.tar.gz @@ -50,3 +52,5 @@ extra: recipe-maintainers: - milot-mirdita - elileka + additional-platforms: + - linux-aarch64 \ No newline at end of file From 72bce2de07be5915601fafb11dedd15fef0aec07 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Wed, 6 Mar 2024 02:36:13 +0900 Subject: [PATCH 0761/1813] Update kalign2 for linux-aarch64 (and enable osx builds again) (#46175) --- recipes/kalign2/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/kalign2/meta.yaml b/recipes/kalign2/meta.yaml index 12287cdb17f9d..0c5f0efab39a6 100644 --- a/recipes/kalign2/meta.yaml +++ b/recipes/kalign2/meta.yaml @@ -6,8 +6,9 @@ package: version: {{ version }} build: - number: 5 - skip: True # [osx] + number: 6 + run_exports: + - {{ pin_subpackage('kalign2', max_pin='x') }} source: url: http://msa.sbc.su.se/downloads/kalign/current.tar.gz @@ -31,3 +32,5 @@ about: extra: identifiers: - doi:10.1186/1471-2105-6-298 + additional-platforms: + - linux-aarch64 \ No newline at end of file From 71d695f7e8080a709abff6de8c854bd90c7f4d90 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Wed, 6 Mar 2024 02:41:32 +0900 Subject: [PATCH 0762/1813] Update spacepharer for linux-aarch64 (#46173) * Update spacepharer for linux-aarch64 * Fix run exports --- recipes/spacepharer/build.sh | 16 +++++++++++++--- recipes/spacepharer/meta.yaml | 6 +++++- 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/recipes/spacepharer/build.sh b/recipes/spacepharer/build.sh index 0d987840efe4b..b06956020200b 100644 --- a/recipes/spacepharer/build.sh +++ b/recipes/spacepharer/build.sh @@ -1,8 +1,18 @@ -#!/bin/bash -e +#!/bin/bash + +ARCH_BUILD="" +case $(uname -m) in + x86_64) ARCH_BUILD="-DHAVE_SSE4_1=1" ;; + arm64|aarch64) ARCH_BUILD="-DHAVE_ARM8=1" ;; +esac + +if [ -z "${ARCH_BUILD}" ]; then + echo "Invalid architecture" + exit 1 +fi mkdir build cd build -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 -DHAVE_SSE4_1=1 -DVERSION_OVERRIDE="${PKG_VERSION}" .. +cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 ${ARCH_BUILD} -DVERSION_OVERRIDE="${PKG_VERSION}" .. make -j${CPU_COUNT} ${VERBOSE_CM} make install - diff --git a/recipes/spacepharer/meta.yaml b/recipes/spacepharer/meta.yaml index b42834234a7ea..ed8c6096e102d 100644 --- a/recipes/spacepharer/meta.yaml +++ b/recipes/spacepharer/meta.yaml @@ -6,7 +6,9 @@ package: version: {{ version|replace("-", ".") }} build: - number: 3 + number: 4 + run_exports: + - {{ pin_subpackage('spacepharer', max_pin="x") }} source: url: https://github.com/soedinglab/spacepharer/archive/{{ version }}.tar.gz @@ -46,3 +48,5 @@ extra: identifiers: - doi:10.1093/bioinformatics/btab222 - biotools:spacepharer + additional-platforms: + - linux-aarch64 \ No newline at end of file From 81ea04a62b0ad7bceee0ca49a609af70dae78c54 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Wed, 6 Mar 2024 02:44:50 +0900 Subject: [PATCH 0763/1813] Update foldseek for linux-aarch64 (#46169) --- recipes/foldseek/build.sh | 16 +++++++++++++--- recipes/foldseek/meta.yaml | 4 +++- 2 files changed, 16 insertions(+), 4 deletions(-) diff --git a/recipes/foldseek/build.sh b/recipes/foldseek/build.sh index 0d987840efe4b..b06956020200b 100644 --- a/recipes/foldseek/build.sh +++ b/recipes/foldseek/build.sh @@ -1,8 +1,18 @@ -#!/bin/bash -e +#!/bin/bash + +ARCH_BUILD="" +case $(uname -m) in + x86_64) ARCH_BUILD="-DHAVE_SSE4_1=1" ;; + arm64|aarch64) ARCH_BUILD="-DHAVE_ARM8=1" ;; +esac + +if [ -z "${ARCH_BUILD}" ]; then + echo "Invalid architecture" + exit 1 +fi mkdir build cd build -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 -DHAVE_SSE4_1=1 -DVERSION_OVERRIDE="${PKG_VERSION}" .. +cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 ${ARCH_BUILD} -DVERSION_OVERRIDE="${PKG_VERSION}" .. make -j${CPU_COUNT} ${VERBOSE_CM} make install - diff --git a/recipes/foldseek/meta.yaml b/recipes/foldseek/meta.yaml index 1c73a8fb35244..7c189ec2f9628 100644 --- a/recipes/foldseek/meta.yaml +++ b/recipes/foldseek/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('foldseek', max_pin="x") }} @@ -53,3 +53,5 @@ extra: recipe-maintainers: - milot-mirdita - martin-steinegger + additional-platforms: + - linux-aarch64 \ No newline at end of file From 79bb61f16a21f68a2d63f510c67318e899f172e6 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Wed, 6 Mar 2024 02:45:34 +0900 Subject: [PATCH 0764/1813] Update metabuli for linux-aarch64 (#46171) --- recipes/metabuli/build.sh | 13 ++++++++++++- recipes/metabuli/meta.yaml | 4 +++- 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/recipes/metabuli/build.sh b/recipes/metabuli/build.sh index dccd8da45922c..b06956020200b 100644 --- a/recipes/metabuli/build.sh +++ b/recipes/metabuli/build.sh @@ -1,7 +1,18 @@ #!/bin/bash +ARCH_BUILD="" +case $(uname -m) in + x86_64) ARCH_BUILD="-DHAVE_SSE4_1=1" ;; + arm64|aarch64) ARCH_BUILD="-DHAVE_ARM8=1" ;; +esac + +if [ -z "${ARCH_BUILD}" ]; then + echo "Invalid architecture" + exit 1 +fi + mkdir build cd build -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 -DHAVE_SSE4_1=1 -DVERSION_OVERRIDE="${PKG_VERSION}" .. +cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 ${ARCH_BUILD} -DVERSION_OVERRIDE="${PKG_VERSION}" .. make -j${CPU_COUNT} ${VERBOSE_CM} make install diff --git a/recipes/metabuli/meta.yaml b/recipes/metabuli/meta.yaml index f096860d05815..584f1202b94a8 100644 --- a/recipes/metabuli/meta.yaml +++ b/recipes/metabuli/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('metabuli', max_pin="x") }} @@ -48,3 +48,5 @@ extra: recipe-maintainers: - milot-mirdita - jaebeom-kim + additional-platforms: + - linux-aarch64 \ No newline at end of file From f310578379541a844d101c7fc77edfc56ceb40d2 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Wed, 6 Mar 2024 02:46:03 +0900 Subject: [PATCH 0765/1813] Update hh-suite for linux-aarch64 (#46170) * Update hh-suite for linux-aarch64 * Missing run-exports --- recipes/hhsuite/build.sh | 14 +++++++++++++- recipes/hhsuite/meta.yaml | 6 +++++- 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/recipes/hhsuite/build.sh b/recipes/hhsuite/build.sh index 7dbbef3e25a4d..17e152530bc6a 100644 --- a/recipes/hhsuite/build.sh +++ b/recipes/hhsuite/build.sh @@ -1,8 +1,20 @@ #!/bin/bash + +ARCH_BUILD="" +case $(uname -m) in + x86_64) ARCH_BUILD="-DHAVE_SSE4_1=1" ;; + arm64|aarch64) ARCH_BUILD="-DHAVE_ARM8=1" ;; +esac + +if [ -z "${ARCH_BUILD}" ]; then + echo "Invalid architecture" + exit 1 +fi + mkdir -p build && cd build cmake -DCHECK_MPI=0 \ -DHAVE_MPI=0 \ - -DHAVE_SSE2=1 \ + ${ARCH_BUILD} \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ .. diff --git a/recipes/hhsuite/meta.yaml b/recipes/hhsuite/meta.yaml index e1b23092e49fa..43639d506e046 100644 --- a/recipes/hhsuite/meta.yaml +++ b/recipes/hhsuite/meta.yaml @@ -6,7 +6,9 @@ package: version: {{ version }} build: - number: 9 + number: 10 + run_exports: + - {{ pin_subpackage('hhsuite', max_pin="x") }} source: url: https://github.com/soedinglab/hh-suite/archive/v{{ version }}.tar.gz @@ -47,3 +49,5 @@ extra: - biotools:hh-suite recipe-maintainers: - milot-mirdita + additional-platforms: + - linux-aarch64 \ No newline at end of file From 56017317c45458dc77712523271f129c21187675 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 13:34:57 -0500 Subject: [PATCH 0766/1813] Update sansa to 0.2.1 (#46182) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/sansa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sansa/meta.yaml b/recipes/sansa/meta.yaml index e22272e18b320..50e1fa53b64ec 100644 --- a/recipes/sansa/meta.yaml +++ b/recipes/sansa/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.1.1" %} -{% set sha256 = "ab477696eca25d3aa84145ba9734f519ea84bea902267836019c3e08aa8b2669" %} +{% set version = "0.2.1" %} +{% set sha256 = "f43b088b8339d3ba395adf922d723b074e31f8bf548c9e9039cccace5acc60ee" %} package: name: sansa From 78930afecbc108f0febb0edf7c2a452bd279e2d2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 13:35:07 -0500 Subject: [PATCH 0767/1813] Update pybiolib to 1.1.1834 (#46181) * Update pybiolib to 1.1.1828 * Update pybiolib to 1.1.1830 * Update pybiolib to 1.1.1834 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 05e1f5613035c..52ee51c6059ce 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1815" %} +{% set version = "1.1.1834" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 53be318613e0eb135d4634fa89841c9b4cd1e085e07fc5ccd2351b82ff2bb5fe + sha256: 9bd04ef7fccae01e8d7d6b49c833fcf5d631e2649889882d10ce52656c62c7e0 build: noarch: python From c498d4d3ea861b92590999095c008becdb753874 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 14:05:20 -0500 Subject: [PATCH 0768/1813] Update mercat2 to 1.4.1 (#46189) --- recipes/mercat2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mercat2/meta.yaml b/recipes/mercat2/meta.yaml index e9ea1d303868d..9de650d4cebc2 100644 --- a/recipes/mercat2/meta.yaml +++ b/recipes/mercat2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mercat2" %} -{% set version = "1.4.0" %} +{% set version = "1.4.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e100287a9772832df1f51295b5f80969aff1010942ecabf24f566083aa31d22c + sha256: 5a090b19db6beecae8d3a1f2014a239b306fa428e92cc8f02e98e0e4b4a89d31 build: number: 0 From eef218d1e5790a58633528390c4f1dda36765a50 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Wed, 6 Mar 2024 08:09:58 +1300 Subject: [PATCH 0769/1813] Build htslib for linux-aarch64 (#46158) * Add additional-platforms entry * Work around old sysroot_linux-aarch64 version This works around samtools/htscodecs#88, whereby conda-forge's older sysroot_linux-aarch64 2.17 does not define HWCAP_* values on ARM and so Neon codec implementations are unused as have_neon() is always 0. Avoid this by including the kernel header to get the desired values. --- recipes/htslib/arm_hwcap.patch | 15 +++++++++++++++ recipes/htslib/meta.yaml | 6 +++++- 2 files changed, 20 insertions(+), 1 deletion(-) create mode 100644 recipes/htslib/arm_hwcap.patch diff --git a/recipes/htslib/arm_hwcap.patch b/recipes/htslib/arm_hwcap.patch new file mode 100644 index 0000000000000..40733dcc33b1d --- /dev/null +++ b/recipes/htslib/arm_hwcap.patch @@ -0,0 +1,15 @@ +Conda-forge's build environment on ARM uses sysroot_linux-aarch64 2.17, which +is based on glibc 2.17 so does not define HWCAP_* values on ARM. +Work around this by including the kernel header to get the desired values. + +--- a/htscodecs/htscodecs/rANS_static4x16pr.c 2023-10-10 02:54:16 ++++ b/htscodecs/htscodecs/rANS_static4x16pr.c 2024-03-06 00:01:14 +@@ -1030,6 +1030,8 @@ + + #if defined(__linux__) || defined(__FreeBSD__) + #include ++// Ensure ARM HWCAP_* values are defined even on old glibc ++#include + #elif defined(_WIN32) + #include + #endif diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml index db620cbb24b61..31e786232b9da 100644 --- a/recipes/htslib/meta.yaml +++ b/recipes/htslib/meta.yaml @@ -5,13 +5,15 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('htslib', max_pin='x.x') }} source: url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 sha256: 222d74d3574fb67b158c6988c980eeaaba8a0656f5e4ffb76b5fa57f035933ec + patches: + - arm_hwcap.patch requirements: build: @@ -46,6 +48,8 @@ about: doc_url: http://www.htslib.org/ extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:HTSlib skip-lints: From c2e38e3609f5f589c4d0becf863d7f8559e887cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 14:39:00 -0500 Subject: [PATCH 0770/1813] Update physiofit to 3.3.3 (#46142) * Update physiofit to 3.3.3 * add pyarrow dependency --------- Co-authored-by: mencian --- recipes/physiofit/meta.yaml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/recipes/physiofit/meta.yaml b/recipes/physiofit/meta.yaml index 097759c293e02..3234da2c1b2b8 100644 --- a/recipes/physiofit/meta.yaml +++ b/recipes/physiofit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "physiofit" %} -{% set version = "3.3.2" %} +{% set version = "3.3.3" %} package: name: {{ name|lower }} @@ -7,16 +7,16 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/physiofit-{{ version }}.tar.gz - sha256: 1512c9926e74255034e4b3bdba7fd72a11e297841f62532b8e835957aa6f0e77 + sha256: a3d16abf8a3da9eb6deacd8ff73a48c21fc22972033bd14afc7edb7cea8fad05 build: entry_points: - physiofit = physiofit.__main__:main noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv number: 0 run_exports: - - {{ pin_subpackage('physiofit', max_pin="x") }} + - {{ pin_subpackage('physiofit', max_pin="x") }} requirements: host: @@ -30,23 +30,26 @@ requirements: - scipy >=1.10.1 - streamlit >=1.20.0 - matplotlib-base >=3.7.1 + - pyarrow >=14.0.1,<15.0.0 - pyyaml >=6.0.0 test: imports: - physiofit commands: - - pip check - physiofit --help - requires: - - pip about: home: https://github.com/MetaSys-LISBP/PhysioFit summary: Calculate extracellular fluxes from metabolite concentrations and biomass data license: GPL-3.0-only + license_family: GPL3 license_file: LICENSE + doc_url: https://physiofit.readthedocs.io/en/latest/ + dev_url: https://github.com/MetaSys-LISBP/PhysioFit extra: recipe-maintainers: - llegregam + identifiers: + - doi:10.1101/2023.10.12.561695 From 40bc097aac1aad5a37fa8022226aa4c67e3809fb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 14:41:59 -0500 Subject: [PATCH 0771/1813] Update ffq to 0.3.1 (#46126) * Update ffq to 0.3.1 * add runexports --------- Co-authored-by: Robert A. Petit III --- recipes/ffq/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ffq/meta.yaml b/recipes/ffq/meta.yaml index 01085e234028f..f1b17c86690cf 100644 --- a/recipes/ffq/meta.yaml +++ b/recipes/ffq/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ffq" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/f/ffq/ffq-{{ version }}.tar.gz - sha256: 247b1da25090519708e3811f849a612c56cdb41eda7845000490992d0a1d98b6 + sha256: 02a82b1130fa1d50558b8e3b9663cc2db1ad95498a7345783e69517f6391884b build: number: 0 @@ -15,6 +15,8 @@ build: - ffq=ffq.main:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " noarch: python + run_exports: + - {{ pin_subpackage('ffq', max_pin="x.x") }} requirements: host: From b68817601e095e93d6c5da6ffe0685684377e29c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 14:42:22 -0500 Subject: [PATCH 0772/1813] Update ncbi-vdb to 3.1.0 (#46190) --- recipes/ncbi-vdb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-vdb/meta.yaml b/recipes/ncbi-vdb/meta.yaml index 61d789b3e0c6f..30242cd443391 100644 --- a/recipes/ncbi-vdb/meta.yaml +++ b/recipes/ncbi-vdb/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.0.10" %} +{% set version = "3.1.0" %} package: name: ncbi-vdb @@ -12,7 +12,7 @@ build: source: url: https://github.com/ncbi/ncbi-vdb/archive/{{ version }}.tar.gz - sha256: 2e088a8542e6c3bc1aad01a5d2fca2ef5b745c36a3aafd3b0b42cb53b42b345d + sha256: eec5a64b8353a201bd4cf2c58cfcbb3622327397c3b11696ae59d827fcfcea9d folder: ncbi-vdb requirements: From fe7a0e2fdacb59a29b5f1e3474c988976ea32943 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 14:44:20 -0500 Subject: [PATCH 0773/1813] Update snakemake-executor-plugin-cluster-generic to 1.0.8 (#46151) * Update snakemake-executor-plugin-cluster-generic to 1.0.8 * add summary --------- Co-authored-by: mencian --- .../meta.yaml | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml b/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml index 0abb031d05075..58af4c99df718 100644 --- a/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml +++ b/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-cluster-generic" %} -{% set version = "1.0.7" %} +{% set version = "1.0.8" %} package: name: {{ name|lower }} @@ -7,11 +7,11 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_cluster_generic-{{ version }}.tar.gz - sha256: 093808e63cc48294a9d1eb0b620cdff8cc970806294a2f6ba127a49f8a81d473 + sha256: 707890e9752a8b711c42fb454430d42a58f39f8cf28ac16e87fe0387b19a29bb build: noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation number: 0 run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -29,15 +29,12 @@ requirements: test: imports: - snakemake_executor_plugin_cluster_generic - commands: - - pip check - requires: - - pip about: home: https://github.com/snakemake/snakemake-executor-plugin-cluster-generic - summary: '' + summary: 'Generic cluster executor for Snakemake' license: MIT + license_family: MIT license_file: LICENSE extra: From 8554145cd563190749c4042251ec4dc0b7cdf52d Mon Sep 17 00:00:00 2001 From: John Marshall Date: Wed, 6 Mar 2024 11:15:50 +1300 Subject: [PATCH 0774/1813] Build bcftools and samtools for linux-aarch64 (#46193) --- recipes/bcftools/meta.yaml | 4 +++- recipes/samtools/meta.yaml | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index cbe333349ad2f..d419fce55b866 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("bcftools", max_pin="x") }} @@ -48,6 +48,8 @@ about: VCF and BCF and streams will work in most, but not all situations. extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:bcftools - usegalaxy-eu:bcftools_merge diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index cd24c1020f76f..8b2987bf9ce72 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("samtools", max_pin="x") }} @@ -35,6 +35,8 @@ test: - samtools view 'https://example.com' 2>&1 | grep 'fail to read the header' -q extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:samtools - usegalaxy-eu:samtools_flagstat From 4e7f63c820615f954d3104b65c6e458112198bc5 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Wed, 6 Mar 2024 11:16:19 +1300 Subject: [PATCH 0775/1813] Build bedtools for linux-aarch64 (#46194) --- recipes/bedtools/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bedtools/meta.yaml b/recipes/bedtools/meta.yaml index 2c96f9e40ecca..d7c60edc863cc 100644 --- a/recipes/bedtools/meta.yaml +++ b/recipes/bedtools/meta.yaml @@ -10,7 +10,7 @@ source: sha256: fc7e660c2279b1e008b80aca0165a4a157daf4994d08a533ee925d73ce732b97 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('bedtools', max_pin="x") }} @@ -35,6 +35,8 @@ about: summary: A powerful toolset for genome arithmetic extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:bedtools - usegalaxy-eu:bedtools_intersectbed From e3d2534814a06bccd1740c70bff1fa69e7e4ba77 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 17:27:05 -0500 Subject: [PATCH 0776/1813] Update sra-tools to 3.1.0 (#46192) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/sra-tools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sra-tools/meta.yaml b/recipes/sra-tools/meta.yaml index a108dacb2488c..48524c74ccba4 100644 --- a/recipes/sra-tools/meta.yaml +++ b/recipes/sra-tools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sra-tools" %} -{% set version = "3.0.10" %} -{% set sha256 = "93cfa802938506866b9d565a18a31ac84fd26f2929636b23f1f8dd9f39cf977d" %} +{% set version = "3.1.0" %} +{% set sha256 = "ce92ce887ee4a7581a7511cfb6b965ac6a5e38841bad9be66a3aee903ec48952" %} package: name: {{ name }} From 6a5ee04a6e438f8fcd537d97ad4c59e5ebf8ff9e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 17:27:15 -0500 Subject: [PATCH 0777/1813] Update ncbi-vdb-py to 3.1.0 (#46191) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ncbi-vdb-py/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-vdb-py/meta.yaml b/recipes/ncbi-vdb-py/meta.yaml index eebd27cd47135..6b8aebde9bebc 100644 --- a/recipes/ncbi-vdb-py/meta.yaml +++ b/recipes/ncbi-vdb-py/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.0.10" %} -{% set sha256 = "2e088a8542e6c3bc1aad01a5d2fca2ef5b745c36a3aafd3b0b42cb53b42b345d" %} +{% set version = "3.1.0" %} +{% set sha256 = "eec5a64b8353a201bd4cf2c58cfcbb3622327397c3b11696ae59d827fcfcea9d" %} package: name: ncbi-vdb-py From bc21aaf0b8e5ff870c1949a380d6e087a6867b27 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 19:08:36 -0500 Subject: [PATCH 0778/1813] Update abritamr to 1.0.17 (#46102) * Update abritamr to 1.0.16 * add run_exports * Update abritamr to 1.0.17 --------- Co-authored-by: mencian --- recipes/abritamr/meta.yaml | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/recipes/abritamr/meta.yaml b/recipes/abritamr/meta.yaml index 6fbc267b65ae6..6d55a4bd9bb53 100644 --- a/recipes/abritamr/meta.yaml +++ b/recipes/abritamr/meta.yaml @@ -1,6 +1,6 @@ {% set name = "abritamr" %} -{% set version = "1.0.14" %} -{% set sha256 = "22600b8cf37c1c4cf5dc5b81f4774907e58ba874a5de968f169101d6829fe6e3" %} +{% set version = "1.0.17" %} +{% set sha256 = "091ddb77afb2a37b4955312887d2ff32669ddc0512b38ab51896139d3c897970" %} package: name: "{{ name|lower }}" @@ -11,24 +11,27 @@ source: sha256: "{{ sha256 }}" build: - number: 1 + number: 0 noarch: python entry_points: - abritamr=abritamr.abritamr:main - script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-build-isolation --no-deps -vvv" + run_exports: + - {{ pin_subpackage('abritamr', max_pin="x") }} requirements: host: - pip - - python =>3.9 + - python >=3.9 + - libcurl + - parallel run: - - pandas =>1.4 + - python >=3.9 + - pandas - xlsxwriter - ncbi-amrfinderplus =3.10.42 - - blast - - hmmer - - libcurl - - parallel + - blast + - hmmer test: imports: @@ -44,9 +47,11 @@ about: license: GPL-3.0-only license_family: GPL3 summary: "Running AMRFinderPlus for MDU" - dev_url: https://github.com/MDU-PHL/abritamr + dev_url: https://github.com/MDU-PHL/abritamr extra: recipe-maintainers: - kristyhoran - andergs + identifiers: + - biotools:abritamr From 5c34d556325fb2ea84a97e65ac975875fd1a45f8 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 5 Mar 2024 18:52:57 -0700 Subject: [PATCH 0779/1813] build fastq-scan for linux-aarch64 (#46168) * build fastq-scan for linux-aarch64 * add empty line at end * Bump build number * improve consistency --- recipes/fastq-scan/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/fastq-scan/meta.yaml b/recipes/fastq-scan/meta.yaml index ecec567b57cf1..5a1e652f87b45 100644 --- a/recipes/fastq-scan/meta.yaml +++ b/recipes/fastq-scan/meta.yaml @@ -11,7 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: build: @@ -30,3 +32,7 @@ about: license: MIT license_file: LICENSE summary: FASTQ summary statistics in JSON format + +extra: + additional-platforms: + - linux-aarch64 From 08e1553e0a46375be68ed7d2b3b9c171502a9083 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Wed, 6 Mar 2024 04:13:54 +0100 Subject: [PATCH 0780/1813] Update MS2PIP to 4.0.0.dev8 (#46195) * Bump ms2pip dev version * add necessary dependency pyopenms --- recipes/ms2pip/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/ms2pip/meta.yaml b/recipes/ms2pip/meta.yaml index 975bda9d85d11..910e321977e0d 100644 --- a/recipes/ms2pip/meta.yaml +++ b/recipes/ms2pip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.0.0.dev4" %} +{% set version = "4.0.0.dev8" %} {% set name = "ms2pip" %} -{% set sha256 = "3342bca48d5163a2fc833065ef1fc43bd349eb3ea32239fb8b74bc759b98ea3d" %} +{% set sha256 = "2a464e00135c875c12c98f6853a4487e193a0730b5bd94f82a44e8d5fb21a7bb" %} package: name: "ms2pip" @@ -49,6 +49,7 @@ requirements: - psm-utils - werkzeug >=2 - pyarrow + - pyopenms test: imports: From cbd85f7c46f7902c4482840036be0eb2b0e38b31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 22:43:10 -0500 Subject: [PATCH 0781/1813] Update pyhmmer to 0.10.8 (#46197) --- recipes/pyhmmer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index bd6805e585491..444948bed41dd 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.7" %} +{% set version = "0.10.8" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 5f738644c413bba5df69aaf6eee8c847bacd34fd58dd69e9ca63cfaa326c19a9 + sha256: b9360a2a97705bbcf4bdf5797241193e0cd81aa384a5d2b2ff5be5b5135c9632 build: number: 0 From 95a83fee23bee1f833e2d10e46a678ff26d434bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Mar 2024 23:48:12 -0500 Subject: [PATCH 0782/1813] Update phold to 0.1.2 (#46200) --- recipes/phold/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phold/meta.yaml b/recipes/phold/meta.yaml index a70b903485b75..3324ee9259f6f 100644 --- a/recipes/phold/meta.yaml +++ b/recipes/phold/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phold" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 73c4045cf7eb847eb43fa91ca79f7d6319d63122b3588279a1d8ea3ec53f7218 + sha256: 4afe2f591f904ea3dd361ad0565e3d837b2d7a0e8eaa717a7208681dfc6f1c35 build: number: 0 From 89212e4e67228d739f9099ea6c5bfc5493ec9a9b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 00:15:22 -0500 Subject: [PATCH 0783/1813] Update rcorrector to 1.0.7 (#46196) * Update rcorrector to 1.0.7 * add run_exports --------- Co-authored-by: mencian --- recipes/rcorrector/build.sh | 2 +- recipes/rcorrector/meta.yaml | 13 ++++++++++--- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/recipes/rcorrector/build.sh b/recipes/rcorrector/build.sh index aca8c80b5e330..d856a68c52db5 100644 --- a/recipes/rcorrector/build.sh +++ b/recipes/rcorrector/build.sh @@ -2,7 +2,7 @@ export C_INCLUDE_PATH=$PREFIX/include export OBJC_INCLUDE_PATH=$PREFIX/include -export CPLUS_INCLUDE_PATH=$PREFIX/include +export CPLUS_INCLUDE_PATH=$PREFIX/include export LD_LIBRARY_PATH=$PATH/lib:$LD_LIBRARY_PATH export CFLAGS="-I$PREFIX/include" export CXXFLAGS="-Wall -O3 -std=c++0x -L$PREFIX/lib" diff --git a/recipes/rcorrector/meta.yaml b/recipes/rcorrector/meta.yaml index 9d532152a0e8e..5d667d2952db5 100644 --- a/recipes/rcorrector/meta.yaml +++ b/recipes/rcorrector/meta.yaml @@ -1,5 +1,5 @@ {% set name = "rcorrector" %} -{% set version = "1.0.6" %} +{% set version = "1.0.7" %} package: name: {{ name }} @@ -7,10 +7,12 @@ package: source: url: https://github.com/mourisl/Rcorrector/archive/refs/tags/v{{ version }}.tar.gz - sha256: 581a7028c68cca20ee045084adabde9f3f896485427c1b7f1c6253fb198cf38a + sha256: cc1a9e82056bdc717b7ac40729c90573caad371899f9a1c61c25b50f019fbedb build: number: 0 + run_exports: + - {{ pin_subpackage('rcorrector', max_pin="x") }} requirements: build: @@ -33,6 +35,11 @@ test: about: home: https://github.com/mourisl/Rcorrector/ license: GPL-3.0-only - license_family: GPL + license_family: GPL3 license_file: LICENSE summary: Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. Rcorrector can also be applied to other type of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. + +extra: + identifiers: + - doi:10.1186/s13742-015-0089-y + - biotools:rcorrector From 8d189101e14f7fb0fd7620141163f327b71d951a Mon Sep 17 00:00:00 2001 From: SegawaTenta <72077055+SegawaTenta@users.noreply.github.com> Date: Wed, 6 Mar 2024 14:56:07 +0900 Subject: [PATCH 0784/1813] add dosage_score (#46166) * Create setup.py * a * add v * addLIVENSE * a * version --- recipes/dosage_score/LICENSE.txt | 674 +++++++++++++++++++++++++++++++ recipes/dosage_score/meta.yaml | 46 +++ 2 files changed, 720 insertions(+) create mode 100644 recipes/dosage_score/LICENSE.txt create mode 100644 recipes/dosage_score/meta.yaml diff --git a/recipes/dosage_score/LICENSE.txt b/recipes/dosage_score/LICENSE.txt new file mode 100644 index 0000000000000..e72bfddabc15b --- /dev/null +++ b/recipes/dosage_score/LICENSE.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. \ No newline at end of file diff --git a/recipes/dosage_score/meta.yaml b/recipes/dosage_score/meta.yaml new file mode 100644 index 0000000000000..99f5fbb7b1edc --- /dev/null +++ b/recipes/dosage_score/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "dosage_score" %} +{% set version = "1.0.0" %} +{% set sha256 = "4d5761a1b0284bba5c0291359b24e7abf9a7e729b06917c324bf846d59b4306c" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/SegawaTenta/Dosage-score/releases/download/v{{ version }}/Dosage-score-main.zip + sha256: {{ sha256 }} + +build: + script: python -m pip install --no-deps --ignore-installed . + noarch: python + number: 0 + run_exports: + - {{ pin_subpackage('dosage_score', max_pin="x") }} + +requirements: + build: + - python >=3.7 + - setuptools + - pip + run: + - python >=3.7 + - pandas =1.5.0 + - samtools >=1.16 + - matplotlib-base + - numpy + +test: + commands: + - dosage_score -h + - dosage_score_plot -h + +about: + home: https://github.com/SegawaTenta/Dosage-score + summary: 'Dosage-score: pipline to estimate dosage of each genomic region' + license: 'GPL-3.0-or-later' + license_family: GPL + license_file: LICENSE.txt + +extra: + identifiers: + - biotools:dosage_score From 6fedcddba8c6dd616554b96ddbd4ca441da64930 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 03:31:46 -0500 Subject: [PATCH 0785/1813] Update jbrowse2 to 2.10.3 (#46201) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 49ca9eeb5caee..46d52e91923e0 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.10.2" %} +{% set version = "2.10.3" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 06e6054086ae0a1aa3bcd55ed6fe475fc23b5960a9907c25c0d3cadfab2c6db7 + sha256: 0257ff74f7c4dd1502158e32238dbe362098292e6825b99b0f95f96c5b3cbce4 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From 68455e17f000263ead283b40254ba74cbeb89f1c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 05:13:45 -0500 Subject: [PATCH 0786/1813] Update hmftools-sage to 3.4.2 (#46202) --- recipes/hmftools-sage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-sage/meta.yaml b/recipes/hmftools-sage/meta.yaml index 46046d1908e61..8fe36d6848773 100644 --- a/recipes/hmftools-sage/meta.yaml +++ b/recipes/hmftools-sage/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.4.1" %} -{% set sha256 = "c81c97fc40aae7b312324e8412daaf2ecf0ee42eb68784ccc642f45a3d46346c" %} +{% set version = "3.4.2" %} +{% set sha256 = "10cf12b1fb8782ad44898fb7ac1e413dc8f9eec3448ae31d03effbd4e01ccc03" %} package: name: hmftools-sage From 68e57ba1d2579bf95e23784b7ebcf98a890a1f74 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 6 Mar 2024 11:44:56 +0100 Subject: [PATCH 0787/1813] moving org for varfish-server-worker (#46206) --- recipes/varfish-server-worker/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/varfish-server-worker/meta.yaml b/recipes/varfish-server-worker/meta.yaml index c895ca635ee19..0b91a19c2abe7 100644 --- a/recipes/varfish-server-worker/meta.yaml +++ b/recipes/varfish-server-worker/meta.yaml @@ -5,13 +5,13 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("varfish-server-worker", max_pin="x.x") }} source: - url: https://github.com/bihealth/varfish-server-worker/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/varfish-org/varfish-server-worker/archive/refs/tags/v{{ version }}.tar.gz sha256: d75f79952215c8be560d864adafd305e46a3694ffe6d9116243bf88c0b1465c4 requirements: @@ -37,7 +37,7 @@ test: - varfish-server-worker --help about: - home: https://github.com/bihealth/varfish-server-worker + home: https://github.com/varfish-org/varfish-server-worker license: MIT summary: | Rust-based tool for the heavy lifting in varfish-server. From f7289be17a834b3bfb82b20d41eacbefecc80bca Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Wed, 6 Mar 2024 11:45:35 +0100 Subject: [PATCH 0788/1813] Bump ms2pip version and build (#46205) --- recipes/ms2rescore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 9f6c9fa2eabb6..dd671a696bd85 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c016f64d76cc0fc6d3ed691d1d8350d2d6e52da5e84e4fc258f4445264a4b9ad build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -33,7 +33,7 @@ requirements: - pyteomics >=4.1.0 - pyopenms - lxml >=4.5 - - ms2pip >=4.0.0-dev4 + - ms2pip >=4.0.0-dev8 - click >=7 - cascade-config >=0.4.0 - deeplc >=2.2 From 8abc0c383edd163e0b287f78e1406e53fdcf03f3 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Wed, 6 Mar 2024 23:46:24 +1300 Subject: [PATCH 0789/1813] Build pysam for linux-aarch64 (#46199) --- recipes/pysam/arm_hwcap.patch | 15 +++++++++++++++ recipes/pysam/meta.yaml | 12 +++++------- 2 files changed, 20 insertions(+), 7 deletions(-) create mode 100644 recipes/pysam/arm_hwcap.patch diff --git a/recipes/pysam/arm_hwcap.patch b/recipes/pysam/arm_hwcap.patch new file mode 100644 index 0000000000000..d7f908ab3d6b4 --- /dev/null +++ b/recipes/pysam/arm_hwcap.patch @@ -0,0 +1,15 @@ +Conda-forge's build environment on ARM uses sysroot_linux-aarch64 2.17, which +is based on glibc 2.17 so does not define HWCAP_* values on ARM. +Work around this by including the kernel header to get the desired values. + +--- a/htslib/htscodecs/htscodecs/rANS_static4x16pr.c 2023-10-10 02:54:16 ++++ b/htslib/htscodecs/htscodecs/rANS_static4x16pr.c 2024-03-06 00:01:14 +@@ -1011,6 +1011,8 @@ + + #if defined(__linux__) || defined(__FreeBSD__) + #include ++// Ensure ARM HWCAP_* values are defined even on old glibc ++#include + #elif defined(_WIN32) + #include + #endif diff --git a/recipes/pysam/meta.yaml b/recipes/pysam/meta.yaml index cb8678b99147c..ae7239552b75a 100644 --- a/recipes/pysam/meta.yaml +++ b/recipes/pysam/meta.yaml @@ -7,9 +7,11 @@ package: source: url: https://github.com/pysam-developers/pysam/archive/v{{ version }}.tar.gz sha256: 61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f + patches: + - arm_hwcap.patch build: - number: 0 + number: 1 skip: True # [py2k] binary_relocation: False # [linux] run_exports: @@ -31,12 +33,6 @@ requirements: - openssl # [not osx] run: - python - - zlib - - xz - - bzip2 - - libdeflate - - libcurl - - openssl # [not osx] about: home: https://github.com/pysam-developers/pysam @@ -44,6 +40,8 @@ about: summary: "Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix." extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:pysam - doi:10.1093/bioinformatics/btp352 From 65a343da20f1bddef989803a85dc55622fa44900 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 6 Mar 2024 12:35:52 +0100 Subject: [PATCH 0790/1813] try to build macs for more than one python version (#46214) * try to build macs for more than one python version * Update meta.yaml --- recipes/macs3/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/macs3/meta.yaml b/recipes/macs3/meta.yaml index 760b2845607d9..c84af572f5f43 100644 --- a/recipes/macs3/meta.yaml +++ b/recipes/macs3/meta.yaml @@ -11,7 +11,8 @@ source: git_rev: 34f9a81398ec2af78317cd0b128f3a1e52a68f17 build: - number: 0 + number: 1 + skip: True # [py < 310] script: python3 -m pip install . --no-deps --ignore-installed -vvv run_exports: - {{ pin_subpackage('macs3', max_pin="x.x") }} @@ -20,7 +21,7 @@ requirements: build: - {{ compiler('c') }} host: - - python >=3.9 + - python - zlib - pip - numpy >=1.25 @@ -30,7 +31,7 @@ requirements: - scikit-learn >=1.3 - cykhash >=2.0,<3.0 run: - - python >=3.9 + - python - numpy >=1.25 - scipy >=1.12 - hmmlearn 0.3 From 9a52d18d6596112ec8f72a1b45b5b7782fb9f663 Mon Sep 17 00:00:00 2001 From: Felix Wiegand Date: Wed, 6 Mar 2024 13:28:39 +0100 Subject: [PATCH 0791/1813] Update alignoth repository url (#46216) * Update alignoth repository url * Increase build number --- recipes/alignoth/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/alignoth/meta.yaml b/recipes/alignoth/meta.yaml index 20b848d111860..f999307688684 100644 --- a/recipes/alignoth/meta.yaml +++ b/recipes/alignoth/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 # TODO fails to build on osx with # Undefined symbols for architecture x86_64: "_SSLCopyALPNProtocols", referenced from: _sectransp_connect_step2 in libcurl_sys-1f07db570920ba9f.rlib(sectransp.o) skip: true #[osx] @@ -13,7 +13,7 @@ build: - {{ pin_subpackage('alignoth', max_pin="x") }} source: - url: https://github.com/koesterlab/alignoth/archive/v{{ version }}.tar.gz + url: https://github.com/alignoth/alignoth/archive/v{{ version }}.tar.gz sha256: b7df1ee950b274c8f1fdfe75b806f47b23a0a9bd8bf2db7b6b762f84a6295f91 requirements: @@ -35,7 +35,7 @@ test: - alignoth --help about: - home: https://github.com/koesterlab/alignoth + home: https://alignoth.github.io license: MIT summary: A tool for creating alignment plots from bam files From 24dfde0f8ce306377ad76ade3193e2aa7c72a6b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Salom=C3=A9=20Brunon?= <91611978+Salome-Brunon@users.noreply.github.com> Date: Wed, 6 Mar 2024 14:18:44 +0100 Subject: [PATCH 0792/1813] UPDATE: Updated ToulligQC to v2.5.2 (#46212) --- recipes/toulligqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/toulligqc/meta.yaml b/recipes/toulligqc/meta.yaml index 2cdff47f0734c..ac481b2417169 100644 --- a/recipes/toulligqc/meta.yaml +++ b/recipes/toulligqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "toulligqc" %} -{% set version = "2.5" %} +{% set version = "2.5.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8c8f5406e8f8dbfaa260ef446b08875a337ef3201dbaad6c8a4e0fa5cbf42f85 + sha256: df12bbd9383857c33a997e44913625a430579e116763c069f38af9de4701d945 build: number: 0 From e283e9e4d5f5b81f5cec60f6de07535ead46a46a Mon Sep 17 00:00:00 2001 From: M Bernt Date: Wed, 6 Mar 2024 14:19:17 +0100 Subject: [PATCH 0793/1813] bump mitos2 (#46213) to avoid broken builds for infernal 1.1.4: https://gitlab.com/Bernt/MITOS/-/issues/44 --- recipes/mitos/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index 65d99c42a65c6..04f527f772168 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b6c6e5173f37a6ff9e5c2b7ac3f45645f0db3093371a7804e3e336e203c5abe4 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " noarch: python run_exports: @@ -25,7 +25,7 @@ requirements: - python >=3 - blast >=2.9 - hmmer =3.2 - - infernal =1.1 + - infernal >=1.1.5 - viennarna - r-base - r-ggplot2 From e5cc87ba22956f08c6c1fa9c0f7fa831c370c85f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 6 Mar 2024 14:25:50 +0100 Subject: [PATCH 0794/1813] Update meta.yaml --- recipes/jbrowse2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 46d52e91923e0..506ab9d42f0f6 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -10,8 +10,8 @@ source: url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: - noarch: generic number: 0 + noarch: generic run_exports: - {{ pin_subpackage('jbrowse2', max_pin="x") }} From 22e141b6487ece57c8609d40866dc48ad6f90024 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 6 Mar 2024 15:25:26 +0100 Subject: [PATCH 0795/1813] reupload jbrowse2 (#46223) --- recipes/jbrowse2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 506ab9d42f0f6..46d52e91923e0 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -10,8 +10,8 @@ source: url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: - number: 0 noarch: generic + number: 0 run_exports: - {{ pin_subpackage('jbrowse2', max_pin="x") }} From 7220908d9627c5f743a879463e139773afefb786 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 09:27:19 -0500 Subject: [PATCH 0796/1813] Update varfish-server-worker to 0.11.0 (#46220) --- recipes/varfish-server-worker/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/varfish-server-worker/meta.yaml b/recipes/varfish-server-worker/meta.yaml index 0b91a19c2abe7..dc77bd2febe35 100644 --- a/recipes/varfish-server-worker/meta.yaml +++ b/recipes/varfish-server-worker/meta.yaml @@ -1,18 +1,18 @@ -{% set version = "0.10.2" %} +{% set version = "0.11.0" %} package: name: varfish-server-worker version: {{ version }} build: - number: 1 + number: 0 skip: True # [osx] run_exports: - {{ pin_subpackage("varfish-server-worker", max_pin="x.x") }} source: url: https://github.com/varfish-org/varfish-server-worker/archive/refs/tags/v{{ version }}.tar.gz - sha256: d75f79952215c8be560d864adafd305e46a3694ffe6d9116243bf88c0b1465c4 + sha256: 81e7c2a35115989eef9e71bd08b56837fea73ac5fe4e6b09115f687d3013915a requirements: build: From 563c3f7c42a7efc05a560433499964da674f75c1 Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Wed, 6 Mar 2024 14:51:39 +0000 Subject: [PATCH 0797/1813] Update TaxonKit to v0.16.0 (#46227) --- recipes/taxonkit/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/taxonkit/meta.yaml b/recipes/taxonkit/meta.yaml index ebb8e35f5e385..959579bd2784a 100644 --- a/recipes/taxonkit/meta.yaml +++ b/recipes/taxonkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.15.1" %} +{% set version = "0.16.0" %} package: name: taxonkit @@ -11,9 +11,9 @@ build: source: - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_amd64.tar.gz # [osx] - md5: cc61492e7642ecf6e0708fb934de7e5f # [osx] + md5: 0f36df3f255caf87004087b4f6a3c718 # [osx] - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_amd64.tar.gz # [linux] - md5: c40825316860d0a23a51fb782561eef7 # [linux] + md5: dcf41d21493a29594b399cdafce16233 # [linux] test: commands: From c508fdad2f29bed03cbfcc0b8c4a12b392ec4ece Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 10:35:03 -0500 Subject: [PATCH 0798/1813] Update alignoth to 0.12.0 (#46222) --- recipes/alignoth/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/alignoth/meta.yaml b/recipes/alignoth/meta.yaml index f999307688684..6777f87490857 100644 --- a/recipes/alignoth/meta.yaml +++ b/recipes/alignoth/meta.yaml @@ -1,11 +1,11 @@ -{% set version = "0.11.0" %} +{% set version = "0.12.0" %} package: name: alignoth version: {{ version }} build: - number: 1 + number: 0 # TODO fails to build on osx with # Undefined symbols for architecture x86_64: "_SSLCopyALPNProtocols", referenced from: _sectransp_connect_step2 in libcurl_sys-1f07db570920ba9f.rlib(sectransp.o) skip: true #[osx] @@ -14,7 +14,7 @@ build: source: url: https://github.com/alignoth/alignoth/archive/v{{ version }}.tar.gz - sha256: b7df1ee950b274c8f1fdfe75b806f47b23a0a9bd8bf2db7b6b762f84a6295f91 + sha256: e430a257f5ab440846756f53a0c618ebec86bd5d6f3627eab1fed11dd68f3b5c requirements: build: From 3a6cb1528e3138b89f90186540af39c6240652a0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 10:47:00 -0500 Subject: [PATCH 0799/1813] Update snakemake to 8.5.4 (#46228) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index e9596071c3f42..d1d081af66ccd 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.5.3" %} +{% set version = "8.5.4" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 6fc39107b395760caf3893106d67859fc70d7de2a8892ddcbcd33611a50abeb1 + sha256: cab6d0df98587ae0d3bcf3861c4ca1bb5cbdcc96809130e9a8c708e6b1601bd8 build: number: 0 From a6da407c0f6780c7c0d61ac622af584e51e99d12 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 11:05:50 -0500 Subject: [PATCH 0800/1813] Update bionumpy to 1.0.7 (#46209) * Update bionumpy to 1.0.5 * Update bionumpy to 1.0.6 * Update bionumpy to 1.0.7 --- recipes/bionumpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index eb79aa91be613..0c0430aca8b82 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.4" %} +{% set version = "1.0.7" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 88d84fd1f18c4406c79bc492963267e837673d961af2dfceb45f65ef27430823 + sha256: 002829bb37d279845546ea953b4d2b206e0dbb956fe981ce8e6ad8647b5b8389 build: noarch: python From cbcc7561f1e64f04479c07f1f5079340ec1a8f20 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 12:31:13 -0500 Subject: [PATCH 0801/1813] Update miniprot to 0.13 (#46229) * Update miniprot to 0.13 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/miniprot/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/miniprot/meta.yaml b/recipes/miniprot/meta.yaml index f8142a26a402f..d3ee72d13b2c3 100644 --- a/recipes/miniprot/meta.yaml +++ b/recipes/miniprot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.12" %} +{% set version = "0.13" %} {% set name = "miniprot" %} -{% set sha256 = "869df52d8a3d350e0a5ba6eb0d1685e78bb7087ace9870d196f5fb4761c3a692" %} +{% set sha256 = "be12d98d998beb78e4e06350c03d2f188bcdf3245d6bcaf43e2cc80785a617a4" %} package: name: "{{ name }}" @@ -8,6 +8,8 @@ package: build: number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} source: url: "https://github.com/lh3/miniprot/archive/refs/tags/v{{ version }}.tar.gz" From f044695927424985e00e88e5f7c652610e31c1fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 12:50:24 -0500 Subject: [PATCH 0802/1813] Update phylophlan to 3.1.1 (#46231) --- recipes/phylophlan/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phylophlan/meta.yaml b/recipes/phylophlan/meta.yaml index 30b9723246e4e..87c643c292cb0 100644 --- a/recipes/phylophlan/meta.yaml +++ b/recipes/phylophlan/meta.yaml @@ -1,6 +1,6 @@ {% set name = "phylophlan" %} -{% set version = "3.1" %} -{% set sha256 = "9428a8fceb2626325fb6b93cc47143b100183c314f50eb96b32467e42a5bc4ad" %} +{% set version = "3.1.1" %} +{% set sha256 = "67df67b60b5a361ee9354db031608213d3ecfa2f9ec78104cb3e81903a8cc07a" %} package: name: "{{ name|lower }}" From c291b9925cb05b69c1a7a23c1203f90574bd766c Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 6 Mar 2024 13:55:24 -0600 Subject: [PATCH 0803/1813] pybigtools update (#46230) --- recipes/pybigtools/build.sh | 2 +- recipes/pybigtools/meta.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybigtools/build.sh b/recipes/pybigtools/build.sh index c42f164e8f033..00b4644361544 100644 --- a/recipes/pybigtools/build.sh +++ b/recipes/pybigtools/build.sh @@ -20,4 +20,4 @@ RUST_BACKTRACE=1 maturin build -b pyo3 --interpreter "${PYTHON}" --release --strip # Install *.whl files using pip -${PYTHON} -m pip install . --no-deps --no-build-isolation -vvv +${PYTHON} -m pip install pybigtools/target/wheels/*.whl --no-deps --no-build-isolation -vvv diff --git a/recipes/pybigtools/meta.yaml b/recipes/pybigtools/meta.yaml index 0660d73d9a205..fbc14f532001a 100644 --- a/recipes/pybigtools/meta.yaml +++ b/recipes/pybigtools/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('pybigtools', max_pin="x.x") }} From 1db8287bba2440e4a788c1c9d421591c9386644f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 14:55:55 -0500 Subject: [PATCH 0804/1813] Update npstructures to 0.2.17 (#46210) --- recipes/npstructures/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/npstructures/meta.yaml b/recipes/npstructures/meta.yaml index 41873871a5cd0..b82ae84aed78b 100644 --- a/recipes/npstructures/meta.yaml +++ b/recipes/npstructures/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.16" %} +{% set version = "0.2.17" %} {% set name = "npstructures" %} package: name: {{ name }} @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 0964520dfb11789635ceae36c9ab477e60cd4fbc99f069656fafbdcb3878a0be + sha256: 403ef65ebafb4a0b34d9571350cdbcf72f3f64a56d3d3e43df421a5f919bef7d build: From 8bbd164800ee8108fa19521d6c6aa02bfb7d48f7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 14:57:05 -0500 Subject: [PATCH 0805/1813] Update pybiolib to 1.1.1846 (#46208) * Update pybiolib to 1.1.1836 * Update pybiolib to 1.1.1846 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 52ee51c6059ce..aa11fdf5ec316 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1834" %} +{% set version = "1.1.1846" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 9bd04ef7fccae01e8d7d6b49c833fcf5d631e2649889882d10ce52656c62c7e0 + sha256: 4023ad085f38531825bf507f9f56fc2ab83236cfcdcaf7ab0802f4f2e375a681 build: noarch: python From b03a5610f6df56c1d9fb9eb51a093cc584cbfbf0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 15:05:02 -0500 Subject: [PATCH 0806/1813] Update tsebra to 1.1.2.4 (#46219) --- recipes/tsebra/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tsebra/meta.yaml b/recipes/tsebra/meta.yaml index 025b3cec0dc83..8b4d1ed9618af 100644 --- a/recipes/tsebra/meta.yaml +++ b/recipes/tsebra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.2.3" %} +{% set version = "1.1.2.4" %} {% set name = "tsebra" %} -{% set sha256 = "bdba8f114a75bd822e7af475f09bc433d1b673902ec09e1ed1f735d21ea80222" %} +{% set sha256 = "b5170dcca85af666d7d158611bee2d8336e57e29fa27d5289ded34b8084bef62" %} package: name: "{{ name }}" From e673d0d8d3ae4f0fec0487e8fd5e09834b2537ca Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 15:07:18 -0500 Subject: [PATCH 0807/1813] Update mehari to 0.25.2 (#46221) * Update mehari to 0.25.1 * Update mehari to 0.25.2 --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 3440fe3cce4b5..ee58ace42a42c 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.25.0" %} -{% set sha256 = "62552913c0a338563e6011a40742f6aba682d6f2842e2af35ea40c3c817d5c5f" %} +{% set version = "0.25.2" %} +{% set sha256 = "9f007e7f564e8428d66d082bfd08eef4a48cafcb2671865152866d9b0c6597a4" %} package: name: mehari From 30713371c631c6e2b8e9557df75ebc0314ef95e4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 15:08:36 -0500 Subject: [PATCH 0808/1813] Update tissuumaps to 3.2.1.1 (#46218) * Update tissuumaps to 3.2.1 * Update tissuumaps to 3.2.1.1 --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index 50e6992dce10d..92de96039697b 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.0.5" %} +{% set version = "3.2.1.1" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 2d0cefff0aa54a8f9bb040cf5537a77c5fec2a40954b8c1b2b2af8a07bb181d9 + sha256: 2367069c3855165f3757079f9b248385003ef8fe7ab2ccf2738493475c11ff76 build: number: 0 From 033e1e30c7e7e3138529e0d789665c53ea19362c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 15:08:52 -0500 Subject: [PATCH 0809/1813] Update bionumpy to 1.0.8 (#46233) --- recipes/bionumpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index 0c0430aca8b82..48b19940c064e 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.7" %} +{% set version = "1.0.8" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 002829bb37d279845546ea953b4d2b206e0dbb956fe981ce8e6ad8647b5b8389 + sha256: 25fcef9da2f95ee2b6152e51cfc0f802c23b2a7dbbba9aeb669f23226d419df7 build: noarch: python From fc23b39ba43643f35bdc781ef943b2b4db335e06 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 15:11:25 -0500 Subject: [PATCH 0810/1813] Update snakemake-storage-plugin-azure to 0.1.5 (#46232) --- recipes/snakemake-storage-plugin-azure/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-storage-plugin-azure/meta.yaml b/recipes/snakemake-storage-plugin-azure/meta.yaml index 0bea4ce30457f..a02ed329f2e5a 100644 --- a/recipes/snakemake-storage-plugin-azure/meta.yaml +++ b/recipes/snakemake-storage-plugin-azure/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-azure" %} -{% set version = "0.1.4" %} +{% set version = "0.1.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_azure-{{ version }}.tar.gz - sha256: dcfcf285c9f1b1aa89db359afbf02b28d9e57a97ddac66747d3e46832e7ddbff + sha256: c200d5ffc1d593083028014becba83ace43749a666f394e567435b7299566568 build: noarch: python From c7e1f5d5326da546c6563762222adfa9df65308b Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Wed, 6 Mar 2024 12:30:37 -0800 Subject: [PATCH 0811/1813] Update nextclade to 3.3.1 (#46234) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index 11b326dcfadd5..67961e351154d 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.3.0" %} +{% set version = "3.3.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 6d2566a510152378e7624104225c29cd765c0f2b8bb8c12bb2d6a161857f05bf # [linux64] + sha256: 9eecdb2e56362d24cfedb510b236f2054c3d02264f3ca7e8c586fe234d25e2f2 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: 330ad12cd1bb20429f49fd00bcd773c453b66662842913ec35bc9e288ab3db2a # [osx and x86_64] + sha256: d8e1604be6a32f34086616ebdf532ec1409d500b5fe72c239b6db2614d75e722 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: 1732681a651de65424f16b8fe5a2582183a4ab0098713e6aa39d63bd760009d3 # [arm64] + sha256: b95e2ed966b08dbd481fe48d7aa1019a748d29ef330daad4773d1c98e6b007ba # [arm64] build: number: 0 From 8ec500b0c9b4ccc9b08eee96e3e587a79c1741be Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren Date: Wed, 6 Mar 2024 15:31:43 -0500 Subject: [PATCH 0812/1813] new: gxf2chrom recipe (#46136) --- recipes/gxf2chrom/build.sh | 9 +++++++++ recipes/gxf2chrom/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/gxf2chrom/build.sh create mode 100644 recipes/gxf2chrom/meta.yaml diff --git a/recipes/gxf2chrom/build.sh b/recipes/gxf2chrom/build.sh new file mode 100644 index 0000000000000..8e10cdc3e3237 --- /dev/null +++ b/recipes/gxf2chrom/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/gxf2chrom/meta.yaml b/recipes/gxf2chrom/meta.yaml new file mode 100644 index 0000000000000..d3925fc4bf0dd --- /dev/null +++ b/recipes/gxf2chrom/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "gxf2chrom" %} +{% set version = "0.1.0" %} + +package: + name: gxf2chrom + version: {{ version }} + +source: + url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 453df8aaff017f2ddb0c977de2e5f494feba8fa17d8f8fcddc908642ecb5fb08 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('gxf2chrom', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.39 + - pkg-config + +test: + commands: + - gxf2chrom --help + - gxf2chrom --version + +about: + home: https://github.com/alejandrogzi/gxf2chrom + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Everything in .chrom from GTF/GFF" + +extra: + recipe-maintainers: + - alejandrogzi From c559f63fc751fea66789575cdc2eaa214c579790 Mon Sep 17 00:00:00 2001 From: Etienne Boileau <32674263+eboileau@users.noreply.github.com> Date: Wed, 6 Mar 2024 21:32:40 +0100 Subject: [PATCH 0813/1813] Add ribotools (#46215) * ADD ribotools recipe * UPD revert changes pbiotools --- recipes/ribotools/meta.yaml | 73 +++++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 recipes/ribotools/meta.yaml diff --git a/recipes/ribotools/meta.yaml b/recipes/ribotools/meta.yaml new file mode 100644 index 0000000000000..c1f71e3bceeb1 --- /dev/null +++ b/recipes/ribotools/meta.yaml @@ -0,0 +1,73 @@ +{% set name = "ribotools" %} +{% set version = "1.0.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ribotools-{{ version }}.tar.gz + sha256: b40767cc80894566708025d5223c2c0dff475ef7d9a4332dc852b4c04388fea4 + +build: + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv" + noarch: python + number: 0 + entry_points: + - get-all-bam-periodic = ribotools.pgrms.get_all_bam_periodic:main + - get-gtf-from-predictions = ribotools.pgrms.get_gtf_from_predictions:main + - run-htseq-workflow = ribotools.htseq_wf.run_htseq_workflow:main + - alignment-workflow = ribotools.htseq_wf.alignment_workflow:main + - get-ribo-periodic = ribotools.htseq_wf.get_ribo_periodic:main + - keep-ribo-periodic = ribotools.htseq_wf.keep_ribo_periodic:main + - call-htseq-count = ribotools.htseq_wf.call_htseq_count:main + - get-sample-table = ribotools.scripts.__main__:get_sample_table + - run-tea = ribotools.scripts.__main__:run_tea + - run-dea = ribotools.scripts.__main__:run_dea + run_exports: + - {{ pin_subpackage('ribotools', max_pin='x') }} + +requirements: + host: + - python >=3.7,<3.11 + - pip + run: + - python >=3.7,<3.11 + - rpbp >=3.0.1 + - htseq >=2.0.2 + - r-base >=4.2.3 + - r-r.utils + - r-devtools + - r-tidyverse + - r-openxlsx + - r-yaml + - r-ashr + - bioconductor-ihw + - bioconductor-apeglm + - bioconductor-deseq2 + +test: + imports: + - ribotools + - ribotools.utils + - ribotools.htseq_wf + - ribotools.pgrms + commands: + - get-all-bam-periodic --help + - get-gtf-from-predictions --help + - run-htseq-workflow --help + - alignment-workflow --help + - get-ribo-periodic --help + - keep-ribo-periodic --help + - call-htseq-count --help + +about: + home: https://github.com/eboileau/ribotools + summary: Ribo-seq analysis tools associated with the Rp-Bp package and more + doc_url: https://ribotools.readthedocs.io/en/latest/ + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - eboileau From 642604cbc91fb0fba625298c41ec50790d7b2f6d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 15:48:30 -0500 Subject: [PATCH 0814/1813] Update clipkit to 2.2.4 (#46235) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index 7c62e3cce5c85..bbde91a49bb3d 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.2.2" %} +{% set version = "2.2.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 76e13db515a951490e9ed6a86955c6207fae3292fb62b6d8adef7ac4a235077a + sha256: 86f33e78f2aa18be093056c92cf69b9853e65022593280876900f1eaaf70daa2 build: number: 0 From 0ccffa06415fd0b6c090495f91a015f00039072d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Mar 2024 16:11:39 -0500 Subject: [PATCH 0815/1813] Update learnmsa to 2.0.1 (#46204) * Update learnmsa to 2.0.0 * Update learnmsa to 2.0.1 * add missing deps --------- Co-authored-by: mencian --- recipes/learnmsa/meta.yaml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/recipes/learnmsa/meta.yaml b/recipes/learnmsa/meta.yaml index 2ddcc263cfca5..393e43a11f17d 100644 --- a/recipes/learnmsa/meta.yaml +++ b/recipes/learnmsa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "learnMSA" %} -{% set version = "1.3.4" %} +{% set version = "2.0.1" %} package: name: "{{ name|lower }}" @@ -7,13 +7,13 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b942cc9f2c6835f8a067ad647e542fe1f2b12517a4b1b81ac70e120b0385637d + sha256: 1f1322d33a83358b989cf26569865cd89235abfecce743aab62c8b8fe3681a51 build: number: 0 entry_points: - learnMSA = learnMSA.run:run_main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python run_exports: - {{ pin_subpackage('learnmsa', max_pin="x") }} @@ -28,9 +28,12 @@ requirements: - seaborn - python >=3.9 - tensorflow >=2.7.0,<2.11 + - tensorflow-probability <=0.18.0 - biopython >=1.69 - pyfamsa - transformers + - imageio + - sentencepiece test: imports: @@ -52,3 +55,6 @@ about: extra: recipe-maintainers: - felbecker + identifiers: + - doi:10.1093/gigascience/giac104 + - biotools:learnMSA From 9e1dd8ac5628bb71365746b033043f2969d911c7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Mar 2024 07:14:05 -0500 Subject: [PATCH 0816/1813] Update semibin to 2.1.0 (#46239) * Update semibin to 2.1.0 * SemiBin: update entry_points Remove fraggenescan as dependency: it's an optional alternative and deprecated upstream. --------- Co-authored-by: Luis Pedro Coelho --- recipes/semibin/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/semibin/meta.yaml b/recipes/semibin/meta.yaml index bdc98bc800525..3904aca49cebb 100644 --- a/recipes/semibin/meta.yaml +++ b/recipes/semibin/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SemiBin" %} -{% set version = "2.0.2" %} +{% set version = "2.1.0" %} package: name: "{{ name|lower }}" @@ -7,13 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b428a68fa9a16e6c713001f8f5afb0b19ae1997a10b66c54076a72d75b1ad8d8 + sha256: 5345982bbc38e283043867d361ca8db727fec34a4c40b3a70e01914154d39bd5 build: noarch: python number: 0 entry_points: - - SemiBin=SemiBin.main:main1 + - SemiBin=SemiBin.main:main_no_version + - SemiBin1=SemiBin.main:main1 - SemiBin2=SemiBin.main:main2 script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv run_exports: @@ -37,7 +38,6 @@ requirements: - mmseqs2 13.45111 - bedtools - hmmer - - fraggenescan - numexpr - prodigal - samtools From fcb3b862975d6d506662c595e9fba1ea239dcaef Mon Sep 17 00:00:00 2001 From: wjunLu <135617475+wjunLu@users.noreply.github.com> Date: Thu, 7 Mar 2024 22:38:33 +0800 Subject: [PATCH 0817/1813] linux-aarch64 build for dart (#46242) * linux-aarch64 build for dart * modify code * correct 'name' * add aarch64 building branch --- recipes/dart/build.sh | 7 ++++++- recipes/dart/meta.yaml | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/recipes/dart/build.sh b/recipes/dart/build.sh index ab1901877606f..641bf8a605d82 100755 --- a/recipes/dart/build.sh +++ b/recipes/dart/build.sh @@ -1,6 +1,11 @@ #!/bin/bash mkdir -p ${PREFIX}/bin +ARCH_BUILD="-m64 -msse4.1" +case $(uname -m) in + arm64|aarch64) ARCH_BUILD="" ;; +esac + #index pushd src/BWT_Index make CC=$CC FLAGS="$CFLAGS" LIBS="$LDFLAGS -lm -lz" @@ -14,6 +19,6 @@ popd #dart pushd src -make CXX=$CXX FLAGS="$CXXFLAGS -Wall -D NDEBUG -O3 -m64 -msse4.1 -fPIC" LIB="$LDFLAGS -lz -lm -lbz2 -llzma -lpthread" +make CXX=$CXX FLAGS="$CXXFLAGS -Wall -D NDEBUG -O3 $ARCH_BUILD -fPIC" LIB="$LDFLAGS -lz -lm -lbz2 -llzma -lpthread" cp dart $PREFIX/bin diff --git a/recipes/dart/meta.yaml b/recipes/dart/meta.yaml index f444a029c9ea5..a6f2aa00531a7 100644 --- a/recipes/dart/meta.yaml +++ b/recipes/dart/meta.yaml @@ -9,7 +9,9 @@ source: sha256: '847d5e0a7e10162583fcf7168d31924d38290b5364e08c4a9cdd6653da73c64f' build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("dart", max_pin='x.x') }} requirements: build: @@ -42,3 +44,6 @@ about: extra: identifiers: - doi:10.1093/bioinformatics/btx558 + + additional-platforms: + - linux-aarch64 From 261c54e71b484810d46e9f9e80071e8f196a3a82 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Mar 2024 10:58:41 -0500 Subject: [PATCH 0818/1813] Update mehari to 0.25.3 (#46247) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index ee58ace42a42c..5610cbb39c241 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.25.2" %} -{% set sha256 = "9f007e7f564e8428d66d082bfd08eef4a48cafcb2671865152866d9b0c6597a4" %} +{% set version = "0.25.3" %} +{% set sha256 = "ec4a5f1fa2135c38207def42e7391414d77ce457be96f3cbdddb5287bdf447c5" %} package: name: mehari From 2feda94ccd690598bb265b96e1350710f40a6305 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Mar 2024 15:02:45 -0500 Subject: [PATCH 0819/1813] Update oakvar to 2.9.91 (#46248) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index a653eae0f46a1..15fd58b64bed5 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.90" %} -{% set sha256 = "5f9a118f57f3bf4477a59d0c3fc2b1c9fdb3aa5a273ba8e7fda463be39da65d4" %} +{% set version = "2.9.91" %} +{% set sha256 = "74a98819e230dc2120752b5f81e194e38d7de46c48e2cd051a4feb62b5fa51da" %} package: name: {{ name|lower }} From e4832a6ef506c5be3dace0bbfbf72167606a04f8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Mar 2024 15:04:18 -0500 Subject: [PATCH 0820/1813] Update snakemake-storage-plugin-irods to 0.1.2 (#46246) --- recipes/snakemake-storage-plugin-irods/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-storage-plugin-irods/meta.yaml b/recipes/snakemake-storage-plugin-irods/meta.yaml index 143d7d1b12075..698ed88bc3071 100644 --- a/recipes/snakemake-storage-plugin-irods/meta.yaml +++ b/recipes/snakemake-storage-plugin-irods/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-irods" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_irods-{{ version }}.tar.gz - sha256: af823c0d18a4e3807d05e9bcfe5687c7ce6c711224fc37259fd74558917ec71d + sha256: e5ceac168095bf7a2ef2d82d9d74ddfc6780c1665ecaa75b16041fc2428ead77 build: noarch: python From 7461e68c8f1312077522bd28c54bc847fbf0f6bb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Mar 2024 15:04:25 -0500 Subject: [PATCH 0821/1813] Update snakemake-interface-storage-plugins to 3.1.1 (#46244) --- recipes/snakemake-interface-storage-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-storage-plugins/meta.yaml b/recipes/snakemake-interface-storage-plugins/meta.yaml index 8ca9b30fbc900..9efb00584f492 100644 --- a/recipes/snakemake-interface-storage-plugins/meta.yaml +++ b/recipes/snakemake-interface-storage-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-storage-plugins" %} -{% set version = "3.1.0" %} +{% set version = "3.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_storage_plugins-{{ version }}.tar.gz - sha256: 26e95be235ef2a9716b890ea96c3a9a2e62061c5d72fbb89c2fad2afada87304 + sha256: d4d2b72ac964f12c5ba343639499c797316d6368dda471fba63610aec8e77cbb build: noarch: python From 1568c5ece77133935d1f84b8e6286cf14d144472 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Mar 2024 15:05:09 -0500 Subject: [PATCH 0822/1813] Update phykit to 1.16.0 (#46240) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index df44afb0cd1f8..d23e0a568312f 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 796a849e9a3dff3c93a7d6e0f3d8145a549340bdc9db7b616190c16e9b7e4f08 + sha256: 7f89a7680d012d756a20f26d395c90ad0b7bd084ee05911da955241611e94656 build: noarch: python From bcdebe214c00217ccf2e6e6ea1431a8947091675 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Mar 2024 15:06:33 -0500 Subject: [PATCH 0823/1813] Update vcfsim to 1.0.10.alpha (#46241) --- recipes/vcfsim/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vcfsim/meta.yaml b/recipes/vcfsim/meta.yaml index 5883749ef127a..39949b080fbfe 100644 --- a/recipes/vcfsim/meta.yaml +++ b/recipes/vcfsim/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcfsim" %} -{% set version = "1.0.9.alpha" %} +{% set version = "1.0.10.alpha" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Pie115/VCFSimulator-SamukLab/archive/{{ version }}.tar.gz - sha256: 364eb81f21b5071450b553649c5be1e2c273a63bb04e9a6e4af2e1455bb8c48e + sha256: 94125b463150246b9b1109a0d989b5a3e2f8c6fd4f33d9ab203106e242c6a345 build: noarch: python From 24ea5d1b1fccb3c150f55b24e3482ca366e553cb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Mar 2024 15:56:16 -0500 Subject: [PATCH 0824/1813] Update mg-toolkit to 0.10.4 (#46245) * Update mg-toolkit to 0.10.4 * add run_exports --------- Co-authored-by: mencian --- recipes/mg-toolkit/meta.yaml | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/recipes/mg-toolkit/meta.yaml b/recipes/mg-toolkit/meta.yaml index 52488ee71a435..f0536f69afb05 100644 --- a/recipes/mg-toolkit/meta.yaml +++ b/recipes/mg-toolkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mg-toolkit" %} -{% set version = "0.10.1" %} +{% set version = "0.10.4" %} package: name: "{{ name|lower }}" @@ -7,26 +7,29 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "19550a3ba8033639822c6f878b799fe6394abc216564012285f84f0a6c19086a" + sha256: "087042ccaac9601fecfdc2e121330b650426ec373ce5353fc32cd5337ef823a9" build: number: 0 entry_points: - mg-toolkit=mg_toolkit.__main__:main noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('mg-toolkit', max_pin="x.x") }} requirements: host: - - python >=3.5 + - python >=3.8 - pip - pytest-runner run: - jsonapi-client >=0.9.9 - - pandas >=0.25.3 - - python >=3.5 - - requests >=2.24.0 + - pandas ==2.0.3 + - python >=3.8 + - requests >=2.31.0 - tqdm >=4.49.0 + - urllib3 >=2.2.1 test: imports: @@ -35,8 +38,13 @@ test: - mg-toolkit --help about: - home: "https://github.com/EBI-metagenomics/emg-toolkit" + home: "https://www.ebi.ac.uk/metagenomics" license: Apache-2.0 license_file: LICENSE license_family: "APACHE" summary: "Metagenomics toolkit." + dev_url: "https://github.com/EBI-metagenomics/emg-toolkit" + +extra: + identifiers: + - biotools:MGnify From f354ec36a1e9741f1a670754d0bc7a802eec6df8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Mar 2024 15:56:51 -0500 Subject: [PATCH 0825/1813] Update viral_consensus to 0.0.5 (#46203) * Update viral_consensus to 0.0.5 * add zlib --------- Co-authored-by: mencian --- recipes/viral_consensus/build.sh | 3 ++- recipes/viral_consensus/meta.yaml | 15 ++++++++++----- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/recipes/viral_consensus/build.sh b/recipes/viral_consensus/build.sh index 94b3d4db60cbe..6637bb02284e0 100644 --- a/recipes/viral_consensus/build.sh +++ b/recipes/viral_consensus/build.sh @@ -1,4 +1,5 @@ #!/bin/bash -make CXX="$CXX" INCLUDE= RELEASEFLAGS="$CPPFLAGS $CXXFLAGS -O3 $LDFLAGS" + +make CXX="$CXX" INCLUDE="-I${PREFIX}/include -Ihtslib" RELEASEFLAGS="$CPPFLAGS $CXXFLAGS -O3 $LDFLAGS" mkdir -p $PREFIX/bin cp viral_consensus $PREFIX/bin/ diff --git a/recipes/viral_consensus/meta.yaml b/recipes/viral_consensus/meta.yaml index 48b6ef887fdee..a326221063cdd 100644 --- a/recipes/viral_consensus/meta.yaml +++ b/recipes/viral_consensus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.0.4" %} +{% set version = "0.0.5" %} package: name: viral_consensus @@ -11,7 +11,7 @@ build: source: url: https://github.com/niemasd/ViralConsensus/archive/refs/tags/{{ version }}.tar.gz - sha256: c1d81a69ff4435f65d1aaac0dc90e3065393a3d11a508629c3fd6aadb63166e7 + sha256: 798fa4d751b3b6b3cde9b6be1b2c55d469c71cd0d030b982980387e9a14011a9 requirements: build: @@ -20,14 +20,19 @@ requirements: - make host: - htslib - run: + - zlib about: - home: https://github.com/niemasd/ViralConsensus - license: GNU General Public License v3 (GPLv3) + home: https://niema.net/ViralConsensus/ + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Fast viral consensus genome reconstruction + dev_url: https://github.com/niemasd/ViralConsensus test: commands: - viral_consensus --version + identifiers: + - doi:10.1093/bioinformatics/btad317 + - doi:10.1093/bioinformatics/btae018 From 15439e4425d22378e0f40e9598e178711b2bed46 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Mar 2024 16:05:19 -0500 Subject: [PATCH 0826/1813] Update ppanggolin to 2.0.4 (#46251) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ppanggolin/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ppanggolin/meta.yaml b/recipes/ppanggolin/meta.yaml index 85280b93ba3e0..b1b30becbd7d7 100644 --- a/recipes/ppanggolin/meta.yaml +++ b/recipes/ppanggolin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.3" %} +{% set version = "2.0.4" %} package: name: ppanggolin @@ -6,7 +6,7 @@ package: source: url: https://github.com/labgem/PPanGGOLiN/archive/{{ version }}.tar.gz - sha256: 0cd44aa30868387fb3617c52658674e57d9bd73efab636e7d8690f5d1a144c5f + sha256: 7ad714d4ab7a81e3a51119aa9ba04d86455eabad175c1da751b0a27501ac76a9 build: number: 0 From cab2797977940c95672090cc30e3212eb99f0885 Mon Sep 17 00:00:00 2001 From: Jose Figueroa Date: Thu, 7 Mar 2024 16:07:45 -0500 Subject: [PATCH 0827/1813] Update MetaCerberus (#46249) --- recipes/metacerberus/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/metacerberus/meta.yaml b/recipes/metacerberus/meta.yaml index 670a203a2f29b..8fac178cb00f0 100644 --- a/recipes/metacerberus/meta.yaml +++ b/recipes/metacerberus/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1140732198b95c0d670fccb213c84464eb80bbe27127e4a85560de30c4873ac6 build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . -vv" run_exports: @@ -29,6 +29,9 @@ requirements: - porechop - bbmap - prodigal + - prodigal-gv + - trnascan-se + - phanotate - hmmer - ray-default - ray-core From ddaf2105e1a3dddc06eccb2b73f222691c815090 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 05:59:09 -0500 Subject: [PATCH 0828/1813] Update agat to 1.3.1 (#46261) --- recipes/agat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/agat/meta.yaml b/recipes/agat/meta.yaml index bae51d9129cd0..15d356d0d9d71 100755 --- a/recipes/agat/meta.yaml +++ b/recipes/agat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "AGAT" %} -{% set version = "1.3.0" %} -{% set sha256 = "4898f83fa214b07f7946c2a8592c11efcbda0db4137a577d2b95206c253981a3" %} +{% set version = "1.3.1" %} +{% set sha256 = "0361f5f5708b0010045a410e3656d6b16571d5ebaf72898f6df846c49f282a3c" %} package: name: "{{ name|lower }}" From 05b4c37dbebecb09ebb19f481cab4d96f6ad4f25 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 06:15:35 -0500 Subject: [PATCH 0829/1813] Update bakta to 1.9.3 (#46260) --- recipes/bakta/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml index cddd0f93850a0..2f9fe0bceefe4 100644 --- a/recipes/bakta/meta.yaml +++ b/recipes/bakta/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.9.2" %} +{% set version = "1.9.3" %} package: name: bakta @@ -6,11 +6,11 @@ package: source: url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz - sha256: '145b0209fe6a0c67a1a1a6e5c108e99bad0a86e3b1db0a9d24261744725fe257' + sha256: '774a60b4fa2032ac4804a37eafdb4c2c67f2573d7f93e785b58963a47d535e70' build: noarch: python - number: 1 + number: 0 script: python -m pip install --no-deps --ignore-installed . entry_points: - bakta = bakta.main:main From bf743831099b68957d758c4577804b493194a4f2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 09:16:33 -0500 Subject: [PATCH 0830/1813] Update resfinder to 4.4.3 (#46263) --- recipes/resfinder/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/resfinder/meta.yaml b/recipes/resfinder/meta.yaml index 4f4e2bcf04abe..d05f4a9a1a066 100644 --- a/recipes/resfinder/meta.yaml +++ b/recipes/resfinder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "resfinder" %} -{% set version = "4.4.2" %} +{% set version = "4.4.3" %} package: name: {{ name|lower }} @@ -7,12 +7,12 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/resfinder-{{ version }}.tar.gz - sha256: 9660e58c3b3f63cf08335c0058f7ef3c56320be852009b714e773c71e8ea2659 + sha256: 8db4f9a41fd55e3f69836094fd8c101751c7a984ed2d8f4c124d756b43f26ee3 patches: - python_path.patch build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage('resfinder', max_pin="x") }} From cc11bf515f270bfee6e20ef08226885ea2958e71 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 10:36:27 -0500 Subject: [PATCH 0831/1813] Update cellsnake to 0.2.0.12 (#45859) * Update cellsnake to 0.2.0.12 * Update meta.yaml (#46217) * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Sinan U. Umu --- recipes/cellsnake/meta.yaml | 37 +++++++++++++------------------------ 1 file changed, 13 insertions(+), 24 deletions(-) diff --git a/recipes/cellsnake/meta.yaml b/recipes/cellsnake/meta.yaml index ceafb17b3f864..012b4037e3037 100644 --- a/recipes/cellsnake/meta.yaml +++ b/recipes/cellsnake/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cellsnake" %} -{% set version = "0.2.0.11" %} +{% set version = "0.2.0.12" %} package: @@ -8,21 +8,22 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cellsnake-{{ version }}.tar.gz - sha256: ceb1779bf0401db27fcfe3b7479d0f8fcd0024d2121e826cc1ca84fa333cfe5f + sha256: d8b812c5063a34cf07da900881517b1946c66f2ad2a89092168edaff5693cb7d build: noarch: python - number: 2 + number: 0 entry_points: - cellsnake=cellsnake.command_line:main - script: python -m pip install . -vv + script: python -m pip install . --ignore-installed -vv run_exports: - - {{ pin_subpackage(name, max_pin="x.x") }} + - {{ pin_compatible(name, max_pin="x.x") }} requirements: host: - pip - python + - r-base ==4.3 run: - python @@ -35,19 +36,19 @@ requirements: - pysam >=0.16.0.1 - regex >=2021.4.4 - scipy - - snakemake >=7.22.0 + - snakemake-minimal ==7.22.0 - umap-learn - plotly - - python-kaleido - - r-base ==4.2.2 + - r-ggraph ==2.1.0 - r-seurat ==4.3.0 - r-seuratobject ==4.1.3 - r-matrix <=1.5_4.1 - - r-igraph ==1.3.4 + - r-igraph - r-ggraph ==2.1.0 - r-clustree ==0.5.0 - r-dbplyr <=2.3.2 - r-ggthemes + - r-gplots - r-viridis - r-librarian - r-patchwork @@ -69,22 +70,9 @@ requirements: - r-r.utils - r-spdep - r-hdf5r - - r-monocle3 - r-rsvd - r-cowplot - r-randomcolor - - bioconductor-rhdf5lib - - bioconductor-clusterprofiler ==4.6.0 - - bioconductor-scater ==1.26.0 - - bioconductor-limma - - bioconductor-complexheatmap - - bioconductor-topgo - - bioconductor-org.hs.eg.db - - bioconductor-miqc - - bioconductor-rhdf5lib - - bioconductor-singler - - bioconductor-celldex - - bioconductor-enhancedvolcano - geos ==3.11.1 - cmake - hdf5 @@ -92,11 +80,12 @@ requirements: - r-xml - bedtools - samtools - - pandoc - kraken2 - - scanpy >=1.9.1 + - scanpy ==1.9.1 - openblas ==0.3.21 + - fastp + test: imports: - cellsnake From 8dba7cf5e3604a7782f1a6635566702c156e6b40 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 10:49:12 -0500 Subject: [PATCH 0832/1813] Update alfred to 0.3.1 (#46268) --- recipes/alfred/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/alfred/meta.yaml b/recipes/alfred/meta.yaml index a1d0b9d8a4038..6aa3e79ccff11 100644 --- a/recipes/alfred/meta.yaml +++ b/recipes/alfred/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.8" %} -{% set sha256 = "5d2583249728184aedd0165e936496a02833221c44eec2243f20ea315fa525e9" %} +{% set version = "0.3.1" %} +{% set sha256 = "6a84eef8cb737e856915c88b340304a22e5cc5013f89d3756026f93720f3c8cb" %} package: name: alfred From 70f69bb5521da3147c943d7fb6a800c39f420c93 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 10:57:50 -0500 Subject: [PATCH 0833/1813] Update gfftk to 24.2.4 (#46255) --- recipes/gfftk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gfftk/meta.yaml b/recipes/gfftk/meta.yaml index 0e92ea547b684..60caeb4b3da4a 100644 --- a/recipes/gfftk/meta.yaml +++ b/recipes/gfftk/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gfftk" %} -{% set version = "23.12.5" %} +{% set version = "24.2.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/gfftk-{{ version }}.tar.gz - sha256: 447280eee990625ea84eab899400ff1be7c38ef818172dc7f4f2a0bebb6cb5e4 + sha256: 053a95204cfcb24b47e0dc23e5983b57cdc0023a37763a4c80a83d7d92598056 build: number: 0 From 2f105882d415abac701a42624b61ebaca2936381 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 10:57:59 -0500 Subject: [PATCH 0834/1813] Update plassembler to 1.6.2 (#46257) --- recipes/plassembler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/plassembler/meta.yaml b/recipes/plassembler/meta.yaml index 96d18ed21a39f..7b7683d2378f5 100644 --- a/recipes/plassembler/meta.yaml +++ b/recipes/plassembler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "plassembler" %} -{% set version = "1.6.1" %} +{% set version = "1.6.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b66b61fda366c80b50eefbd68b93d8fdbc0cdefb0441093ed1ed9e571a549817 + sha256: 1433253aa9fb9305b8eb55ac3a19b46c4064d01147adbda077bc34da82509e46 build: number: 0 From 1805eb82698a3e429a63a712991e9ab4a81362e7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 11:09:55 -0500 Subject: [PATCH 0835/1813] Update pybiolib to 1.1.1855 (#46267) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index aa11fdf5ec316..ea610c7a56df2 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1846" %} +{% set version = "1.1.1855" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 4023ad085f38531825bf507f9f56fc2ab83236cfcdcaf7ab0802f4f2e375a681 + sha256: 49a230993446ceafcd3401cb578b09b18e6c936ed5935220f7564f0bada6d453 build: noarch: python From 1f8c2d969f494d31aa3244c54436efe644c89554 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 8 Mar 2024 13:42:17 -0600 Subject: [PATCH 0836/1813] Update pybigtools source URL (#46254) * Update pybigtools source URL * edit pip install command --- recipes/pybigtools/build.sh | 4 ++-- recipes/pybigtools/meta.yaml | 9 +++++---- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/pybigtools/build.sh b/recipes/pybigtools/build.sh index 00b4644361544..9bb1e5cebea29 100644 --- a/recipes/pybigtools/build.sh +++ b/recipes/pybigtools/build.sh @@ -17,7 +17,7 @@ fi # build statically linked binary with Rust RUST_BACKTRACE=1 # Build the package using maturin - should produce *.whl files. -maturin build -b pyo3 --interpreter "${PYTHON}" --release --strip +maturin build -m pybigtools/Cargo.toml -b pyo3 --interpreter "${PYTHON}" --release --strip # Install *.whl files using pip -${PYTHON} -m pip install pybigtools/target/wheels/*.whl --no-deps --no-build-isolation -vvv +${PYTHON} -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/pybigtools/meta.yaml b/recipes/pybigtools/meta.yaml index fbc14f532001a..50743e489df2e 100644 --- a/recipes/pybigtools/meta.yaml +++ b/recipes/pybigtools/meta.yaml @@ -1,16 +1,17 @@ {% set name = "pybigtools" %} {% set version = "0.1.2" %} +{% set sha256 = "ecc46cbfac71a4c10b7c14b4b280742db9d6ef6cecd5e595bb361027c47ea670" %} package: name: {{ name }} version: {{ version }} source: - url: "https://pypi.io/packages/source/p/pybigtools/{{ name }}-{{ version }}.tar.gz" - sha256: "0f21bc8b4f2dce67c6e5287af895f5f28a8c6eb123d809e3ab5679e2131dbf58" + url: "https://github.com/jackh726/bigtools/archive/refs/tags/{{ name }}@v{{ version }}.tar.gz" + sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('pybigtools', max_pin="x.x") }} @@ -35,7 +36,7 @@ about: license: MIT summary: 'pybigtools: Python bindings to the Bigtools Rust library for high-performance BigWig and BigBed I/O' license_family: MIT - license_file: pybigtools/LICENSE + license_file: LICENSE doc_url: https://bigtools.readthedocs.io dev_url: https://github.com/jackh726/bigtools/ From cf5637e5d3eac6b7faee9146965d5834b53fda77 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 15:24:22 -0500 Subject: [PATCH 0837/1813] Update snakemake to 8.5.5 (#46250) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index d1d081af66ccd..db57d5f200241 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.5.4" %} +{% set version = "8.5.5" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: cab6d0df98587ae0d3bcf3861c4ca1bb5cbdcc96809130e9a8c708e6b1601bd8 + sha256: a6e962ea72a060a6541253db59d3f1f44d52b6cac1bb1282a6f1e5cf11b3929f build: number: 0 From 591f3c411db2cb334511f0f13e60b4d4d9cadb2f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 16:08:42 -0500 Subject: [PATCH 0838/1813] Update deeptools to 3.5.5 (#46270) * Update deeptools to 3.5.5 * edit license to MIT and add entry_points --------- Co-authored-by: mencian --- recipes/deeptools/meta.yaml | 61 ++++++++++++++++++++++++++++++++----- 1 file changed, 53 insertions(+), 8 deletions(-) diff --git a/recipes/deeptools/meta.yaml b/recipes/deeptools/meta.yaml index 805ccb38e5137..a6e95ba34a6cb 100644 --- a/recipes/deeptools/meta.yaml +++ b/recipes/deeptools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.5.4" %} +{% set version = "3.5.5" %} package: name: deeptools @@ -6,23 +6,47 @@ package: source: url: https://github.com/deeptools/deepTools/archive/refs/tags/{{ version }}.tar.gz - sha256: 4554a2e9cfa264b181e4847be93a070e7ffe4ad5cb3988bc2606da4d59b2f3ea + sha256: f6dda39f552624758a9830cd4589ef43e7047284759b103cf833271cfa564dd1 build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage("deeptools", max_pin="x") }} - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + entry_points: + - alignmentSieve = deeptools.alignmentSieve:main + - bamCompare = deeptools.bamCompare:main + - bamCoverage = deeptools.bamCoverage:main + - bamPEFragmentSize = deeptools.bamPEFragmentSize:main + - bigwigAverage = deeptools.bigwigAverage:main + - bigwigCompare = deeptools.bigwigCompare:main + - computeGCBias = deeptools.computeGCBias:main + - computeMatrix = deeptools.computeMatrix:main + - computeMatrixOperations = deeptools.computeMatrixOperations:main + - correctGCBias = deeptools.correctGCBias:main + - deeptools = deeptools.deeptools_list_tools:main + - estimateReadFiltering = deeptools.estimateReadFiltering:main + - estimateScaleFactor = deeptools.estimateScaleFactor:main + - multiBamSummary = deeptools.multiBamSummary:main + - multiBigwigSummary = deeptools.multiBigwigSummary:main + - plotCorrelation = deeptools.plotCorrelation:main + - plotCoverage = deeptools.plotCoverage:main + - plotEnrichment = deeptools.plotEnrichment:main + - plotFingerprint = deeptools.plotFingerprint:main + - plotHeatmap = deeptools.plotHeatmap:main + - plotPCA = deeptools.plotPCA:main + - plotProfile = deeptools.plotProfile:main requirements: host: - - python >=3.7 + - python >=3.8 - pip run: - - python >=3.7 + - python >=3.8 - pybigwig >=0.2.3 - numpy >=1.9.0 + - numpydoc >=0.5 - scipy >=0.17.0 - matplotlib-base >=3.5.0 - pysam >=0.14.0 @@ -34,18 +58,39 @@ requirements: test: imports: - deeptools - commands: - bamCompare --version about: home: https://github.com/deeptools/deepTools - license: GPL3 + license: MIT + license_family: MIT license_file: LICENSE.txt summary: A set of user-friendly tools for normalization and visualzation of deep-sequencing data + doc_url: https://deeptools.readthedocs.io/en/latest/ + dev_url: https://github.com/deeptools/deepTools extra: identifiers: - biotools:deeptools - doi:10.1093/nar/gkw257 - usegalaxy-eu:deeptools_plot_heatmap + - usegalaxy-eu:deeptools_plot_pca + - usegalaxy-eu:deeptools_plot_profile + - usegalaxy-eu:deeptools_plot_correlation + - usegalaxy-eu:deeptools_plot_coverage + - usegalaxy-eu:deeptools_plot_fingerprint + - usegalaxy-eu:deeptools_plot_enrichment + - usegalaxy-eu:deeptools_bam_compare + - usegalaxy-eu:deeptools_bam_pe_fragmentsize + - usegalaxy-eu:deeptools_bigwig_compare + - usegalaxy-eu:deeptools_correct_gc_bias + - usegalaxy-eu:deeptools_multi_bam_summary + - usegalaxy-eu:deeptools_compute_matrix + - usegalaxy-eu:deeptools_compute_gc_bias + - usegalaxy-eu:deeptools_multi_bigwig_summary + - usegalaxy-eu:deeptools_compute_matrix_operations + - usegalaxy-eu:deeptools_alignmentsieve + - usegalaxy-eu:deeptools_estimatereadfiltering + - usegalaxy-eu:hicup_deduplicator + - usegalaxy-eu:deeptools_bigwig_average From 9c7120bb899f22d10234f559b501ec9d06bc3951 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 8 Mar 2024 15:26:17 -0600 Subject: [PATCH 0839/1813] Add recipe for pybarrnap v0.3.0 (#46273) --- recipes/pybarrnap/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/pybarrnap/meta.yaml diff --git a/recipes/pybarrnap/meta.yaml b/recipes/pybarrnap/meta.yaml new file mode 100644 index 0000000000000..61d75e0356930 --- /dev/null +++ b/recipes/pybarrnap/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "pybarrnap" %} +{% set version = "0.3.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybarrnap-{{ version }}.tar.gz + sha256: 07a1b8b4d33f0064b6471b874dbf43189a1ada370ddac5b092d57dd4e8b4cb4b + +build: + number: 0 + noarch: python + entry_points: + - pybarrnap = pybarrnap.scripts.pybarrnap:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('pybarrnap', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.8 + - biopython >=1.79 + - pyhmmer >=0.10.8 + +test: + imports: + - pybarrnap + commands: + - pybarrnap --help + +about: + home: https://github.com/moshi4/pybarrnap/ + summary: "Python implementation of barrnap (Bacterial ribosomal RNA predictor)" + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + +extra: + recipe-maintainers: + - moshi4 From 5c3aea80e856c348fe3be2a49c065ceeac527e4b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 18:25:53 -0500 Subject: [PATCH 0840/1813] Update alevin-fry to 0.9.0 (#46276) * Update alevin-fry to 0.9.0 * fix yaml --------- Co-authored-by: Rob Patro --- recipes/alevin-fry/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/alevin-fry/meta.yaml b/recipes/alevin-fry/meta.yaml index 2b773c2e1497a..446695091e5e6 100644 --- a/recipes/alevin-fry/meta.yaml +++ b/recipes/alevin-fry/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.2" %} +{% set version = "0.9.0" %} package: name: alevin-fry @@ -6,14 +6,16 @@ package: build: number: 0 - + run_exports: + - {{ pin_subpackage("alevin-fry", max_pin="x.x") }} + source: url: https://github.com/COMBINE-lab/alevin-fry/archive/v{{ version }}.tar.gz - sha256: 7feaa5b59c6537eee9d1a2a07797f151ba6a50955a969fa1807dcb7aeb357ab1 + sha256: 80fa964ba998c21dfd1190629015924e53d633be64cb8c8ee105bd7e3a33ac21 requirements: build: - - rust >=1.60 + - {{ compiler('rust') }} - cmake - autoconf - make From d83bb8121e8290addbbea08851678b84d5c833e6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Mar 2024 22:04:49 -0500 Subject: [PATCH 0841/1813] Update mehari to 0.25.4 (#46278) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 5610cbb39c241..1ba7525a1d0fa 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.25.3" %} -{% set sha256 = "ec4a5f1fa2135c38207def42e7391414d77ce457be96f3cbdddb5287bdf447c5" %} +{% set version = "0.25.4" %} +{% set sha256 = "bd33b8942d51352151785a49ebcfb2f9ea076747ed110cc966d1f8778ad029cb" %} package: name: mehari From e0bc8090d7c803d5f6429ba7b03e5d0b10ea501c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Mar 2024 09:55:47 -0500 Subject: [PATCH 0842/1813] Update pango-designation to 1.26 (#46280) --- recipes/pango-designation/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pango-designation/meta.yaml b/recipes/pango-designation/meta.yaml index 7dcdda6f72e20..f19439657e130 100644 --- a/recipes/pango-designation/meta.yaml +++ b/recipes/pango-designation/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.25" %} +{% set version = "1.26" %} package: name: pango-designation @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pango-designation/archive/refs/tags/v{{ version }}.tar.gz - sha256: f57bc2dee34d39ac73d27782357a4332f899bf45a495c8c279c6905c8b0130be + sha256: 15e2b6c22f4022385b67acf58638d89b9aa39e5c17f0f6f44beefc2f4bec10ff build: number: 0 From 7b08fc74b01ad246174dd8615b2280b61aa43616 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Sun, 10 Mar 2024 03:36:54 +0900 Subject: [PATCH 0843/1813] colabfold: fix incompatibility with jax and dm-tree (#46256) * Fix incompatibility with jax and dm-tree within colabfold * Stick to jax <=0.4.23 / dm-haiku 0.0.10 for now * Try to build with newer packages one more time --- recipes/colabfold/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/colabfold/meta.yaml b/recipes/colabfold/meta.yaml index c8c5024145ad6..5b02beb3331bb 100644 --- a/recipes/colabfold/meta.yaml +++ b/recipes/colabfold/meta.yaml @@ -14,7 +14,7 @@ build: python -m pip install --no-deps --ignore-installed alphafold/ run_exports: - {{ pin_subpackage('colabfold', max_pin="x") }} - number: 0 + number: 1 source: - url: https://github.com/sokrypton/ColabFold/archive/refs/tags/v{{ cf_version }}.tar.gz @@ -43,11 +43,11 @@ requirements: - dm-tree - ml-collections - importlib-metadata - - dm-haiku ==0.0.10 + - dm-haiku >=0.0.12 - biopython <=1.82 - - jax >=0.4.14 - - jaxlib >=0.4.14 - - tensorflow >=2.12.1=cpu* + - jax >=0.4.23 + - jaxlib >=0.4.23 + - tensorflow-base >=2.12.1=cpu* - mmseqs2 >=15.6f452 - kalign2 >=2.04 - hhsuite >=3.3.0 From 8a314dd97a8ac22e1948bbae29a489ef3da2609f Mon Sep 17 00:00:00 2001 From: Vladimir Mikryukov Date: Sat, 9 Mar 2024 22:01:36 +0200 Subject: [PATCH 0844/1813] Update `RDP Classifier` to 2.14 (#46265) * upd RDP Classifier to 2.14 * start build number with 0 * add `run_exports` * RDP - Home page Old home page (rdp.cme.msu.edu/classifier/classifier.jsp) is dead, change to SourceForge (https://sourceforge.net/projects/rdp-classifier/) --- recipes/rdp_classifier/meta.yaml | 10 ++++++---- recipes/rdp_classifier/rdp_classifier.sh | 4 ++-- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/rdp_classifier/meta.yaml b/recipes/rdp_classifier/meta.yaml index 2f1fc33e086f3..5341085f3b312 100644 --- a/recipes/rdp_classifier/meta.yaml +++ b/recipes/rdp_classifier/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.13" %} +{% set version = "2.14" %} package: name: rdp_classifier @@ -6,11 +6,13 @@ package: source: url: https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_{{ version }}.zip - sha256: d2eb9a989d7e31ff824de6876bc1d8ab70d97112ece167afe8d87a3cd412086a + sha256: 2aac7ba2bf602eb025e1791f356c0c437200486ece6905f93219d51395504b2b build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('rdp_classifier', max_pin='x.x') }} requirements: run: @@ -21,6 +23,6 @@ test: - rdp_classifier about: - home: 'http://rdp.cme.msu.edu/classifier/' + home: 'https://sourceforge.net/projects/rdp-classifier/' license: GPL-2.0-only summary: "Naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus" diff --git a/recipes/rdp_classifier/rdp_classifier.sh b/recipes/rdp_classifier/rdp_classifier.sh index 1bbc9b3f9e0bb..1596d5df830e7 100644 --- a/recipes/rdp_classifier/rdp_classifier.sh +++ b/recipes/rdp_classifier/rdp_classifier.sh @@ -36,10 +36,10 @@ for arg in "$@"; do '-XX'*) jvm_prop_opts="$jvm_prop_opts $arg" ;; - '-Xm'*) + '-Xm'*) jvm_mem_opts="$jvm_mem_opts $arg" ;; - *) + *) pass_args="$pass_args $arg" ;; esac From f88a164ac28489ca9ab4c0ff7c79093709b16e93 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sun, 10 Mar 2024 07:13:54 +0100 Subject: [PATCH 0845/1813] Update Nextclade: Enable linux-aarch64 (#46185) * Add linux-aarch64 to Nextclade platforms * fix sha256 --- recipes/nextclade/meta.yaml | 15 ++++++++++----- recipes/nextclade/run_test.sh | 7 +++++++ 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index 67961e351154d..2ceb70785f55a 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -8,22 +8,25 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] sha256: 9eecdb2e56362d24cfedb510b236f2054c3d02264f3ca7e8c586fe234d25e2f2 # [linux64] + - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-unknown-linux-gnu # [aarch64] + sha256: 63b38aac186b9b9776761bb1a321b87382044d01c17e6b4a2ba76ca614d04ed1 # [aarch64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: d8e1604be6a32f34086616ebdf532ec1409d500b5fe72c239b6db2614d75e722 # [osx and x86_64] - - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: b95e2ed966b08dbd481fe48d7aa1019a748d29ef330daad4773d1c98e6b007ba # [arm64] + sha256: 330ad12cd1bb20429f49fd00bcd773c453b66662842913ec35bc9e288ab3db2a # [osx and x86_64] + - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [osx and arm64] + sha256: b95e2ed966b08dbd481fe48d7aa1019a748d29ef330daad4773d1c98e6b007ba # [osx and arm64] build: - number: 0 + number: 1 binary_relocation: False run_exports: - {{ pin_compatible(name, max_pin='x') }} requirements: +# Disable test for aarch64, as nextclade requires glibc 2.18 not available on aarch64 test: commands: - - nextclade --help + - nextclade --help # [not aarch64] about: home: https://github.com/nextstrain/nextclade @@ -34,6 +37,8 @@ about: dev_url: https://github.com/nextstrain/nextclade extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - pvanheus - corneliusroemer diff --git a/recipes/nextclade/run_test.sh b/recipes/nextclade/run_test.sh index 7fe8383073ee4..fff9dde423c45 100644 --- a/recipes/nextclade/run_test.sh +++ b/recipes/nextclade/run_test.sh @@ -5,6 +5,13 @@ set -e MAJOR_VERSION=$(echo "$PKG_VERSION" | cut -d. -f1) +# Skip if aarch64 on linux +# Because Nextclade requires glibc >= 2.18 not available yet on aarch64 builder +if [[ $target_platform == linux-aarch64 ]]; then + echo "Skipping test on aarch64" + exit 0 +fi + for BIN in nextclade nextclade$MAJOR_VERSION; do "$BIN" --version From b343d22b07a5ac712bc2dd079f5e82cb1315471f Mon Sep 17 00:00:00 2001 From: John Marshall Date: Mon, 11 Mar 2024 03:02:05 +1300 Subject: [PATCH 0846/1813] Build hmmer for linux-aarch64 (#46288) --- recipes/hmmer/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/hmmer/meta.yaml b/recipes/hmmer/meta.yaml index f6561a1f17117..a5b3120a4bd0d 100644 --- a/recipes/hmmer/meta.yaml +++ b/recipes/hmmer/meta.yaml @@ -7,7 +7,7 @@ source: sha256: ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3 build: - number: 0 + number: 1 run_exports: # commands/options have been removed or replaced between minor versions - {{ pin_subpackage('hmmer', max_pin="x.x") }} @@ -43,3 +43,7 @@ about: home: http://hmmer.org/ license: BSD license_file: LICENSE + +extra: + additional-platforms: + - linux-aarch64 From 9e6353dda0c27f0910da544f6f3edb544c3a67af Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Mar 2024 10:02:21 -0400 Subject: [PATCH 0847/1813] Update virstrain to 1.17 (#46281) * Update virstrain to 1.15 * Update virstrain to 1.17 --- recipes/virstrain/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/virstrain/meta.yaml b/recipes/virstrain/meta.yaml index 6f527c19bffa1..6b76a92afa455 100644 --- a/recipes/virstrain/meta.yaml +++ b/recipes/virstrain/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virstrain" %} -{% set version = "1.14" %} +{% set version = "1.17" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: f9247a696892c75ded21e93ba60a2a4d6a63d3ecacd18b8d002fd8d7560227d5 + sha256: 76b71f73eb6fc92f61e495ee28ada438092bb70e33cf6f5d211c9a82922fd7a9 build: number: 0 From b27b731d56c654986dee922ccd989a053423c959 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Mar 2024 10:03:59 -0400 Subject: [PATCH 0848/1813] Update pybarrnap to 0.4.1 (#46286) * Update pybarrnap to 0.4.0 * Update pybarrnap to 0.4.1 --- recipes/pybarrnap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybarrnap/meta.yaml b/recipes/pybarrnap/meta.yaml index 61d75e0356930..1f4e67ed04198 100644 --- a/recipes/pybarrnap/meta.yaml +++ b/recipes/pybarrnap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybarrnap" %} -{% set version = "0.3.0" %} +{% set version = "0.4.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybarrnap-{{ version }}.tar.gz - sha256: 07a1b8b4d33f0064b6471b874dbf43189a1ada370ddac5b092d57dd4e8b4cb4b + sha256: d20c05a027f8b16a32855c5d63be0cff79150b1cb5f642037f31faf02a721679 build: number: 0 From 4de48a728a505a23c6ae75153353f6685ebc86f8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Mar 2024 10:04:45 -0400 Subject: [PATCH 0849/1813] Update pybiolib to 1.1.1879 (#46282) * Update pybiolib to 1.1.1866 * Update pybiolib to 1.1.1874 * Update pybiolib to 1.1.1879 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index ea610c7a56df2..0b30582e2b188 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1855" %} +{% set version = "1.1.1879" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 49a230993446ceafcd3401cb578b09b18e6c936ed5935220f7564f0bada6d453 + sha256: 09c1c44e4128bdf41798d6327c6cf58192df0a489cfbe5976dc24c4570824f47 build: noarch: python From c053eee912fac88b005fc0c90d8b74b8d23a9a2c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Mar 2024 10:04:54 -0400 Subject: [PATCH 0850/1813] Update liftover to 1.2.1 (#46277) * Update liftover to 1.2.0 * Update liftover to 1.2.1 --- recipes/liftover/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/liftover/meta.yaml b/recipes/liftover/meta.yaml index 13f38da8679fa..4fee1d42574a2 100644 --- a/recipes/liftover/meta.yaml +++ b/recipes/liftover/meta.yaml @@ -1,6 +1,6 @@ {% set name = "liftover" %} -{% set version = "1.1.18" %} -{% set sha256 = "a4bf896c5dd59a284929d68f446a78c426827efbec430d35da1ec7bcd29eac44" %} +{% set version = "1.2.1" %} +{% set sha256 = "43d89d929288b0f2031f6200958a920d6ec71a0929a91abcfd73b15032f20116" %} package: name: {{ name|lower }} From a6f69588478435218c53cd4e58d6bb59d1c5a24f Mon Sep 17 00:00:00 2001 From: Christian Diener Date: Sun, 10 Mar 2024 15:08:50 +0100 Subject: [PATCH 0851/1813] Add architeuthis (#46264) * add architeuthis * add run_exports * add taxonkit as dep * move run_exports to the right place * hardcode package name --- recipes/architeuthis/meta.yaml | 44 ++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 recipes/architeuthis/meta.yaml diff --git a/recipes/architeuthis/meta.yaml b/recipes/architeuthis/meta.yaml new file mode 100644 index 0000000000000..6ef0a4385567a --- /dev/null +++ b/recipes/architeuthis/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "architeuthis" %} +{% set version = "0.2.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/cdiener/{{ name }}/archive/{{ version }}.tar.gz + sha256: af522d822ed2dcf3bc386c8cb5ea42772ade1826b998ca0f1cd1d825f1a114ab + +build: + number: 0 + script: + - go build -v -ldflags "-w -s -X 'main.version={{ version }}'" -o $PREFIX/bin/architeuthis + run_exports: + - {{ pin_subpackage('architeuthis', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('go') }} + run: + - taxonkit >=0.16.0 + +test: + commands: + - architeuthis -v + +about: + home: https://github.com/cdiener/{{ name }} + license: Apache-2.0 + license_file: LICENSE + summary: Tool to analyze and summarize data for Kraken. + description: | + architeuthis is a fast standalone command to supplement the Kraken suite of software + tools such like Kraken2, KrakenUniq, and Bracken. I saw myself repeatedly rewriting + the same code in my pipelines when dealing with Kraken output, like merging files or + maninpulating lineage annotations. It also adds some functionality to dive deeper + into the individual k-mer classifications for reads. + dev_url: https://github.com/cdiener/architeuthis.git + +extra: + recipe-maintainers: + - cdiener \ No newline at end of file From 288618d5934825cb24c63520f2a500bbbef2c3bb Mon Sep 17 00:00:00 2001 From: Reid Wagner <74672860+reid-wagner@users.noreply.github.com> Date: Sun, 10 Mar 2024 09:23:11 -0500 Subject: [PATCH 0852/1813] Add FragPipe Recipe (#46105) * Add initial fragpipe recipe. * Add msfragger and philosopher recipes. * Add license agreement requirement to msfragger.py. * Add wrapper script for FragPipe that requires user to pass --accept_license flag. * Progress with MSFragger, IonQuant, FragPipe recipes. * Delete msfragger recipe. * FragPipe: Incorporate existing IonQuant and MSFragger recipes. * Add subpackage pin for FragPipe. * FragPipe: Remove philosopher recipe. * Remove redundant build section. Add maintainer. * Fix argument handling in FragPipe wrapper script. * Remove conda_build_config.yaml. * Fix MSFragger and IonQuant versions. * Constrain python and openjdk versions. * - Use latest Philosopher, version 5.10 - Install philosopher into $CONDA_PREFIX/share - Fix meta.yaml test to ensure FragPipe runs properly - Fix wrapper script to properly call FragPipe - Grep for 'License key verified' from MSFragger and IonQuant * Remove unused host section. * Fix typos. * Update description with latest from FragPipe site. * - Add licenses for FragPipe and components - Disallow DIA-NN as its license is not included - Do not pin JDK, IonQuant, or MSFragger versions - Update ionquant key --------- Co-authored-by: Jim Johnson --- recipes/fragpipe/build.sh | 21 + recipes/fragpipe/fragpipe | 64 ++ .../fragpipe/licenses/dia-umpire_LICENSE.txt | 674 ++++++++++++++++++ recipes/fragpipe/licenses/easypqp_LICENSE.txt | 29 + .../fragpipe/licenses/fragpipe_LICENSE.txt | 2 + .../fragpipe/licenses/msbooster_LICENSE.txt | 165 +++++ .../licenses/ptm-shepherd_LICENSE.txt | 202 ++++++ recipes/fragpipe/meta.yaml | 70 ++ 8 files changed, 1227 insertions(+) create mode 100644 recipes/fragpipe/build.sh create mode 100755 recipes/fragpipe/fragpipe create mode 100644 recipes/fragpipe/licenses/dia-umpire_LICENSE.txt create mode 100644 recipes/fragpipe/licenses/easypqp_LICENSE.txt create mode 100644 recipes/fragpipe/licenses/fragpipe_LICENSE.txt create mode 100644 recipes/fragpipe/licenses/msbooster_LICENSE.txt create mode 100644 recipes/fragpipe/licenses/ptm-shepherd_LICENSE.txt create mode 100644 recipes/fragpipe/meta.yaml diff --git a/recipes/fragpipe/build.sh b/recipes/fragpipe/build.sh new file mode 100644 index 0000000000000..9ea5f09a40436 --- /dev/null +++ b/recipes/fragpipe/build.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +# Copy entire FragPipe installation including workflows into share location. +TARGET="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +mkdir -p "$TARGET" + +# DIA-NN license is currently incompatible with bioconda +rm -rf fragpipe_source/tools/diann{,_so} +rm -rf fragpipe_source/tools/diann{,_so} +cp -rp fragpipe_source/* "$TARGET" + +# Copy wrapper script, which checks license keys, into bin. +mkdir "$PREFIX/bin" +cp "$RECIPE_DIR/fragpipe" "$PREFIX/bin" + +# Copy Philosopher installation into share and link to bin. +PHILOSOPHER_DIR="$TARGET/philosopher" +mkdir "$PHILOSOPHER_DIR" +cp philosopher_source/philosopher philosopher_source/philosopher.yml "$PHILOSOPHER_DIR" +ln -s "$PHILOSOPHER_DIR/philosopher" "$PREFIX/bin/philosopher" +chmod ugo+x "$PHILOSOPHER_DIR/philosopher" diff --git a/recipes/fragpipe/fragpipe b/recipes/fragpipe/fragpipe new file mode 100755 index 0000000000000..0de8efde2f0d9 --- /dev/null +++ b/recipes/fragpipe/fragpipe @@ -0,0 +1,64 @@ +#!/bin/bash + +# Wrapper script for command-line FragPipe. Ensures the user agrees to MSFragger and IonQuant academic licenses. + +license_agreement_text=' +Please accept the academic license. + +FragPipe uses tools that are available freely for academic research and educational purposes only. + +Please provide license keys for MSFragger and IonQuant with the --msfragger_key and --ionquant_key flags. By passing these, you verify that you have read the ACADEMIC licenses for the MSFragger and IonQuant tools. You may obtain these keys by agreeing to the terms at http://msfragger-upgrader.nesvilab.org/upgrader/ and https://msfragger.arsci.com/ionquant/.' + +declare -a fragpipe_args + +while [[ $# -gt 0 ]]; do + case "$1" in + --msfragger_key) + shift + msfragger_key=$1 + ;; + --ionquant_key) + shift + ionquant_key=$1 + ;; + --workflow) + fragpipe_args+=("$1") + shift + workflow_file="$1" + fragpipe_args+=("$1") + ;; + *) + fragpipe_args+=("$1") + ;; + esac + shift +done + +if [[ ! -z "$workflow_file" ]]; then + # Because the DIA-NN license is incompatible with bioconda, we remove the feature. + grep 'diann.run-dia-nn=true' "$workflow_file" >/dev/null + if [[ $? -eq 0 ]]; then + echo "Error: DIA-NN is disabled in the FragPipe bioconda package." + exit 1 + fi +fi + +if [[ -z $msfragger_key || -z $ionquant_key ]]; then + echo "$license_agreement_text" + exit 1 +else + msfragger --key $msfragger_key --help | grep 'License key verified' >/dev/null 2>&1 + if [[ $? -ne 0 ]]; then + echo "Error: Invalid MSFragger license key" + echo "$license_agreement_text" + exit 1 + fi + ionquant --key $ionquant_key --help | grep 'License key verified' >/dev/null 2>&1 + if [[ $? -ne 0 ]]; then + echo "Error: Invalid IonQuant license key" + echo "$license_agreement_text" + exit 1 + fi +fi + +sh "$CONDA_PREFIX"/share/fragpipe*/bin/fragpipe "${fragpipe_args[@]}" diff --git a/recipes/fragpipe/licenses/dia-umpire_LICENSE.txt b/recipes/fragpipe/licenses/dia-umpire_LICENSE.txt new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/fragpipe/licenses/dia-umpire_LICENSE.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/recipes/fragpipe/meta.yaml b/recipes/fragpipe/meta.yaml new file mode 100644 index 0000000000000..a093ff8dc5456 --- /dev/null +++ b/recipes/fragpipe/meta.yaml @@ -0,0 +1,70 @@ +{% set name = "FragPipe" %} +{% set version = "20.0" %} +{% set philosopher_version = "5.1.0" %} + +# These keys were generated ONLY for the testing of this bioconda package. +# Users must generate their own key by agreeing to the terms at https://msfragger-upgrader.nesvilab.org/upgrader/ and https://msfragger.arsci.com/ionquant/. +{% set msfragger_academic_use_only_key = "f28c4be2-759b0a11-6c1ea652-1240565a" %} +{% set ionquant_academic_use_only_key = "b6c0ad83-9a4e8900-3e83d29c-aeba3bfb" %} + +package: + name: fragpipe + version: {{ version }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('fragpipe', max_pin="x.x") }} + +source: + - url: https://github.com/Nesvilab/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}.zip + sha256: 0d77db85ae26c190a915823e1c68238f3a19533810734b008564b2a8d85d1bd6 + folder: fragpipe_source + - url: https://github.com/Nesvilab/philosopher/releases/download/v{{ philosopher_version }}/philosopher_v{{ philosopher_version }}_linux_amd64.zip + sha256: cf15a2d6321ecb530170b2410f5873f89e283b52d5f1ab0f27eebc124f4f4a1a + folder: philosopher_source + +requirements: + run: + - openjdk >=9 + - python =3.9 + - msfragger >=4.0 + - ionquant >=1.10.12 + +test: + commands: + - fragpipe --msfragger_key {{ msfragger_academic_use_only_key }} --ionquant_key {{ ionquant_academic_use_only_key }} --help | grep "FragPipe v{{ version }}" + +about: + home: https://github.com/Nesvilab/FragPipe + license: GPL-3.0 + LICENSE files + license_file: + - licenses/fragpipe_LICENSE.txt + - licenses/dia-umpire_LICENSE.txt + - licenses/easypqp_LICENSE.txt + - licenses/msbooster_LICENSE.txt + - licenses/ptm-shepherd_LICENSE.txt + - philosopher_source/License + summary: Pipeline for comprehensive analysis of shotgun proteomics data + description: | + FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools + enabling comprehensive analysis of mass spectrometry-based proteomics data. + It is powered by MSFragger - an ultrafast proteomic search engine suitable + for both conventional and "open" (wide precursor mass tolerance) peptide identification. + FragPipe includes the Philosopher toolkit for downstream post-processing of + MSFragger search results (PeptideProphet, iProphet, ProteinProphet), FDR filtering, + label-based quantification, and multi-experiment summary report generation. + Crystal-C and PTM-Shepherd are included to aid interpretation of open search results. + Also included in FragPipe binary are TMT-Integrator for TMT/iTRAQ isobaric + labeling-based quantification, IonQuant for label-free quantification with + match-between-run (MBR) functionality, spectral library building with EasyPQP, + and MSFragger-DIA and DIA-Umpire SE modules for direct analysis of data independent + acquisition (DIA) data. + +extra: + recipe-maintainers: + - reid-wagner + identifiers: + - biotools:fragpipe + - doi:10.1074/mcp.TIR120.002048 From dcbb102ccf590d1f2d86b30a7eb78c254afca196 Mon Sep 17 00:00:00 2001 From: Timothee Cezard Date: Sun, 10 Mar 2024 14:25:28 +0000 Subject: [PATCH 0853/1813] Add VCF-Validator (#46115) * Retrieve the prebuilt binaries * Add run_export * Add back noarch ? * Skip noarch linter --- recipes/vcf-validator/LICENSE | 203 ++++++++++++++++++++++++++++++ recipes/vcf-validator/LICENSE_ODB | 71 +++++++++++ recipes/vcf-validator/build.sh | 11 ++ recipes/vcf-validator/meta.yaml | 44 +++++++ 4 files changed, 329 insertions(+) create mode 100644 recipes/vcf-validator/LICENSE create mode 100644 recipes/vcf-validator/LICENSE_ODB create mode 100644 recipes/vcf-validator/build.sh create mode 100644 recipes/vcf-validator/meta.yaml diff --git a/recipes/vcf-validator/LICENSE b/recipes/vcf-validator/LICENSE new file mode 100644 index 0000000000000..6b0b1270ff0ca --- /dev/null +++ b/recipes/vcf-validator/LICENSE @@ -0,0 +1,203 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + diff --git a/recipes/vcf-validator/LICENSE_ODB b/recipes/vcf-validator/LICENSE_ODB new file mode 100644 index 0000000000000..52e36215fc329 --- /dev/null +++ b/recipes/vcf-validator/LICENSE_ODB @@ -0,0 +1,71 @@ + +ODB License Exception for vcf-validator (Validator for the Variant Call +Format (VCF)) Software + Version 1.0 + +1. Intent + +The intent of this License Exception is to allow the vcf-validator software +to use ODB without the "copyleft" restrictions that would normally be +imposed by the GPL, the license under which ODB is distributed. + +Specifically, the intent is to allow you to use the original vcf-validator +software in your open source or proprietary works without imposing +any additional restrictions to the terms and conditions of the +Apache 2.0 license used by vcf-validator. + +If you wish to modify the vcf-validator software in such a way that it +requires changes to the persistent object model handled by ODB, you can +continue enjoying the terms of this exception provided that you are +prepared to release your modifications under Apache 2.0 or another open +source license and you obtain a separate license exception for your +modifications from Code Synthesis Tools CC. + +While this exception is specific to vcf-validator, any open source software +project licensed under a more liberal than the GPL license can obtain +a similar exception free of charge by contacting Code Synthesis Tools CC. + +2. Definitions + +"Original Software" is the vcf-validator software, Copyright (c) EMBL - +European Bioinformatics Institute, distributed under the terms of the +Apache 2.0 license, and available to any third party from: + + https://github.com/ebivariation/vcf-validator + +"ODB-Extended Software" are any modifications to the Original Software +that require additions or changes to the persistent object model of +the Original Software that is handled by ODB. + +"Work Based on the Original Software" is any derivative work under the +copyright law that is either based on the Original Software or any +modified version of the Original Software that does not constitute +ODB-Extended Software. + +"Work Based on the ODB-Extended Software" is any derivative work under +the copyright law that is based on any modified version of the Original +Software that constitutes ODB-Extended Software. + +3. Legal Terms and Conditions + +As a special exception to the terms and conditions of version 2 of the +GPL you may use the ODB runtime libraries in Original Software and in +Works Based on the Original Software and distribute the resulting works +in object code or executable form and without making source code for +such works available to any third party, provided that all of the +following conditions are met: + + a) Original Software was licensed as a whole at no charge to all third + parties under the terms of the Apache 2.0 license. + + b) The ODB runtime libraries in Works Based on the Original Software + are used solely for the purpose of supporting the functionality of + the Original Software. + +The same exception does not apply automatically to ODB-Extended Software +or Works Based on the ODB-Extended Software. If you wish to enjoy this +exception for such works, then you will need to license ODB-Extended +Software at no charge to all third parties under the terms of the Apache 2.0 +license or another open source license. You will also need to obtain a +separate License Exception for ODB-Extended Software from Code Synthesis +Tools CC. diff --git a/recipes/vcf-validator/build.sh b/recipes/vcf-validator/build.sh new file mode 100644 index 0000000000000..acd838e4eac4f --- /dev/null +++ b/recipes/vcf-validator/build.sh @@ -0,0 +1,11 @@ +mkdir -p ${PREFIX}/bin +# Check if linux or osx +if [ -z ${OSX_ARCH+x} ]; then + mv vcf_validator_linux ${PREFIX}/bin/vcf_validator + mv vcf_assembly_checker_linux ${PREFIX}/bin/vcf_assembly_checker +else + mv vcf_validator_macos ${PREFIX}/bin/vcf_validator + mv vcf_assembly_checker_macos ${PREFIX}/bin/vcf_assembly_checker +fi + +chmod 755 ${PREFIX}/bin/vcf_assembly_checker ${PREFIX}/bin/vcf_validator diff --git a/recipes/vcf-validator/meta.yaml b/recipes/vcf-validator/meta.yaml new file mode 100644 index 0000000000000..252a24c4013d0 --- /dev/null +++ b/recipes/vcf-validator/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "vcf-validator" %} +{% set version = "0.9.6" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_validator_linux # [linux] + sha256: 33fc99334e77a90e99415daebfa877a9bc0375a3d7c18809082ace64d8373cdd # [linux] + - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_assembly_checker_linux # [linux] + sha256: 7913a6b3f12fdf5a66c98026ef144be4f8964f981f80eca4b509e06e6b8282ab # [linux] + - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_validator_macos # [osx] + sha256: 68f50e38323260dcd77e236c27872e1a0eb5c6407736baf003cbc755c87bab94 # [osx] + - url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_assembly_checker_macos # [osx] + sha256: afb7383468fa08d597fc8f7588918dbcdafc8d6d41eb7d33d37ae71a30860cb7 # [osx] + +build: + script: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +test: + commands: + - vcf_validator --help + - vcf_assembly_checker --help + +about: + home: https://github.com/EBIVariation/vcf-validator + summary: EBI EVA - Validation tool to ensure VCF specification compliance + license: Apache-2.0 + license_file: + - LICENSE + - LICENSE_ODB + +extra: + recipe-maintainers: + - apriltuesday + - tcezard + - ebi-variation + skip-lints: + - should_be_noarch_generic + - should_not_be_noarch_source From d4b10fa66de7191763892a1f4b20671de0950a03 Mon Sep 17 00:00:00 2001 From: Meltpinkg <47966870+Meltpinkg@users.noreply.github.com> Date: Sun, 10 Mar 2024 22:26:12 +0800 Subject: [PATCH 0854/1813] Add cuteFC recipe (#46174) * add cuteFC * add cutefc recipe * pin run to python3 --------- Co-authored-by: Robert A. Petit III --- recipes/cutefc/meta.yaml | 49 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/cutefc/meta.yaml diff --git a/recipes/cutefc/meta.yaml b/recipes/cutefc/meta.yaml new file mode 100644 index 0000000000000..39c976a89d87d --- /dev/null +++ b/recipes/cutefc/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} + +package: + name: cutefc + version: {{ version }} + +source: + url: https://pypi.io/packages/source/c/cuteFC/cuteFC-{{ version }}.tar.gz + sha256: c8cfc36d2b2195760d8feee2e3a8e79a885622c3e50f8ceb903d945d4e41e0ef + +build: + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage("cutefc", max_pin="x.x") }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - scipy + - pysam + - biopython + - cigar + - numpy + - pyvcf3 + - scikit-learn + +test: + imports: + - benchmarks + - cuteFC + commands: + - cuteFC -h + requires: + - pip + +about: + home: https://github.com/tjiangHIT/cuteFC + summary: Regenotyping structural variants through an accurate and efficient force-calling method + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - Meltpinkg From 8ed4d499f2317c3daad52a1ea07d720255d6a6d2 Mon Sep 17 00:00:00 2001 From: lspindler2509 <83402447+lspindler2509@users.noreply.github.com> Date: Sun, 10 Mar 2024 15:30:14 +0100 Subject: [PATCH 0855/1813] Add recipe for robust-bias-aware (#46056) * create new recipe for robust-bias-aware * correct version * adjusted run requirements * correct synthax * different dependencies * updated dependencies * updated recipe * correct filepath in tar * deleted unnecessary logs in tar --- recipes/robust-bias-aware/meta.yaml | 49 +++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/robust-bias-aware/meta.yaml diff --git a/recipes/robust-bias-aware/meta.yaml b/recipes/robust-bias-aware/meta.yaml new file mode 100644 index 0000000000000..dcfc453f25cb6 --- /dev/null +++ b/recipes/robust-bias-aware/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "robust-bias-aware" %} +{% set version = "0.0.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://github.com/lspindler2509/robust_bias_aware_pip_package/archive/refs/tags/v{{ version }}-xi.tar.gz" + sha256: 182c413b2f39b34d89fec657afdcf350a1c1a7b9f75b799746a3c0a18ce40744 + +build: + number: 0 + script: + - "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" + - mkdir -p $PREFIX/site-packages + - cp -r $SRC_DIR/robust_bias_aware/* $PREFIX/site-packages + noarch: python + run_exports: + - {{ pin_subpackage('robust-bias-aware', max_pin="x.x") }} + +requirements: + build: + - python + - setuptools + host: + - pip >=3.7 + - python + + run: + - numpy >=1.26.4 + - matplotlib-base >=3.2.2 + - pandas >=1.3.5 + - networkx >=2.6.3 + - pcst-fast + - python >=3.7 + + +test: + commands: + - robust-bias-aware --help + + +about: + home: https://github.com/bionetslab/robust_bias_aware_pip_package + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: "Robust bias aware." From 826220fb120b84f59afb6b6df00968081a281847 Mon Sep 17 00:00:00 2001 From: pvanheus Date: Sun, 10 Mar 2024 16:30:33 +0200 Subject: [PATCH 0856/1813] Add recipe for merge-genbank-records (#46289) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Add recipe for merge-genbank-records * Add run_exports section * Fix Jinja2 * Stop use of name variable * fix linting * now for real * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/merge-gbk-records/meta.yaml | 42 +++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 recipes/merge-gbk-records/meta.yaml diff --git a/recipes/merge-gbk-records/meta.yaml b/recipes/merge-gbk-records/meta.yaml new file mode 100644 index 0000000000000..38aaf9585a484 --- /dev/null +++ b/recipes/merge-gbk-records/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "merge-gbk-records" %} +{% set version = "0.2.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: "4e204552a87787e1fbe3eba629c0e05dbe0cd6bddc81c256cc813066d67b8be4" + +build: + noarch: python + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps -vv" + run_exports: + - {{ pin_subpackage("merge-gbk-records", max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.7 + - biopython >=1.79 + +test: + commands: + - merge-gbk-records --help + +about: + home: http://github.com/kblin/{{ name }} + license: Apache-2.0 + license_family: Apache + license_file: LICENSE + summary: 'Turn multiple GenBank records (either in multiple files or a single multi-record file) into a single record' + description: | + A small script to turn multiple GenBank records (either in multiple files or a single multi-record file) into a + single record. + Sequences are merged by concatenating them in order, and putting a spacer sequence between them. + Spacer sequence length can be given in kbp. It is possible to pick an all-N spacer, or using a spacer + consisting of all-frame stop codons. From ccdeb5760ceb59e1db08a52f61cdfb225b518306 Mon Sep 17 00:00:00 2001 From: Ray <851836818@qq.com> Date: Mon, 11 Mar 2024 00:07:34 +0800 Subject: [PATCH 0857/1813] Update meta.yaml (#46290) * Update meta.yaml * Update meta.yaml --- recipes/virstrain/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/virstrain/meta.yaml b/recipes/virstrain/meta.yaml index 6b76a92afa455..62e80eec94e1d 100644 --- a/recipes/virstrain/meta.yaml +++ b/recipes/virstrain/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 76b71f73eb6fc92f61e495ee28ada438092bb70e33cf6f5d211c9a82922fd7a9 build: - number: 0 + number: 1 entry_points: - virstrain = VirStrain.VirStrain:main - virstrain_build = VirStrain.VirStrain_build:main @@ -31,6 +31,7 @@ requirements: - pandas ==1.0.1 - plotly ==3.10.0 - python ==3.7.3 + - bowtie2 test: imports: @@ -38,6 +39,8 @@ test: commands: - virstrain --help - virstrain_build --help + - virstrain_contig --help + - virstrain_merge --help about: home: https://github.com/liaoherui/VirStrain From 7d9e796ffd88c7c99c83f8a9657a65edc73fa023 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 01:13:03 -0400 Subject: [PATCH 0858/1813] Update metacache to 2.4.0 (#46291) * Update metacache to 2.4.0 * Update metacache to 2.4.0 --- recipes/metacache/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metacache/meta.yaml b/recipes/metacache/meta.yaml index b56fab267d2cd..d06a2a2a03ea6 100644 --- a/recipes/metacache/meta.yaml +++ b/recipes/metacache/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.3.2" %} +{% set version = "2.4.0" %} package: name: metacache @@ -6,7 +6,7 @@ package: source: url: https://github.com/muellan/metacache/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3d5bb4e49a0fd3e59a4c60ba1100c162912a52e15e9a8aea4316a2e5d01d4b66 + sha256: 8d5eea5aedd6ce36befef0371cf5906533a70ed17e1e12d7cd26658673f7d954 build: number: 0 From ebd10985b81c34fbefe501899e34a44fb386b25c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 01:55:32 -0400 Subject: [PATCH 0859/1813] Update snakemake-storage-plugin-gcs to 0.1.4 (#46287) * Update snakemake-storage-plugin-gcs to 0.1.4 * add missing deps --------- Co-authored-by: mencian --- recipes/snakemake-storage-plugin-gcs/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-storage-plugin-gcs/meta.yaml b/recipes/snakemake-storage-plugin-gcs/meta.yaml index d9da699d0876f..ce5f67acc91ae 100644 --- a/recipes/snakemake-storage-plugin-gcs/meta.yaml +++ b/recipes/snakemake-storage-plugin-gcs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-gcs" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: {{ name|lower }} @@ -7,11 +7,11 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_gcs-{{ version }}.tar.gz - sha256: f0315596120160656b8c8afec66e3b31b4a2889b9d0cead2102f9d924ec0b326 + sha256: f8c2ebbc2b44ff5a87f7507b26bd1176de98ae80e93339b2ae65f722d17dbc24 build: noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -23,6 +23,8 @@ requirements: - pip run: - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.14.2,<2.0.0 + - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 - google-cloud-storage >=2.12.0,<3.0.0 - google-crc32c >=1.1.2,<2.0.0 @@ -38,6 +40,7 @@ about: home: https://github.com/snakemake/snakemake-storage-plugin-gcs summary: A Snakemake storage plugin for Google Cloud Storage license: MIT + license_family: MIT license_file: LICENSE extra: From 443dafb2361b52989dee425ce22c94901c424a99 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 01:55:58 -0400 Subject: [PATCH 0860/1813] Update pytaxonkit to 0.9 (#46275) * Update pytaxonkit to 0.9 * Pin new minimum taxonkit version * Add run_exports * restrict python to <3.12 --------- Co-authored-by: Daniel Standage Co-authored-by: mencian --- recipes/pytaxonkit/meta.yaml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/recipes/pytaxonkit/meta.yaml b/recipes/pytaxonkit/meta.yaml index 2f82b3f837c92..8da2b003b8ae3 100644 --- a/recipes/pytaxonkit/meta.yaml +++ b/recipes/pytaxonkit/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8" %} -{% set sha256 = "414793a8ddc40c03c8c63512114c613153b31ff4c7da1feb015c2f3191f4d8d0" %} +{% set version = "0.9" %} +{% set sha256 = "539ae750fef3d213b669645359dbd4758e28950981a72a35755a852cd8f50358" %} package: name: pytaxonkit @@ -10,19 +10,21 @@ source: sha256: '{{sha256}}' build: + run_exports: + - {{ pin_subpackage("pytaxonkit", max_pin="x.x") }} noarch: python - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv number: 0 requirements: host: - - python >=3 + - python >=3,<3.12 - pip run: - - python >=3 + - python >=3,<3.12 - pandas >=1.0 - pytest >=5.4 - - taxonkit >=0.8 + - taxonkit >=0.16 test: imports: @@ -33,11 +35,13 @@ test: about: home: https://github.com/bioforensics/pytaxonkit/ - license: BSD License + license: BSD-3-Clause license_family: BSD + license_file: LICENSE summary: Python bindings for the TaxonKit library. dev_url: https://github.com/bioforensics/pytaxonkit/ extra: recipe-maintainers: - standage + - RyanBerger98 From 8e42d81d87358b91840411dbbd7a56ed29fcb55e Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Mon, 11 Mar 2024 16:14:13 +0100 Subject: [PATCH 0861/1813] Update ms2rescore: Constraint pyteomics version (#46301) * Bump ms2pip version and build * Fix pyteomics version to prevent issues with most recent version * bump build number --- recipes/ms2rescore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index dd671a696bd85..c9fd49da47b4d 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c016f64d76cc0fc6d3ed691d1d8350d2d6e52da5e84e4fc258f4445264a4b9ad build: - number: 1 + number: 2 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -30,7 +30,7 @@ requirements: - numpy >=1.16.0 - pandas >=1.0 - rich >=12 - - pyteomics >=4.1.0 + - pyteomics >=4.1.0,<=4.6.3 - pyopenms - lxml >=4.5 - ms2pip >=4.0.0-dev8 From 23cc206e8ff44c83c03d2ffccf013ddf8b5cd18b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 13:42:15 -0400 Subject: [PATCH 0862/1813] Update thapbi-pict to 1.0.12 (#46316) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 234e1a3470a50..3d0df49663cbd 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.11" %} +{% set version = "1.0.12" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: d0f087d07b584a5a6e5aa9a6a077cfc60a339f3f37c43e09343adda41beadcc2 + sha256: 638c8d11b5071895381fcb5cf59f8cbe4dc1b2426f796f636131dcd3e63f55c4 build: noarch: python From 64f23d6819a8aa60109dec8ee19449e96d51e310 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 16:55:49 -0400 Subject: [PATCH 0863/1813] Update snakemake-interface-executor-plugins to 9.0.0 (#46319) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index a52840165b3ea..aeea231e43ace 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "8.2.0" %} +{% set version = "9.0.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: 4c74e3e1751bab6b266baf8688e854b8b4c5c5e10f5e34c581f42d69af4ff13b + sha256: 22b7337d9ea4f9e32679b96fa873337608d73f2d41443cc6bde18de4549acdb7 build: noarch: python From 8723bf9c45e49eff6144411d45d18596c1d6f41b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 17:01:36 -0400 Subject: [PATCH 0864/1813] Update vcfdist to 2.5.0 (#46318) --- recipes/vcfdist/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vcfdist/meta.yaml b/recipes/vcfdist/meta.yaml index bd4e85ad61cf7..855ce4f6f418c 100644 --- a/recipes/vcfdist/meta.yaml +++ b/recipes/vcfdist/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.4.0" %} -{% set sha256 = "bdb1bc84229f2bb81c9a4b5ee005b4f586895c320f504fbd1f983a0ef1cd6bb6" %} +{% set version = "2.5.0" %} +{% set sha256 = "d48c95902c9a700049003018ae28a9684d6b320235cf152f418a544f63aa6e7d" %} package: name: vcfdist From 2a8f37ed5c14f5dd838030ad98385cf719603834 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 17:01:44 -0400 Subject: [PATCH 0865/1813] Update tissuumaps to 3.2.1.2 (#46307) --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index 92de96039697b..d1bb21fe16d35 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.1.1" %} +{% set version = "3.2.1.2" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 2367069c3855165f3757079f9b248385003ef8fe7ab2ccf2738493475c11ff76 + sha256: 5565f8abb5d1cde13dd6a1daa19c8fbff6bc69f49247ae0d95208352b1212a5c build: number: 0 From 791baff76410688fde0f2b47d24afa7a96e11ce2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 17:01:56 -0400 Subject: [PATCH 0866/1813] Update bamdash to 0.2.4 (#46299) --- recipes/bamdash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bamdash/meta.yaml b/recipes/bamdash/meta.yaml index 549a5ab5d04bd..2a77d75331151 100644 --- a/recipes/bamdash/meta.yaml +++ b/recipes/bamdash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bamdash" %} -{% set version = "0.2.3" %} +{% set version = "0.2.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/bamdash-{{ version }}.tar.gz - sha256: da43cd3539ba86b4d2800aded8a3361ba34f325f803b5acd2991c69473c0f398 + sha256: 9e9d81cb5cefbb2f356d1a1e05ffc84bcaee0cfbfd16b5e92d905817337ea4e8 build: entry_points: From 5c897b9774227c625708855c9a390c99f0f56a37 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 17:02:15 -0400 Subject: [PATCH 0867/1813] Update metacache to 2.4.2 (#46297) * Update metacache to 2.4.1 * Update metacache to 2.4.2 --- recipes/metacache/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metacache/meta.yaml b/recipes/metacache/meta.yaml index d06a2a2a03ea6..6960be24fcb92 100644 --- a/recipes/metacache/meta.yaml +++ b/recipes/metacache/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.4.0" %} +{% set version = "2.4.2" %} package: name: metacache @@ -6,7 +6,7 @@ package: source: url: https://github.com/muellan/metacache/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8d5eea5aedd6ce36befef0371cf5906533a70ed17e1e12d7cd26658673f7d954 + sha256: 2062de4c13cc9ed3962c8903b81dca05ccabd5820305362229bc446c11c9b111 build: number: 0 From 63403e8573157ea116fca4799332f23dae7c8e62 Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Mon, 11 Mar 2024 21:33:32 +0000 Subject: [PATCH 0868/1813] Update SeqKit to v2.8.0 (#46317) --- recipes/seqkit/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index a3be4a4ee909e..7d426309ab185 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.7.0" %} +{% set version = "2.8.0" %} package: name: seqkit @@ -6,10 +6,10 @@ package: source: url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx] - md5: 2d0bd16060b100c90abd216eaf6c9947 # [osx] + md5: f8310b1ff14e49c7506080e75d97e5dc # [osx] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux] - md5: 78311f53ecebbcd4acd5455ae46debbe # [linux] + md5: d53457672a8f7873bc17698bad9e8514 # [linux] build: number: 0 From bfbb53148d623ca28bcf6b10962ceb4ad45fbc65 Mon Sep 17 00:00:00 2001 From: richard-burhans Date: Mon, 11 Mar 2024 18:00:55 -0400 Subject: [PATCH 0869/1813] segalign-full does not need twoBitToFa (#46279) Co-authored-by: Richard C. Burhans --- recipes/segalign-full/meta.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/recipes/segalign-full/meta.yaml b/recipes/segalign-full/meta.yaml index ef44b90632061..ead1a962ea78a 100644 --- a/recipes/segalign-full/meta.yaml +++ b/recipes/segalign-full/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_compatible('segalign-full', max_pin='x.x') }} @@ -15,7 +15,6 @@ requirements: - segalign - lastz - ucsc-fatotwobit - - ucsc-twobittofa test: commands: @@ -23,7 +22,6 @@ test: - segalign_repeat_masker --help - lastz --version 2>&1 | grep released - which faToTwoBit - - which twoBitToFa about: home: https://github.com/gsneha26/SegAlign From 897545c6e56bd8d397aaeb9a5f984a497c1e163a Mon Sep 17 00:00:00 2001 From: Timofey Prodanov Date: Mon, 11 Mar 2024 23:03:43 +0100 Subject: [PATCH 0870/1813] Add Locityper (#46269) * Add Locityper recipe * Add build number and run_export * Fix minor mistake in meta.yaml * Update summary * Add more dependencies * Add libclang dependency * Try clangdev * Add openmp dep * Remove comments and host section --- recipes/locityper/build.sh | 13 ++++++++++++ recipes/locityper/meta.yaml | 41 +++++++++++++++++++++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 recipes/locityper/build.sh create mode 100644 recipes/locityper/meta.yaml diff --git a/recipes/locityper/build.sh b/recipes/locityper/build.sh new file mode 100644 index 0000000000000..0563cd7748405 --- /dev/null +++ b/recipes/locityper/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash -euo + +if [ "$(uname)" == "Darwin" ]; then + export HOME="/Users/distiller" + export HOME=`pwd` +fi + +export C_INCLUDE_PATH="$BUILD_PREFIX/include:$C_INCLUDE_PATH" +export LIBRARY_PATH="$BUILD_PREFIX/lib:$LIBRARY_PATH" + +git clone https://github.com/smarco/WFA2-lib WFA2 +cargo install --no-track --verbose --root "${PREFIX}" --path . + diff --git a/recipes/locityper/meta.yaml b/recipes/locityper/meta.yaml new file mode 100644 index 0000000000000..556ab0c9d5398 --- /dev/null +++ b/recipes/locityper/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "0.13.4" %} + +package: + name: locityper + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("locityper", max_pin="x.x") }} + +source: + url: https://github.com/tprodanov/locityper/archive/refs/tags/v{{ version }}.tar.gz + sha256: 2e7290d6a6a63f594906de02a30e3f1f1e495bbb5f99640ac66708ac37c1113e + +requirements: + build: + - {{ compiler('rust') }} + - {{ compiler('cxx') }} + - cmake + - make + - clangdev + - llvm-openmp + run: + - samtools >=1.18 + - jellyfish >=1.0 + - minimap2 >=2.25 + - strobealign >=0.12 + - python + - pysam + +test: + commands: + - locityper version + +about: + summary: Targeted genotyper for complex polymorphic loci from short and long read WGS. + home: https://github.com/tprodanov/locityper + license: MIT + license_file: LICENSE + From 52d882265adb01fb13bb99c6ba1dcde8a57020c6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 18:14:53 -0400 Subject: [PATCH 0871/1813] Update snakemake-executor-plugin-cluster-generic to 1.0.9 (#46320) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake-executor-plugin-cluster-generic to 1.0.9 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake-executor-plugin-cluster-generic/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml b/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml index 58af4c99df718..a49c5bcab174a 100644 --- a/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml +++ b/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-cluster-generic" %} -{% set version = "1.0.8" %} +{% set version = "1.0.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_cluster_generic-{{ version }}.tar.gz - sha256: 707890e9752a8b711c42fb454430d42a58f39f8cf28ac16e87fe0387b19a29bb + sha256: ad0dc2d8bde7d4f336364bebe11a3b2209653c481ce8fbb0ae8bec81016a9a14 build: noarch: python @@ -23,7 +23,7 @@ requirements: - pip run: - python >=3.11.0,<4.0.0 - - snakemake-interface-executor-plugins >=8.1.0,<9.0.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 - snakemake-interface-common >=1.13.0,<2.0.0 test: From b2b8e6efa59d78a695d284a2871cd4a7e4572ffb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 18:26:17 -0400 Subject: [PATCH 0872/1813] Update snakemake-executor-plugin-slurm-jobstep to 0.1.11 (#46324) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake-executor-plugin-slurm-jobstep to 0.1.11 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml b/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml index 0674423f6262c..6c518d608ee27 100644 --- a/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm-jobstep" %} -{% set version = "0.1.10" %} +{% set version = "0.1.11" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm_jobstep-{{ version }}.tar.gz - sha256: 321b6bdf7883a8fb40ff4aeeb88633502e4db8394e40b6628db41a430c2eae2b + sha256: cafdac937796ab0dfc0354c42380167a44a1db00c4edc98ab736a6ace2201a94 build: noarch: python @@ -24,7 +24,7 @@ requirements: run: - python >=3.11.0,<4.0.0 - snakemake-interface-common >=1.13.0,<2.0.0 - - snakemake-interface-executor-plugins >=8.2.0,<9.0.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 test: imports: From e7857d1feed9e821eff2c25c0a59a6dbc974d5e8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 18:26:33 -0400 Subject: [PATCH 0873/1813] Update snakemake to 8.6.0 (#46322) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake to 8.6.0 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index db57d5f200241..330e389b6dcb9 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.5.5" %} +{% set version = "8.6.0" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: a6e962ea72a060a6541253db59d3f1f44d52b6cac1bb1282a6f1e5cf11b3929f + sha256: dafcd6e6aab257f6712ab7e9931164e7114a96a3b83cb0d97effd8db7b2d3295 build: number: 0 @@ -101,7 +101,7 @@ outputs: - requests >=2.8.1 - reretry - smart_open >=3.0,<4.0 - - snakemake-interface-executor-plugins >=8.1.3,<9.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 - snakemake-interface-common >=1.17.0,<2.0 - snakemake-interface-storage-plugins >=3.1.0,<4.0 - snakemake-interface-report-plugins >=1.0.0,<2.0.0 From 8ba6e4052afaba7e0b8a6fd61a8bd8677e6420b4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 21:12:46 -0400 Subject: [PATCH 0874/1813] Update liftover to 1.2.2 (#46315) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/liftover/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/liftover/meta.yaml b/recipes/liftover/meta.yaml index 4fee1d42574a2..8c484a1d7355b 100644 --- a/recipes/liftover/meta.yaml +++ b/recipes/liftover/meta.yaml @@ -1,6 +1,6 @@ {% set name = "liftover" %} -{% set version = "1.2.1" %} -{% set sha256 = "43d89d929288b0f2031f6200958a920d6ec71a0929a91abcfd73b15032f20116" %} +{% set version = "1.2.2" %} +{% set sha256 = "f858aed016227882263d369969790adf6df2c07399e16f063aec8a248a2b4513" %} package: name: {{ name|lower }} From 364367806e2acd378df6ccca5fc4a1c4d2ead303 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 21:13:06 -0400 Subject: [PATCH 0875/1813] Update phykit to 1.17.0 (#46326) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index d23e0a568312f..c762c75156615 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.16.0" %} +{% set version = "1.17.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7f89a7680d012d756a20f26d395c90ad0b7bd084ee05911da955241611e94656 + sha256: eb4087ff616aeb8935016f2f5b929fe49731190e99d6c4df89da2f49252bdd2a build: noarch: python From 71f828267efbf949424b9387a06b09d810dda362 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 21:13:42 -0400 Subject: [PATCH 0876/1813] Update baredsc to 1.1.3 (#46327) --- recipes/baredsc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/baredsc/meta.yaml b/recipes/baredsc/meta.yaml index d9b7c9290d414..3816c34d391ee 100644 --- a/recipes/baredsc/meta.yaml +++ b/recipes/baredsc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "baredSC" %} -{% set version = "1.1.2" %} +{% set version = "1.1.3" %} package: name: {{ name | lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/lldelisle/baredSC/archive/v{{ version }}.tar.gz - sha256: 9c1ac38cebdb6e9183ee208f86021e3c80bbd98a3bff8a078327c4c8420f4fba + sha256: 96b4eee8d959ab4d30350ae7ac91d89501bb7175ab4c3bd3e3e9ff6b0c1dcfcf build: number: 0 From 42f36a97b7bed1dd184c8c271dc90e88f5bb2706 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 21:39:09 -0400 Subject: [PATCH 0877/1813] Update bioframe to 0.6.2 (#46329) --- recipes/bioframe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioframe/meta.yaml b/recipes/bioframe/meta.yaml index 81590d40e0556..0080c41f04ada 100644 --- a/recipes/bioframe/meta.yaml +++ b/recipes/bioframe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioframe" %} -{% set version = "0.6.1" %} +{% set version = "0.6.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 63aec69ac37aebcdc8298ed41154a875ba99652cc7ef081dd1458bc90537f73b + sha256: b9519206115ae435c18ec57f9ae49768851202684949caa7d183ac76f812e5c7 build: noarch: python From 5c76fe8dbe8b21f0af40f20b29feacd5db13c7b8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 21:39:17 -0400 Subject: [PATCH 0878/1813] Update snakemake-executor-plugin-slurm to 0.4.2 (#46323) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake-executor-plugin-slurm to 0.4.2 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index ed2edf2bc4eb0..57c874c53a5b3 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: bd05fd3908530cb3d542090ee4123de8d7515082f48b37bded6339f1967e43d6 + sha256: 265ffff24cdaa7929769bdbe822c39d8ac059b0642e92fc6fa9e55c9cdc7d018 build: noarch: python @@ -24,7 +24,7 @@ requirements: run: - python >=3.11.0,<4.0.0 - snakemake-interface-common >=1.13.0,<2.0.0 - - snakemake-interface-executor-plugins >=8.2.0,<9.0.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 - snakemake-executor-plugin-slurm-jobstep >=0.1.10,<0.2.0 - throttler >=1.2.2,<2.0.0 From 86d66854001c546d1c816a84d13d2348ca44d705 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Mar 2024 23:55:17 -0400 Subject: [PATCH 0879/1813] Update bioframe to 0.6.3 (#46330) --- recipes/bioframe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioframe/meta.yaml b/recipes/bioframe/meta.yaml index 0080c41f04ada..50aa16011fa1f 100644 --- a/recipes/bioframe/meta.yaml +++ b/recipes/bioframe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioframe" %} -{% set version = "0.6.2" %} +{% set version = "0.6.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b9519206115ae435c18ec57f9ae49768851202684949caa7d183ac76f812e5c7 + sha256: dfc1e94ae7bbd22e8fe1bb80b28ff4d1fcd6ce791e1166a64a8e7b6db08d61ff build: noarch: python From 56308b04aa92cbbe4af394c428a6b55d7b2b7185 Mon Sep 17 00:00:00 2001 From: Niema Moshiri Date: Mon, 11 Mar 2024 21:41:17 -0700 Subject: [PATCH 0880/1813] Update viralmsa meta.yaml (#46311) * Update meta.yaml * Bumping build number --- recipes/viralmsa/meta.yaml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 7f8cf82f1cbac..acbbb36202cf5 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -6,7 +6,7 @@ package: build: noarch: python - number: 0 + number: 1 run_exports: - {{ pin_subpackage('viralmsa', max_pin="x.x.x") }} @@ -38,3 +38,10 @@ about: test: commands: - ViralMSA.py -h + +extra: + identifiers: + - biotools:viralmsa + - doi:10.1093/bioinformatics/btaa743 + maintainers: + - niemasd From 44f254d2668173acda047b9224f5b0c4e542bcca Mon Sep 17 00:00:00 2001 From: Niema Moshiri Date: Mon, 11 Mar 2024 21:41:55 -0700 Subject: [PATCH 0881/1813] Update viral_consensus meta.yaml (#46310) * Update meta.yaml * Bumping build number --- recipes/viral_consensus/meta.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/viral_consensus/meta.yaml b/recipes/viral_consensus/meta.yaml index a326221063cdd..873dff8a59be7 100644 --- a/recipes/viral_consensus/meta.yaml +++ b/recipes/viral_consensus/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('viral_consensus', max_pin="x.x.x") }} @@ -33,6 +33,11 @@ about: test: commands: - viral_consensus --version + +extra: identifiers: + - biotools:viral_consensus - doi:10.1093/bioinformatics/btad317 - doi:10.1093/bioinformatics/btae018 + maintainers: + - niemasd From 61d11cd98e14d8e19ec9626e3734a1e909fa81c2 Mon Sep 17 00:00:00 2001 From: Niema Moshiri Date: Mon, 11 Mar 2024 21:43:57 -0700 Subject: [PATCH 0882/1813] Update meta.yaml (#46314) --- recipes/tn93/meta.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/tn93/meta.yaml b/recipes/tn93/meta.yaml index 37df7d1f5e9e2..dd0aa8184536d 100644 --- a/recipes/tn93/meta.yaml +++ b/recipes/tn93/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 58f26807cd762cfc5cb6f088b57dfb26c69e8dd8e59a3e3db42a51ddea03bb3c build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('tn93', max_pin="x") }} @@ -32,3 +32,8 @@ about: license_family: MIT license_file: LICENSE summary: This is a simple program meant to compute pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance. + +extra: + identifiers: + - biotools:tn93 + - doi:10.1093/molbev/msy016 From 234b5be021d8274080d586d568a41d33ceed89ee Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Tue, 12 Mar 2024 05:46:08 +0100 Subject: [PATCH 0883/1813] perl-digest-sha1: enable linux-aarch64 builds (#46302) * perl-digest-sha1: enable linux-aarch64 builds * Add run_exports * Bugfix --- recipes/perl-digest-sha1/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/perl-digest-sha1/meta.yaml b/recipes/perl-digest-sha1/meta.yaml index ecd9d4fc4b247..26ad2a3951131 100644 --- a/recipes/perl-digest-sha1/meta.yaml +++ b/recipes/perl-digest-sha1/meta.yaml @@ -11,7 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: @@ -33,3 +35,7 @@ about: home: http://metacpan.org/pod/Digest::SHA1 license: perl_5 summary: 'Perl interface to the SHA-1 algorithm' + +extra: + additional-platforms: + - linux-aarch64 From 2a1681ec2238da35ace37b16a6c0dbc58d894cd2 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 12 Mar 2024 00:06:44 -0500 Subject: [PATCH 0884/1813] Update MACS3 recipe to build on python 3.9 (#46333) --- recipes/macs3/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/macs3/meta.yaml b/recipes/macs3/meta.yaml index c84af572f5f43..53b070ffb72c9 100644 --- a/recipes/macs3/meta.yaml +++ b/recipes/macs3/meta.yaml @@ -11,9 +11,9 @@ source: git_rev: 34f9a81398ec2af78317cd0b128f3a1e52a68f17 build: - number: 1 - skip: True # [py < 310] - script: python3 -m pip install . --no-deps --ignore-installed -vvv + number: 2 + skip: True # [py < 39] + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv run_exports: - {{ pin_subpackage('macs3', max_pin="x.x") }} From fe7454fb867f979da677cd33fea8e85fbb10cb02 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 01:10:18 -0400 Subject: [PATCH 0885/1813] Update aviary to 0.9.0 (#46331) * Update aviary to 0.9.0 * add entry_points --------- Co-authored-by: mencian --- recipes/aviary/meta.yaml | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/recipes/aviary/meta.yaml b/recipes/aviary/meta.yaml index eba258abc566c..72560874ce8f3 100644 --- a/recipes/aviary/meta.yaml +++ b/recipes/aviary/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "0.8.3" %} +{% set version = "0.9.0" %} {% set name = "aviary" %} -{% set sha256 = "c484f2bef8ac783e2fbb93270b8a8e034e1139eef2bf641ccfa3a4f17e78abcb" %} +{% set sha256 = "60a13bc4b5053dda041a2f2f677eb518c454b88225b53431dc65ae6ff0f2baa9" %} package: name: aviary version: {{ version }} +source: + url: https://github.com/rhysnewell/{{ name }}/releases/download/v{{ version }}/aviary-genome-{{ version }}.tar.gz + sha256: {{ sha256 }} + build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + entry_points: + - aviary = aviary.aviary:main run_exports: - - {{ pin_subpackage('aviary', max_pin="x") }} - -source: - url: https://github.com/rhysnewell/{{ name }}/releases/download/v{{ version }}/aviary-genome-{{ version }}.tar.gz - sha256: {{ sha256 }} + - {{ pin_subpackage('aviary', max_pin="x.x") }} requirements: host: - - python >=3.8 + - python >=3.8,<3.12 - pip run: - - python >=3.8,<=3.11 - - snakemake >=7.0.0,<=7.32.3 + - python >=3.8,<3.12 + - snakemake-minimal >=7.0.0,<=7.32.3 - ruamel.yaml >=0.15.99 - numpy - pandas @@ -41,11 +43,12 @@ test: about: home: https://github.com/rhysnewell/aviary/ doc_url: https://rhysnewell.github.io/aviary/ - license: GPL3 + dev_url: https://github.com/rhysnewell/aviary/ + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: End-to-end metagenomics hybrid assembly and binning pipeline. description: | Aviary is an easy to use hybrid assembler and metagenomic pipeline For more details see documentation: https://rhysnewell.github.io/aviary/. - From 5ff4cd1fbae712abb216e81ddc162d1a870758b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 01:41:54 -0400 Subject: [PATCH 0886/1813] Update wgd to 2.0.27 (#46334) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index 106a69c3b0845..039ed9ad26df7 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.26" %} +{% set version = "2.0.27" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: eca2e580095b1857868a31fb58b02eb886e0de500569afa44930e8469bb1c12d + sha256: c596d18d59621194ba3d7db2e40c04ef302c376b2d1349e9ef2fde21938beec7 build: number: 0 From 3e29a1a5961763278b5ee47ba10112187fa6a9cd Mon Sep 17 00:00:00 2001 From: Leonid Kostrykin Date: Tue, 12 Mar 2024 09:28:39 +0100 Subject: [PATCH 0887/1813] Add `orientationpy` recipe (#46321) --- recipes/orientationpy/build.sh | 3 +++ recipes/orientationpy/meta.yaml | 44 +++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 recipes/orientationpy/build.sh create mode 100644 recipes/orientationpy/meta.yaml diff --git a/recipes/orientationpy/build.sh b/recipes/orientationpy/build.sh new file mode 100644 index 0000000000000..9b117d644a325 --- /dev/null +++ b/recipes/orientationpy/build.sh @@ -0,0 +1,3 @@ +#!/usr/bin/env bash + +"${PYTHON}" -m pip install --no-deps --ignore-installed --no-cache-dir -vvv *.whl diff --git a/recipes/orientationpy/meta.yaml b/recipes/orientationpy/meta.yaml new file mode 100644 index 0000000000000..11b7b6ed31b4b --- /dev/null +++ b/recipes/orientationpy/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "orientationpy" %} +{% set version = "0.2.0.4" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: "https://files.pythonhosted.org/packages/0a/f5/ab88217f2b8a14bf10959de073d0fb2ca631c6ca00a953184cefec66a003/orientationpy-{{ version }}-py3-none-any.whl" + sha256: 918654b71c28824c0b19f67d4a9fb20d45f72f41566dc51d63f835076f7cd744 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + host: + - python >=3.8 + - pip + run: # see https://gitlab.com/epfl-center-for-imaging/orientationpy/-/blob/main/pyproject.toml?ref_type=heads#L32 + - python >=3.8 + - matplotlib-base >=3.1.3 + - numpy + - scipy + - numba + - numba-progress + +test: + commands: + - python -c "import orientationpy" + +about: + home: "https://pypi.org/project/orientationpy" + license: GNU General Public License v3 (GPL-3.0) + license_family: GPL + summary: "OrientationPy is the pythonic successor to the well-loved OrientationJ Fiji Plugin. It is a library that takes in 2D images or 3D volumes and computes the orientation of the greylevels." + dev_url: "https://gitlab.com/epfl-center-for-imaging/orientationpy" + doc_url: "https://epfl-center-for-imaging.gitlab.io/orientationpy/introduction.html" + +extra: + recipe-maintainers: + - kostrykin From 718fe126e7fe619fd4d11c42832a01e95c1a9946 Mon Sep 17 00:00:00 2001 From: Brian Fulton-Howard Date: Tue, 12 Mar 2024 04:35:25 -0400 Subject: [PATCH 0888/1813] Add Snakemake 8 executor plugins for LSF (#46328) * add Snakemake 8 executor plugins for LSF * add run_exports for linter --- .../meta.yaml | 41 ++++++++++++++++++ .../snakemake-executor-plugin-lsf/meta.yaml | 43 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 recipes/snakemake-executor-plugin-lsf-jobstep/meta.yaml create mode 100644 recipes/snakemake-executor-plugin-lsf/meta.yaml diff --git a/recipes/snakemake-executor-plugin-lsf-jobstep/meta.yaml b/recipes/snakemake-executor-plugin-lsf-jobstep/meta.yaml new file mode 100644 index 0000000000000..27f1ea3595b3f --- /dev/null +++ b/recipes/snakemake-executor-plugin-lsf-jobstep/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "snakemake-executor-plugin-lsf-jobstep" %} +{% set version = "0.1.10" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_lsf_jobstep-{{ version }}.tar.gz + sha256: 72d29f3cd22061a61f138bba0ab6803b3fb7017f9475276acfa40ad20d23f44d + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.17.1,<2.0.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 + +test: + imports: + - snakemake_executor_plugin_lsf_jobstep + +about: + home: https://github.com/BEFH/snakemake-executor-plugin-lsf-jobstep + summary: A Snakemake executor plugin for running bjobs jobs inside of LSF jobs (meant for internal use by snakemake-executor-plugin-lsf) + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - BFH diff --git a/recipes/snakemake-executor-plugin-lsf/meta.yaml b/recipes/snakemake-executor-plugin-lsf/meta.yaml new file mode 100644 index 0000000000000..fef6a217b9517 --- /dev/null +++ b/recipes/snakemake-executor-plugin-lsf/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "snakemake-executor-plugin-lsf" %} +{% set version = "0.2.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_lsf-{{ version }}.tar.gz + sha256: 2e03b98b29cf1469add3114046b5a1662e07879a8606914f4fe4c01f1fd53aea + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.17.1,<2.0.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 + - snakemake-executor-plugin-lsf-jobstep >=0.1.10,<0.2.0 + - throttler >=1.2.2,<2.0.0 + +test: + imports: + - snakemake_executor_plugin_lsf + +about: + home: https://github.com/befh/snakemake-executor-plugin-lsf + summary: A Snakemake executor plugin for submitting jobs to a LSF cluster. + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - BEFH From 98db16b8c79ea9a1876a095f263099fc77001771 Mon Sep 17 00:00:00 2001 From: Matt McGuffie Date: Tue, 12 Mar 2024 01:36:06 -0700 Subject: [PATCH 0889/1813] Update plannotate patch version (#46293) --- recipes/plannotate/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/plannotate/meta.yaml b/recipes/plannotate/meta.yaml index 37eeb74fca738..ebb56cfdfd40c 100644 --- a/recipes/plannotate/meta.yaml +++ b/recipes/plannotate/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: plannotate @@ -7,10 +7,12 @@ package: build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('plannotate', max_pin="x") }} source: - url: https://github.com/mmcguffi/pLannotate/archive/refs/tags/v{{version}}.tar.gz - sha256: 7525ca5fa0309b4a579e46a6f9e167ed86751f7d3d07aba2c9d0468c53bcbaed + sha256: 423ad78a90d2fa13eed538b2ecdd939342388a5137b75de0c5d50c12974be3d6 - url: https://github.com/mmcguffi/pLannotate/releases/download/v1.2.0/BLAST_dbs.tar.gz sha256: 34c7bacb1c73bd75129e16990653f73b3eba7e3cdb3816a55d3989a7601f2137 folder: BLAST_dbs @@ -26,7 +28,7 @@ requirements: - biopython >=1.78 - blast >=2.10.1 - diamond >=2.0.13 - - pandas >=1.3.5 + - pandas >=1.3.5,<2.0.0 - python >=3.9 - ripgrep >=13.0.0 - tabulate >=0.8.9 From f81026ca7fcf188c0e447111b4e8c2c7079d0cca Mon Sep 17 00:00:00 2001 From: Jens-Uwe Ulrich <46562264+JensUweUlrich@users.noreply.github.com> Date: Tue, 12 Mar 2024 10:19:49 +0100 Subject: [PATCH 0890/1813] update taxor to version 0.1.2 (#46339) --- recipes/taxor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxor/meta.yaml b/recipes/taxor/meta.yaml index cc994c4012da7..b7846fe6d4640 100755 --- a/recipes/taxor/meta.yaml +++ b/recipes/taxor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: taxor @@ -6,7 +6,7 @@ package: source: url: https://github.com/JensUweUlrich/Taxor/archive/refs/tags/{{ version }}.tar.gz # [linux] - md5: ad6a34b6c3d2c114bed5181af8f69ad3 # [linux] + md5: 9c4ce8562b17c21035433233ceb98d66 # [linux] build: number: 0 From f606ad49c3c1a857818e8b2b3462fddf579ca02b Mon Sep 17 00:00:00 2001 From: John Lees Date: Tue, 12 Mar 2024 10:36:59 +0000 Subject: [PATCH 0891/1813] Bump poppunk to v2.6.4 (#46343) --- recipes/poppunk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index 57b87d23fbd98..fe463f0193781 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.6.3" %} +{% set version = "2.6.4" %} {% set name = "PopPUNK" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 4a305da07482a8d500213823b29c48b9be5465194f25beae53ee986f0ae111d0 + sha256: 3cbedaea29807752e008f627d916d035a2c75522de19ea5a0b9c447d558f0e70 build: number: 0 From 2e6c0e8866c08fbca3c2ae699ccd2159c3ed77b3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 07:06:01 -0400 Subject: [PATCH 0892/1813] Update snakemake-executor-plugin-googlebatch to 0.3.1 (#46352) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake-executor-plugin-googlebatch to 0.3.1 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake-executor-plugin-googlebatch/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml index 1cc605247f4ba..fce87b3ef78b0 100644 --- a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml +++ b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml @@ -1,5 +1,6 @@ {% set name = "snakemake-executor-plugin-googlebatch" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} +# Upon version update, requirements have to be checked! package: name: {{ name|lower }} @@ -7,14 +8,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_googlebatch-{{ version }}.tar.gz - sha256: b143fcaeffceec682bc0f7e3f13eece3596a5d6faaf41fab94977f4a93948c16 + sha256: 292c024534e98aecf6a5a2be8a24db104d8038831b6a55fe50c87c1e4fdb28af build: noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 run_exports: - - {{ pin_subpackage(name, max_pin='x') }} + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: host: @@ -28,7 +29,7 @@ requirements: - google-api-core >=2.12.0,<3.0.0 - google-cloud-storage >=2.12.0,<3.0.0 - snakemake-interface-common >=1.14.0,<2.0.0 - - snakemake-interface-executor-plugins >=8.1.1,<9.0.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 - jinja2 >=3.1.2,<4.0.0 - google-cloud-logging >=3.8.0,<4.0.0 From 53a938f6ca544e2922a2891b6370a0a41d5cfb3e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 07:08:08 -0400 Subject: [PATCH 0893/1813] Update snakemake-executor-plugin-cluster-sync to 0.1.4 (#46351) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake-executor-plugin-cluster-sync to 0.1.4 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake-executor-plugin-cluster-sync/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-executor-plugin-cluster-sync/meta.yaml b/recipes/snakemake-executor-plugin-cluster-sync/meta.yaml index 8c85124cc99e3..04a8c2b648553 100644 --- a/recipes/snakemake-executor-plugin-cluster-sync/meta.yaml +++ b/recipes/snakemake-executor-plugin-cluster-sync/meta.yaml @@ -1,5 +1,6 @@ {% set name = "snakemake-executor-plugin-cluster-sync" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} +# Upon version update, requirements have to be checked! package: name: {{ name|lower }} @@ -7,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_cluster_sync-{{ version }}.tar.gz - sha256: c30fca6ccb98a3f7ca52ca8a95414c71360a3d4a835bd4a097a13445d6fce2ac + sha256: 6a6dcb2110d4c2ee74f9a48ea68e0fd7ddd2800672ebef00a01faa4affa835ad build: noarch: python @@ -24,7 +25,7 @@ requirements: run: - python >=3.11.0,<4.0.0 - snakemake-interface-common >=1.14.0,<2.0.0 - - snakemake-interface-executor-plugins >=8.1.0,<9.0.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 test: imports: From 1cd50655be3ab4d31e1676d2b1068de35362ab5d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 07:14:08 -0400 Subject: [PATCH 0894/1813] Update snakemake-executor-plugin-kubernetes to 0.1.5 (#46350) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake-executor-plugin-kubernetes to 0.1.5 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake-executor-plugin-kubernetes/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/snakemake-executor-plugin-kubernetes/meta.yaml b/recipes/snakemake-executor-plugin-kubernetes/meta.yaml index c355b079a0b3e..c4ffe95046b1e 100644 --- a/recipes/snakemake-executor-plugin-kubernetes/meta.yaml +++ b/recipes/snakemake-executor-plugin-kubernetes/meta.yaml @@ -1,5 +1,6 @@ {% set name = "snakemake-executor-plugin-kubernetes" %} -{% set version = "0.1.4" %} +{% set version = "0.1.5" %} +# Upon version update, requirements have to be checked! package: name: {{ name|lower }} @@ -7,14 +8,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_kubernetes-{{ version }}.tar.gz - sha256: c3aeac87939ec5d038efdc3ba7dbbef5eeb3171c1b718b8af850b6287b9c54ff + sha256: 7984ef057c25ce1ff46ceac5839dfad01e2938faa649e59fa439e8154e8025eb build: noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 run_exports: - - {{ pin_subpackage(name, max_pin='x') }} + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: host: @@ -24,7 +25,7 @@ requirements: run: - python >=3.11.0,<4.0.0 - snakemake-interface-common >=1.14.1,<2.0.0 - - snakemake-interface-executor-plugins >=8.0.2,<9.0.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 - python-kubernetes >=27.2.0,<28.0.0 test: From f0e9955b14b562d4df79fca7b305ab83ee7b8b47 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 08:33:57 -0400 Subject: [PATCH 0895/1813] Update r-cellosaurus to 0.8.2 (#46325) --- recipes/r-cellosaurus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-cellosaurus/meta.yaml b/recipes/r-cellosaurus/meta.yaml index 0a6c31bd625d5..303e14d510275 100644 --- a/recipes/r-cellosaurus/meta.yaml +++ b/recipes/r-cellosaurus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.1" %} +{% set version = "0.8.2" %} {% set github = "https://github.com/acidgenomics/r-cellosaurus" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: c18ed889a603e15332afdc71cd7fb1ab13701fe892e5247c55ba6fbb630c2677 + sha256: 83d730b19dfe21ca7447d8eaf674b991010300918bb17dad70f25458617b33a3 build: noarch: generic From 2bd42537a98b5b4ea6c3984aa7fc209901913b41 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 14:04:28 -0400 Subject: [PATCH 0896/1813] Update physiofit to 3.3.4 (#46353) --- recipes/physiofit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/physiofit/meta.yaml b/recipes/physiofit/meta.yaml index 3234da2c1b2b8..090a51968a5a4 100644 --- a/recipes/physiofit/meta.yaml +++ b/recipes/physiofit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "physiofit" %} -{% set version = "3.3.3" %} +{% set version = "3.3.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/physiofit-{{ version }}.tar.gz - sha256: a3d16abf8a3da9eb6deacd8ff73a48c21fc22972033bd14afc7edb7cea8fad05 + sha256: 03b5e801096d9622429944ee4987ad404ffbf301db7167071f9e92d6b7c9e1f3 build: entry_points: From 8f9427ef28c568c3a6812ba50285605b7b9fb9cd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 14:25:32 -0400 Subject: [PATCH 0897/1813] Update pyhmmer to 0.10.9 (#46370) --- recipes/pyhmmer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 444948bed41dd..113bc216794fa 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.8" %} +{% set version = "0.10.9" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b9360a2a97705bbcf4bdf5797241193e0cd81aa384a5d2b2ff5be5b5135c9632 + sha256: c78c6f547fb3e37f537d7f87d543e4c61584e688023d0f004107c1df157d36c5 build: number: 0 From 9aa572774e51361e8b5edb9ba05e9784feca939f Mon Sep 17 00:00:00 2001 From: Kez Cleal <42997789+kcleal@users.noreply.github.com> Date: Tue, 12 Mar 2024 18:42:33 +0000 Subject: [PATCH 0898/1813] Reduce requirements for GW (#46259) --- recipes/gw/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gw/meta.yaml b/recipes/gw/meta.yaml index b76079b337bc9..5594f0a8c7aa8 100644 --- a/recipes/gw/meta.yaml +++ b/recipes/gw/meta.yaml @@ -13,7 +13,7 @@ source: build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('gw', max_pin="x") }} @@ -34,7 +34,7 @@ requirements: host: - fontconfig - libcurl - - libdeflate >=1.8 + - libdeflate >=1.0 - htslib >=1.12 - glfw >=3.3 - freetype From 5b2447f794abbc1de178ff41a2591cf7733f484a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 15:28:06 -0400 Subject: [PATCH 0899/1813] Update minimap2 to 2.27 (#46371) --- recipes/minimap2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/minimap2/meta.yaml b/recipes/minimap2/meta.yaml index ca802bfd9cb0c..5a16eeea80c0a 100644 --- a/recipes/minimap2/meta.yaml +++ b/recipes/minimap2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.26" %} +{% set version = "2.27" %} package: name: minimap2 @@ -6,10 +6,10 @@ package: source: url: https://github.com/lh3/minimap2/archive/v{{ version }}.tar.gz - sha256: f4c8c3459c7b87e9de6cbed7de019b48d9337c2e46b87ba81b9f72d889420b3c + sha256: ca9ceb07e3b388858ebc2d7d91a6c74e996659402d16aa759ecedd63588b1ef7 build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('minimap2', max_pin="x") }} From 26a2c4e3abfb798e2187fdfc129ad58bfa5cfdc9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 17:04:54 -0400 Subject: [PATCH 0900/1813] Update pangolin-data to 1.26 (#46372) --- recipes/pangolin-data/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangolin-data/meta.yaml b/recipes/pangolin-data/meta.yaml index 172b1dbf9901b..8f6e62a645bd9 100644 --- a/recipes/pangolin-data/meta.yaml +++ b/recipes/pangolin-data/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.25.1" %} +{% set version = "1.26" %} package: name: pangolin-data @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pangolin-data/archive/refs/tags/v{{ version }}.tar.gz - sha256: d92af7f5563cf8b3c0db4fa16748476d0033153865d75711a2dec46039c2473a + sha256: 6aed4738a29260d616654d69c79c540de1b547139cb51b54670970b023aba4bd build: number: 0 From 149cea472bea08727ab22099e6941d43f83d4347 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 17:16:28 -0400 Subject: [PATCH 0901/1813] Update snakemake-executor-plugin-drmaa to 0.1.4 (#46365) * Update snakemake-executor-plugin-drmaa to 0.1.4 * bump deps --------- Co-authored-by: mencian --- recipes/snakemake-executor-plugin-drmaa/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/snakemake-executor-plugin-drmaa/meta.yaml b/recipes/snakemake-executor-plugin-drmaa/meta.yaml index ecc427cb7d15e..7937a06afe146 100644 --- a/recipes/snakemake-executor-plugin-drmaa/meta.yaml +++ b/recipes/snakemake-executor-plugin-drmaa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-drmaa" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: {{ name|lower }} @@ -7,14 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_drmaa-{{ version }}.tar.gz - sha256: 1250d0f307bf3db3aa3f26f85ea5ecc7ae00b2598ea1e1afceab7a457042fa12 + sha256: 93ddefc3fcb5ee2241e4622d04fd1ffcfc58776ff9e723e958a0da2cc2c5fcb7 build: noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation number: 0 run_exports: - - {{ pin_subpackage(name, max_pin='x') }} + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: host: @@ -24,7 +24,7 @@ requirements: run: - python >=3.11.0,<4.0.0 - snakemake-interface-common >=1.13.0,<2.0.0 - - snakemake-interface-executor-plugins >=8.1.0,<9.0.0 + - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 - drmaa >=0.7.9,<0.8.0 test: @@ -39,6 +39,7 @@ about: home: https://github.com/snakemake/snakemake-executor-plugin-drmaa summary: A snakemake executor plugin for submission of jobs via DRMAA. license: MIT + license_family: MIT license_file: LICENSE extra: From c7e3c730cf84ae551dd8b11f83b7a3f8bc24f155 Mon Sep 17 00:00:00 2001 From: Niema Moshiri Date: Tue, 12 Mar 2024 15:28:20 -0700 Subject: [PATCH 0902/1813] Update CoaTran to v0.0.4 (#46308) * Update meta.yaml * Delete recipes/coatran/LICENSE * Update build.sh * edit recipe-maintainer * edit tests * revert changes --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian --- recipes/coatran/LICENSE | 674 -------------------------------------- recipes/coatran/build.sh | 2 +- recipes/coatran/meta.yaml | 52 +-- 3 files changed, 27 insertions(+), 701 deletions(-) delete mode 100644 recipes/coatran/LICENSE diff --git a/recipes/coatran/LICENSE b/recipes/coatran/LICENSE deleted file mode 100644 index f288702d2fa16..0000000000000 --- a/recipes/coatran/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. By contrast, -the GNU General Public License is intended to guarantee your freedom to -share and change all versions of a program--to make sure it remains free -software for all its users. We, the Free Software Foundation, use the -GNU General Public License for most of our software; it applies also to -any other work released this way by its authors. You can apply it to -your programs, too. - - When we speak of free software, we are referring to freedom, not -price. Our General Public Licenses are designed to make sure that you -have the freedom to distribute copies of free software (and charge for -them if you wish), that you receive source code or can get it if you -want it, that you can change the software or use pieces of it in new -free programs, and that you know you can do these things. - - To protect your rights, we need to prevent others from denying you -these rights or asking you to surrender the rights. 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But first, please read -. diff --git a/recipes/coatran/build.sh b/recipes/coatran/build.sh index b0e17ef5d4f51..3fb84cb72e5d8 100644 --- a/recipes/coatran/build.sh +++ b/recipes/coatran/build.sh @@ -2,4 +2,4 @@ mkdir -p ${PREFIX}/bin make CXX=${CXX} -cp {coatran_constant,coatran_expgrowth,coatran_transtree,coatran_inftime} ${PREFIX}/bin +cp coatran_* ${PREFIX}/bin diff --git a/recipes/coatran/meta.yaml b/recipes/coatran/meta.yaml index 92dea311f4897..73c066d76d605 100644 --- a/recipes/coatran/meta.yaml +++ b/recipes/coatran/meta.yaml @@ -1,43 +1,43 @@ -{% set name = "CoaTran" %} -{% set version = "0.0.1" %} -{% set commit = "e0d34b0" %} -{% set sha256 = "a20c263675ec34ecbfd08eecfaa639aa5b6fb7648b5d27fdf41cec9f8eb8cce0" %} +{% set name = "coatran" %} +{% set version = "0.0.4" %} package: - name: "{{ name|lower }}" - version: "{{ version }}" - -source: - url: "https://github.com/niemasd/CoaTran/archive/{{ commit }}.zip" - sha256: {{ sha256}} + name: {{ name }} + version: {{ version }} build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage('coatran', max_pin="x.x.x") }} + +source: + url: https://github.com/niemasd/CoaTran/archive/refs/tags/{{ version }}.tar.gz + sha256: b0af9eff5c78a7126ce5f36386c3c514e811d3470392a7a18566195e40765456 requirements: build: - - make + - {{ compiler('c') }} - {{ compiler('cxx') }} - host: - run: - -test: - commands: - - coatran_constant --help 2>&1 | grep CoaTran - - coatran_expgrowth --help 2>&1 | grep CoaTran - - coatran_transtree --help 2>&1 | grep CoaTran - - coatran_inftime --help 2>&1 | grep CoaTran + - make about: - home: "https://github.com/niemasd/CoaTran" - license: GPLv3 - license_family: GPL + home: https://github.com/niemasd/CoaTran + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE - summary: "CoaTran: Coalescent tree simulation along a transmission network" - dev_url: "https://github.com/niemasd/CoaTran" + summary: Coalescent tree simulation along a transmission network + dev_url: https://github.com/niemasd/CoaTran + +test: + commands: + - coatran_constant -h 2>&1 | grep "CoaTran" + - coatran_inftime -h 2>&1 | grep "CoaTran" + - coatran_transtree -h 2>&1 | grep "CoaTran" extra: identifiers: - biotools:coatran + - doi:10.1101/2020.11.10.377499 recipe-maintainers: - acaprez + - niemasd From a2b04ef1506e06370ee584ffeed11e4764bccaf7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 18:28:54 -0400 Subject: [PATCH 0903/1813] Update ms2deepscore to 1.0.0 (#46369) * Update ms2deepscore to 1.0.0 * add run_exports * remove licence --------- Co-authored-by: mencian --- recipes/ms2deepscore/LICENCE | 201 --------------------------------- recipes/ms2deepscore/meta.yaml | 19 +++- 2 files changed, 13 insertions(+), 207 deletions(-) delete mode 100644 recipes/ms2deepscore/LICENCE diff --git a/recipes/ms2deepscore/LICENCE b/recipes/ms2deepscore/LICENCE deleted file mode 100644 index 261eeb9e9f8b2..0000000000000 --- a/recipes/ms2deepscore/LICENCE +++ /dev/null @@ -1,201 +0,0 @@ - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/recipes/ms2deepscore/meta.yaml b/recipes/ms2deepscore/meta.yaml index ee8f51bf196d1..c631294d07e8b 100644 --- a/recipes/ms2deepscore/meta.yaml +++ b/recipes/ms2deepscore/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ms2deepscore" %} -{% set version = "0.5.0" %} -{% set sha256 = "7adcc18260b37291f525a263cb4d46c68b2e326718c36fde78cbb88d7ddd03a7" %} +{% set version = "1.0.0" %} +{% set sha256 = "76f88b8e4b0d296df77262c1d8078f7f902852608ca50f259f12d407047d52db" %} package: name: {{ name|lower }} @@ -13,19 +13,22 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('ms2deepscore', max_pin="x") }} requirements: host: - python >=3.8 + - pip run: - python >=3.8 - - matchms >=0.14 + - matchms >=0.14.0 - numba - numpy >=1.20.3 - pandas - tqdm - - tensorflow + - tensorflow <2.14 test: imports: @@ -34,15 +37,19 @@ test: about: home: https://github.com/matchms/ms2deepscore license: Apache-2.0 + license_family: APACHE license_file: LICENSE + dev_url: https://github.com/matchms/ms2deepscore summary: "Deep learning similarity measure for comparing MS/MS spectra with respect to their chemical similarity" description: | ms2deepscore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. + extra: identifiers: - - doi:https://doi.org/10.1186/s13321-021-00558-4 + - doi:10.1186/s13321-021-00558-4 + - biotools:ms2deepscore recipe-maintainers: - niekdejonge - hechth From d4d3ba1a08bb2a109fef9e95a9d000c541f5dfcc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 18:29:13 -0400 Subject: [PATCH 0904/1813] Update ska2 to 0.3.7 (#46358) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ska2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ska2/meta.yaml b/recipes/ska2/meta.yaml index 575802314f7b1..5351d482863ab 100644 --- a/recipes/ska2/meta.yaml +++ b/recipes/ska2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ska2" %} -{% set version = "0.3.6" %} +{% set version = "0.3.7" %} package: name: {{ name|lower}} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/ska.rust/archive/v{{ version }}.tar.gz - sha256: b1f7aecec7ff50c982d4dabceeb091b4c00071bfb4385aa5ea931fdbdca32e1e + sha256: ea7234428f253638b2093abdd6c8b1e8362ecad0ba56e3b29700af9a4481d911 build: number: 0 From 457c721422f7bb045a2e9594108f3b15da49fbc8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 18:29:30 -0400 Subject: [PATCH 0905/1813] Update tajimas_d to 2.0.1 (#46356) * Update tajimas_d to 2.0.1 * add run_exports --------- Co-authored-by: mencian --- recipes/tajimas_d/meta.yaml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/recipes/tajimas_d/meta.yaml b/recipes/tajimas_d/meta.yaml index a9d4c00070e44..6b5cc9f32216f 100644 --- a/recipes/tajimas_d/meta.yaml +++ b/recipes/tajimas_d/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tajimas_d" %} -{% set version = "2.0.0" %} +{% set version = "2.0.1" %} package: name: {{ name }} @@ -7,12 +7,16 @@ package: source: url: https://github.com/not-a-feature/tajimas_d/archive/refs/tags/v{{ version }}.tar.gz - sha256: c877bc1e1ca78c2e8bd4b4f5fd37aa40fcd5a91880e508c9038eb5f8479015e9 + sha256: 11fd47453836d9dc9470a426d52f4889d4c49248dd5c931f66b8907ad9c66656 build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + entry_points: + - tajimas_d = tajimas_d._tajimas_d:run_cli + run_exports: + - {{ pin_subpackage('tajimas_d', max_pin="x") }} requirements: host: @@ -24,16 +28,13 @@ requirements: test: imports: - tajimas_d - commands: - - pip check requires: - - pip - miniFasta about: home: https://github.com/not-a-feature/tajimas_d license: GPL-3.0-or-later - license_family: GPL + license_family: GPL3 license_file: LICENSE summary: 'Computes Tajimas D, the Pi- or Watterson-Estimator for multiple sequences.' description: | From c40e6ba576e7b2638f67d4f3f8afcd24657e062a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 18:30:11 -0400 Subject: [PATCH 0906/1813] Update blosum to 2.0.3 (#46354) * Update blosum to 2.0.3 * add run_exports --------- Co-authored-by: mencian --- recipes/blosum/meta.yaml | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/recipes/blosum/meta.yaml b/recipes/blosum/meta.yaml index 88e1045f87f16..c20c944256cbd 100644 --- a/recipes/blosum/meta.yaml +++ b/recipes/blosum/meta.yaml @@ -1,5 +1,5 @@ {% set name = "blosum" %} -{% set version = "2.0.2" %} +{% set version = "2.0.3" %} package: name: {{ name }} @@ -7,12 +7,14 @@ package: source: url: https://github.com/not-a-feature/blosum/archive/refs/tags/v{{ version }}.tar.gz - sha256: a0e4a44471d6f70b19ec6b936cdf57cf9849bc5f21ef7d3a698b9e9c2e20a00f + sha256: 7e061dd6934333068b87d0d900eb437574f3c4acda26de7179c2422dcff74033 build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('blosum', max_pin="x") }} requirements: host: @@ -24,15 +26,11 @@ requirements: test: imports: - blosum - commands: - - pip check - requires: - - pip about: home: https://github.com/not-a-feature/blosum license: GPL-3.0-or-later - license_family: GPL + license_family: GPL3 license_file: LICENSE summary: 'A small module for easy access to BLOSUM matrices without dependencies.' description: | @@ -43,4 +41,3 @@ about: extra: recipe-maintainers: - not-a-feature - From 8c32c479d00b15566342ab437b7426a50af4f98e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 18:30:22 -0400 Subject: [PATCH 0907/1813] Update tissuumaps to 3.2.1.3 (#46349) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index d1bb21fe16d35..ee3fe1375a10d 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.1.2" %} +{% set version = "3.2.1.3" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 5565f8abb5d1cde13dd6a1daa19c8fbff6bc69f49247ae0d95208352b1212a5c + sha256: b15b12bcac2005ef9d2c542e8275324680ae93f981e5ddd4860cf89be0463f9f build: number: 0 From e6b530d72f033ccf4977b93c947f220ea7b17da9 Mon Sep 17 00:00:00 2001 From: Mikko Rautiainen Date: Wed, 13 Mar 2024 00:52:16 +0200 Subject: [PATCH 0908/1813] Update ribotin to version 1.3 (#46357) * Update ribotin to version 1.3 * fix makefile version patch --- recipes/ribotin/build.sh | 1 + recipes/ribotin/makefile.patch | 8 ++++++-- recipes/ribotin/meta.yaml | 8 ++++---- 3 files changed, 11 insertions(+), 6 deletions(-) diff --git a/recipes/ribotin/build.sh b/recipes/ribotin/build.sh index 3b102e3f455cb..19adc930d88f8 100644 --- a/recipes/ribotin/build.sh +++ b/recipes/ribotin/build.sh @@ -4,6 +4,7 @@ cd $SRC_DIR make all cp bin/ribotin-ref $PREFIX/bin cp bin/ribotin-verkko $PREFIX/bin +cp bin/ribotin-hifiasm $PREFIX/bin mkdir -p $PREFIX/share/${PKG_NAME}-${PKG_VERSION} cp template_seqs/rDNA_one_unit.fasta $PREFIX/share/${PKG_NAME}-${PKG_VERSION}/rDNA_one_unit.fasta diff --git a/recipes/ribotin/makefile.patch b/recipes/ribotin/makefile.patch index c01ea1f0fbf7d..8f9192ef79578 100644 --- a/recipes/ribotin/makefile.patch +++ b/recipes/ribotin/makefile.patch @@ -1,5 +1,5 @@ diff --git a/makefile b/makefile -index 40a23f7..b35510c 100644 +index 5166dd0..83ff306 100644 --- a/makefile +++ b/makefile @@ -15,8 +15,8 @@ OBJ = $(patsubst %, $(ODIR)/%, $(_OBJ)) @@ -13,11 +13,15 @@ index 40a23f7..b35510c 100644 $(shell mkdir -p bin) $(shell mkdir -p obj) -@@ -30,10 +30,10 @@ $(BINDIR)/ribotin-ref: $(OBJ) $(ODIR)/ribotin-ref.o +@@ -33,13 +33,13 @@ $(BINDIR)/ribotin-ref: $(OBJ) $(ODIR)/ribotin-ref.o $(GPP) -o $@ $^ $(LINKFLAGS) $(ODIR)/ribotin-verkko.o: $(SRCDIR)/ribotin-verkko.cpp $(DEPS) $(OBJ) - $(GPP) -c -o $@ $< $(CPPFLAGS) -DVERSION="\"$(VERSION)\"" -DRIBOTIN_TEMPLATE_PATH="\"$(TEMPLATEPATH)\"" ++ $(GPP) -c -o $@ $< $(CPPFLAGS) -DVERSION="\"$(VERSION)\"" -DRIBOTIN_TEMPLATE_PATH="$(TEMPLATEPATH)" + + $(ODIR)/ribotin-hifiasm.o: $(SRCDIR)/ribotin-hifiasm.cpp $(DEPS) $(OBJ) +- $(GPP) -c -o $@ $< $(CPPFLAGS) -DVERSION="\"$(VERSION)\"" -DRIBOTIN_TEMPLATE_PATH="\"$(TEMPLATEPATH)\"" + $(GPP) -c -o $@ $< $(CPPFLAGS) -DVERSION="\"$(VERSION)\"" -DRIBOTIN_TEMPLATE_PATH="$(TEMPLATEPATH)" $(ODIR)/ribotin-ref.o: $(SRCDIR)/ribotin-ref.cpp $(DEPS) $(OBJ) diff --git a/recipes/ribotin/meta.yaml b/recipes/ribotin/meta.yaml index a362932854381..1acdf0e771f91 100644 --- a/recipes/ribotin/meta.yaml +++ b/recipes/ribotin/meta.yaml @@ -1,18 +1,18 @@ {% set name = "ribotin" %} -{% set version = "1.2" %} +{% set version = "1.3" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/maickrau/{{ name }}/files/13435950/{{ name }}.tar.gz - sha256: 88d7be40dc641b96ef6f36cd2e464e8d65395ab50158efa1d2d49203b42ffa79 + url: https://github.com/maickrau/{{ name }}/files/14571457/{{ name }}.tar.gz + sha256: 7eda750e4fd1064eedf3016f5a49d6b6994e336619fc3b5e4afe4655b2873b70 patches: - makefile.patch build: - number: 1 + number: 0 skip: True # [osx] run_exports: - {{ pin_subpackage('ribotin', max_pin="x.x") }} From a7b1d290f01d7c4bd67b9c073b19a498afab8f65 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 19:27:58 -0400 Subject: [PATCH 0909/1813] Update mappy to 2.27 (#46373) * Update mappy to 2.27 * add run_exports * retrigger CI --------- Co-authored-by: mencian --- recipes/mappy/build.sh | 2 +- recipes/mappy/meta.yaml | 17 +++++++++++------ 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/recipes/mappy/build.sh b/recipes/mappy/build.sh index b574ab80d53e9..f8457f291b1a6 100644 --- a/recipes/mappy/build.sh +++ b/recipes/mappy/build.sh @@ -3,4 +3,4 @@ export C_INCLUDE_PATH=$PREFIX/include export LIBRARY_PATH=$PREFIX/lib -$PYTHON setup.py install --single-version-externally-managed --record=record.txt +${PYTHON} -m pip install . --no-build-isolation --no-deps -vvv diff --git a/recipes/mappy/meta.yaml b/recipes/mappy/meta.yaml index 8125b86d3352f..fd0f7edcf8930 100644 --- a/recipes/mappy/meta.yaml +++ b/recipes/mappy/meta.yaml @@ -1,15 +1,18 @@ -{% set version = "2.26" %} +{% set name = "mappy" %} +{% set version = "2.27" %} package: - name: mappy + name: {{ name }} version: {{ version }} source: - url: https://pypi.io/packages/source/m/mappy/mappy-{{ version }}.tar.gz - sha256: e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mappy-{{ version }}.tar.gz + sha256: 47df11e7cecee9138680d6d2312e44397d0484a02ecf1f5908dea50d94a0efe4 build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('mappy', max_pin="x") }} requirements: build: @@ -17,7 +20,7 @@ requirements: host: - python - cython - - setuptools + - pip - zlib run: - python @@ -30,4 +33,6 @@ test: about: home: https://github.com/lh3/minimap2 license: MIT + license_family: MIT + license_file: LICENSE.txt summary: 'Minimap2 Python binding' From 234d3e1d9af23634cb320fe2cbbaa329a32d27ae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 19:57:55 -0400 Subject: [PATCH 0910/1813] Update fastq to 2.0.4 (#46355) * Update fastq to 2.0.4 * add run_exports * add miniFasta back to run section --------- Co-authored-by: mencian --- recipes/fastq/meta.yaml | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/recipes/fastq/meta.yaml b/recipes/fastq/meta.yaml index 4201b44ec8ee4..936ef2639cd24 100644 --- a/recipes/fastq/meta.yaml +++ b/recipes/fastq/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fastq" %} -{% set version = "2.0.2" %} +{% set version = "2.0.4" %} package: name: {{ name }} @@ -7,33 +7,31 @@ package: source: url: https://github.com/not-a-feature/fastq/archive/refs/tags/v{{ version }}.tar.gz - sha256: 855f2347f3a566fde44ba1d91d033dc0de9e0c1ce72dfe7085c6f92f7eeb7cd4 + sha256: 677a5d2eb2b70d0d90da7bf9c52fabd327e5522cb7a7004a011940a3014c0562 build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" + run_exports: + - {{ pin_subpackage('fastq', max_pin="x") }} requirements: host: - - python >=3.7 + - python >=3.8 - pip run: - - python >=3.7 - - miniFasta >=2.1 + - python >=3.8 + - miniFasta >=3.0.1 test: imports: - fastq - commands: - - pip check - requires: - - pip about: home: https://github.com/not-a-feature/fastq license: GPL-3.0-or-later - license_family: GPL + license_family: GPL3 license_file: LICENSE summary: 'A simple FASTQ toolbox for small to medium size projects without dependencies.' description: | From 83f4d3a51a1778cfcef25235f26cb723d9ef3a0e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Mar 2024 21:48:03 -0400 Subject: [PATCH 0911/1813] Update pharokka to 1.7.1 (#46375) --- recipes/pharokka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pharokka/meta.yaml b/recipes/pharokka/meta.yaml index 9463fd547e901..61abbc4f7282e 100644 --- a/recipes/pharokka/meta.yaml +++ b/recipes/pharokka/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.7.0" %} +{% set version = "1.7.1" %} {% set name = "pharokka" %} -{% set sha256 = "4637e70116c621872f6aea71548c8155312540d84ec8fc007f9729010287a948" %} +{% set sha256 = "54fb44fd3ab9693a7625fffa19f3201651a6cdf04455342e6f4266266f1ac139" %} {% set user = "gbouras13" %} package: From e6dde6670424628427dea42c53d85b58ce77c206 Mon Sep 17 00:00:00 2001 From: Niema Moshiri Date: Wed, 13 Mar 2024 00:05:44 -0700 Subject: [PATCH 0912/1813] Add FAVITES-Lite v1.0.1 and its dependencies (#46292) * Added NiemaGraphGen * Updated CoaTran * Updated NiemaGraphGen meta * Added FAVITES-Lite * Added GEMF_FAVITES * Updated FAVITES-Lite meta * Added TreeSAP * Finished first attempt at FAVITES-Lite meta * Added quotes to string * Attempt to fix GEMF compilation * Added imports to TreeSAP recipe * Fixed FAVITES-Lite folder copy * Attempt to fix NGG compilation in Mac OS X * Attempt to fix NGG compilation * Attempt to fix NGG compilation * Reverted CoaTran recipe (will submit separate PR) * Fixed meta.yaml extra sections * Reverting CoaTran meta.yaml to how it was before this PR * Added noarch: generic to build: --- recipes/favites_lite/build.sh | 5 ++++ recipes/favites_lite/meta.yaml | 41 ++++++++++++++++++++++++++++ recipes/gemf_favites/build.sh | 5 ++++ recipes/gemf_favites/meta.yaml | 39 +++++++++++++++++++++++++++ recipes/niemagraphgen/build.sh | 5 ++++ recipes/niemagraphgen/meta.yaml | 47 +++++++++++++++++++++++++++++++++ recipes/treesap/meta.yaml | 44 ++++++++++++++++++++++++++++++ 7 files changed, 186 insertions(+) create mode 100644 recipes/favites_lite/build.sh create mode 100644 recipes/favites_lite/meta.yaml create mode 100644 recipes/gemf_favites/build.sh create mode 100644 recipes/gemf_favites/meta.yaml create mode 100644 recipes/niemagraphgen/build.sh create mode 100644 recipes/niemagraphgen/meta.yaml create mode 100644 recipes/treesap/meta.yaml diff --git a/recipes/favites_lite/build.sh b/recipes/favites_lite/build.sh new file mode 100644 index 0000000000000..b6efe41d72ed0 --- /dev/null +++ b/recipes/favites_lite/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +mkdir -p ${PREFIX}/bin/FAVITES-Lite +cp -r * ${PREFIX}/bin/FAVITES-Lite/ +ln -s ${PREFIX}/bin/FAVITES-Lite/favites_lite.py ${PREFIX}/bin/favites_lite.py diff --git a/recipes/favites_lite/meta.yaml b/recipes/favites_lite/meta.yaml new file mode 100644 index 0000000000000..8cf7408c77ce3 --- /dev/null +++ b/recipes/favites_lite/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.1" %} + +package: + name: favites_lite + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('favites_lite', max_pin="x.x.x") }} + noarch: generic + +source: + url: https://github.com/niemasd/FAVITES-Lite/archive/refs/tags/{{ version }}.tar.gz + sha256: a93435b263a7d9825ab8624c828e569112b4845ca7fafc97e77ee3919053563a + +requirements: + run: + - python >=3.7 + - numpy + - scipy + - treesap + - treeswift + - coatran + - gemf_favites + - niemagraphgen + - seq-gen + +about: + home: https://github.com/niemasd/FAVITES-Lite + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: "FAVITES-Lite: A lightweight framework for viral transmission and evolution simulation" + dev_url: https://github.com/niemasd/FAVITES-Lite + +test: + commands: + - favites_lite.py -h + identifiers: + - doi:10.1093/bioinformatics/bty921 diff --git a/recipes/gemf_favites/build.sh b/recipes/gemf_favites/build.sh new file mode 100644 index 0000000000000..f3ceea26ca6f1 --- /dev/null +++ b/recipes/gemf_favites/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +mkdir -p ${PREFIX}/bin +make CC=${CC} +cp GEMF GEMF_FAVITES.py ${PREFIX}/bin diff --git a/recipes/gemf_favites/meta.yaml b/recipes/gemf_favites/meta.yaml new file mode 100644 index 0000000000000..12f628887e00f --- /dev/null +++ b/recipes/gemf_favites/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.3" %} + +package: + name: gemf_favites + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('gemf_favites', max_pin="x.x.x") }} + +source: + url: https://github.com/niemasd/GEMF/archive/refs/tags/{{ version }}.tar.gz + sha256: 6a342852ff196501022d8814eb86a76fcb1d4ef1c2405ef24e8f4c79e2e1edf5 + +requirements: + build: + - {{ compiler('c') }} + - make + run: + - python >=3.7 + +about: + home: https://github.com/niemasd/GEMF + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: User-friendly epidemic simulations + dev_url: https://github.com/niemasd/GEMF + +test: + commands: + - GEMF_FAVITES.py -h | grep "usage:" + +extra: + identifiers: + - biotools:gemf_favites + recipe-maintainers: + - niemasd diff --git a/recipes/niemagraphgen/build.sh b/recipes/niemagraphgen/build.sh new file mode 100644 index 0000000000000..1fd3513e1fa7d --- /dev/null +++ b/recipes/niemagraphgen/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +mkdir -p ${PREFIX}/bin +make CXX="$CXX" INCLUDE="-I${PREFIX}/include" RELEASEFLAGS="-Wall -pedantic -std=c++11 -DOUTFAVITES -DNGG_UINT_32 -O3 $LDFLAGS" +cp ngg_* ${PREFIX}/bin diff --git a/recipes/niemagraphgen/meta.yaml b/recipes/niemagraphgen/meta.yaml new file mode 100644 index 0000000000000..12c498054c879 --- /dev/null +++ b/recipes/niemagraphgen/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.6" %} + +package: + name: niemagraphgen + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('niemagraphgen', max_pin="x.x.x") }} + +source: + url: https://github.com/niemasd/NiemaGraphGen/archive/refs/tags/{{ version }}.tar.gz + sha256: 65789a45c126cbeb385e5b36550b3c3ed2588943b2e1ac779d433fd3026974c1 + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + +about: + home: https://github.com/niemasd/NiemaGraphGen + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: Niema's C++ implementations of graph generators + dev_url: https://github.com/niemasd/NiemaGraphGen + +test: + commands: + - ngg_barabasi_albert -h 2>&1 | grep "NiemaGraphGen" + - ngg_barbell -h 2>&1 | grep "NiemaGraphGen" + - ngg_complete -h 2>&1 | grep "NiemaGraphGen" + - ngg_cycle -h 2>&1 | grep "NiemaGraphGen" + - ngg_empty -h 2>&1 | grep "NiemaGraphGen" + - ngg_erdos_renyi -h 2>&1 | grep "NiemaGraphGen" + - ngg_newman_watts_strogatz -h 2>&1 | grep "NiemaGraphGen" + - ngg_path -h 2>&1 | grep "NiemaGraphGen" + - ngg_ring_lattice -h 2>&1 | grep "NiemaGraphGen" + +extra: + identifiers: + - biotools:niemagraphgen + - doi:10.46471/gigabyte.37 + maintainers: + - niemasd diff --git a/recipes/treesap/meta.yaml b/recipes/treesap/meta.yaml new file mode 100644 index 0000000000000..d4ec8012f3251 --- /dev/null +++ b/recipes/treesap/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.0.10" %} + +package: + name: "treesap" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/t/treesap/treesap-{{ version }}.tar.gz + sha256: 74d2d6f1106f5345ec6408a443be6d2a9b983fb83e4957d04e22be88659905ab + +build: + noarch: python + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('treesap', max_pin="x") }} + +requirements: + host: + - pip + - python + run: + - python + - numpy + - scipy + - treeswift + +test: + imports: + - treesap + +about: + home: https://github.com/niemasd/TreeSAP + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: "TreeSAP: Tree SAmpling under Phylogenetic models" + dev_url: https://github.com/niemasd/TreeSAP + +extra: + identifiers: + - biotools:treesap + maintainers: + - niemasd From 84e0a315d1d86abab991a195b3e6cf6a4a4f6b9d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Mar 2024 03:07:22 -0400 Subject: [PATCH 0913/1813] Update mafft to 7.525 (#46385) --- recipes/mafft/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mafft/meta.yaml b/recipes/mafft/meta.yaml index 132c40b37520a..9f79b00a30dc4 100644 --- a/recipes/mafft/meta.yaml +++ b/recipes/mafft/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mafft" %} -{% set version = "7.520" %} +{% set version = "7.525" %} package: name: {{ name|lower }} @@ -8,10 +8,10 @@ package: source: # url: https://mafft.cbrc.jp/alignment/software/mafft-{{ version }}-without-extensions-src.tgz url: https://gitlab.com/sysimm/mafft/-/archive/v{{ version }}/mafft-v{{ version }}.zip - sha256: "986042f7eb9d5aba237b7b9701974e20b6952cb7d585c66fd979137ed4a34c9b" + sha256: "fbd94516539c3401243d80f0c33ee247362120b0efc92b31260b2d5db484b2a6" build: - number: 3 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x") }} From b9493d980965c06b22858035710f8935f0c05fb2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Mar 2024 03:07:31 -0400 Subject: [PATCH 0914/1813] Update hybracter to 0.7.1 (#46383) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index cee091ee7a396..c3620151f7ed6 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: ae2ea5fcfc525b1b4d71975d56ead81015afed342e54f1cc3e232f7671033278 + sha256: 1edd91904d91d9fd17889f7e762acda33f92fe5f8553d2e055a2b6bff8778c45 build: number: 0 From 4188403ab6e234cc45c6859d5f4b83c0ad5ca780 Mon Sep 17 00:00:00 2001 From: Po-E Li Date: Wed, 13 Mar 2024 01:08:15 -0600 Subject: [PATCH 0915/1813] add gottcha2 (#46386) --- recipes/gottcha2/meta.yaml | 42 +++++++++++++++++++++++++++++++++++ recipes/gottcha2/post-link.sh | 5 +++++ 2 files changed, 47 insertions(+) create mode 100644 recipes/gottcha2/meta.yaml create mode 100644 recipes/gottcha2/post-link.sh diff --git a/recipes/gottcha2/meta.yaml b/recipes/gottcha2/meta.yaml new file mode 100644 index 0000000000000..b86da3424f743 --- /dev/null +++ b/recipes/gottcha2/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "GOTTCHA2" %} +{% set version = "2.1.8.5p1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +build: + noarch: generic + number: 0 + script: {{ PYTHON }} -m pip install -vv --no-deps . + run_exports: + - {{ pin_subpackage('gottcha2', max_pin='x.x') }} + +source: + url: https://github.com/poeli/GOTTCHA2/archive/refs/tags/{{ version }}.tar.gz + sha256: 81107fdb32c4da753c02a9973cc7d8ba540ac8255006c57e2f133dbc4c833351 + +requirements: + host: + - python + run: + - minimap2 >=2.17 + - gawk + - biom-format >=2.1.7 + - requests + - tqdm + +test: + commands: + - minimap2 -h + - gawk -h + - gottcha2.py --version + +about: + home: https://github.com/poeli/gottcha2 + license: BSD 3-clause + summary: 'Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) v2' + +extra: + identifiers: + - biotools:gottcha2 \ No newline at end of file diff --git a/recipes/gottcha2/post-link.sh b/recipes/gottcha2/post-link.sh new file mode 100644 index 0000000000000..11273771bc6f1 --- /dev/null +++ b/recipes/gottcha2/post-link.sh @@ -0,0 +1,5 @@ +echo " +GOTTCHA2 installed. The database can be download at: + +https://ref-db.edgebioinformatics.org/gottcha2/ +" > $PREFIX/.messages.txt \ No newline at end of file From 209c8bb8fec452053e7c1ae94814f80238d702dc Mon Sep 17 00:00:00 2001 From: John Marshall Date: Wed, 13 Mar 2024 23:22:46 +1300 Subject: [PATCH 0916/1813] Build entrez-direct from source code (#46258) Rewrite the recipe to build the Go executables from edirect.tar.gz rather than using prebuilt executables. Add Linux-aarch64 support by patching the various scripts that switch on architecture and building the executables as .ARM64 on this platform. Update to the current 21.6. --- recipes/entrez-direct/aarch64.patch | 115 ++++++++++++++++++++++++++++ recipes/entrez-direct/build.sh | 26 ++++--- recipes/entrez-direct/meta.yaml | 21 +++-- recipes/entrez-direct/xtract.patch | 30 -------- 4 files changed, 145 insertions(+), 47 deletions(-) create mode 100644 recipes/entrez-direct/aarch64.patch delete mode 100644 recipes/entrez-direct/xtract.patch diff --git a/recipes/entrez-direct/aarch64.patch b/recipes/entrez-direct/aarch64.patch new file mode 100644 index 0000000000000..897f38f6818d7 --- /dev/null +++ b/recipes/entrez-direct/aarch64.patch @@ -0,0 +1,115 @@ +diff -urN edirect.orig/cmd/build.sh edirect/cmd/build.sh +--- edirect.orig/cmd/build.sh 2022-11-12 07:25:55 ++++ edirect/cmd/build.sh 2024-03-08 22:13:47 +@@ -13,6 +13,7 @@ + Darwin-*arm* ) platform=Silicon ;; + CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;; + Linux-*arm* ) platform=ARM ;; ++ Linux-*aarch64* ) platform=ARM64 ;; + * ) platform=UNSUPPORTED ;; + esac + +@@ -94,7 +95,7 @@ + fi + + # erase any existing executables in current directory +-for plt in Darwin Silicon Linux CYGWIN_NT ARM ++for plt in Darwin Silicon Linux CYGWIN_NT ARM ARM64 + do + rm -f *.$plt + done +@@ -103,6 +104,7 @@ + mods="darwin amd64 Darwin \ + darwin arm64 Silicon \ + linux amd64 Linux \ ++ linux arm64 ARM64 \ + windows 386 CYGWIN_NT \ + linux arm ARM" + +@@ -126,13 +128,13 @@ + if [ "$cleanup" = true ] + then + # remove old executables from target +- for plt in Darwin Silicon Linux CYGWIN_NT ARM ++ for plt in Darwin Silicon Linux CYGWIN_NT ARM ARM64 + do + rm -f $target/*.$plt + done + fi + # copy new executables to target +- for plt in Darwin Silicon Linux CYGWIN_NT ARM ++ for plt in Darwin Silicon Linux CYGWIN_NT ARM ARM64 + do + for exc in xtract rchive transmute + do +@@ -145,7 +147,7 @@ + fi + + # erase any remaining executables after compiling +-for plt in Darwin Silicon Linux CYGWIN_NT ARM ++for plt in Darwin Silicon Linux CYGWIN_NT ARM ARM64 + do + rm -f *.$plt + done +diff -urN edirect.orig/extern/build.sh edirect/extern/build.sh +--- edirect.orig/extern/build.sh 2024-03-04 11:00:38 ++++ edirect/extern/build.sh 2024-03-08 22:14:43 +@@ -13,6 +13,7 @@ + Darwin-*arm* ) platform=Silicon ;; + CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;; + Linux-*arm* ) platform=ARM ;; ++ Linux-*aarch64* ) platform=ARM64 ;; + * ) platform=UNSUPPORTED ;; + esac + +@@ -51,7 +52,7 @@ + fi + + # erase any existing executables in current directory +-for plt in Darwin Silicon Linux CYGWIN_NT ARM ++for plt in Darwin Silicon Linux CYGWIN_NT ARM ARM64 + do + rm -f *.$plt + done +@@ -64,7 +65,7 @@ + done + + # will be using "go run", erase executables after test complication +-for plt in Darwin Silicon Linux CYGWIN_NT ARM ++for plt in Darwin Silicon Linux CYGWIN_NT ARM ARM64 + do + rm -f *.$plt + done +diff -urN edirect.orig/rchive edirect/rchive +--- edirect.orig/rchive 2022-01-29 07:25:44 ++++ edirect/rchive 2024-03-08 22:16:43 +@@ -62,6 +62,7 @@ + Darwin-*arm* ) platform=Silicon ;; + CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;; + Linux-*arm* ) platform=ARM ;; ++ Linux-*aarch64* ) platform=ARM64 ;; + * ) platform=UNSUPPORTED ;; + esac + compiled=$0."$platform" +diff -urN edirect.orig/transmute edirect/transmute +--- edirect.orig/transmute 2023-02-22 07:25:33 ++++ edirect/transmute 2024-03-08 22:16:43 +@@ -402,6 +402,7 @@ + Darwin-*arm* ) platform=Silicon ;; + CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;; + Linux-*arm* ) platform=ARM ;; ++ Linux-*aarch64* ) platform=ARM64 ;; + * ) platform=UNSUPPORTED ;; + esac + compiled=$0."$platform" +diff -urN edirect.orig/xtract edirect/xtract +--- edirect.orig/xtract 2024-02-28 09:25:34 ++++ edirect/xtract 2024-03-08 22:16:43 +@@ -110,6 +110,7 @@ + Darwin-*arm* ) platform=Silicon ;; + CYGWIN_NT-* | MINGW*-* ) platform=CYGWIN_NT ;; + Linux-*arm* ) platform=ARM ;; ++ Linux-*aarch64* ) platform=ARM64 ;; + * ) platform=UNSUPPORTED ;; + esac + compiled=$0."$platform" diff --git a/recipes/entrez-direct/build.sh b/recipes/entrez-direct/build.sh index 9771c20b4c018..99a82f92a55e0 100644 --- a/recipes/entrez-direct/build.sh +++ b/recipes/entrez-direct/build.sh @@ -3,18 +3,24 @@ # Keep track of the process set -uex +mkdir bin nobin +# Don't install these most bespoke scripts +mv custom-* idx-* pm-* xy-* nobin +# Move ordinary scripts into a subdirectory for convenience +mv $(find * -type d -prune -o -print | sed '/^[A-Z]/d;/[.]pdf$/d;/[.]pem$/d;/[.]py$/d;/conda/d;/build/d') bin + mkdir -p $PREFIX/bin -mv * $PREFIX/bin -mkdir -p "$PREFIX/home" -export HOME="$PREFIX/home" +(cd cmd && sh -ex ./build.sh $PREFIX/bin) +(cd extern && sh -ex ./build.sh $PREFIX/bin) -# Needs to run in the install folder -cd ${PREFIX}/bin +# Ensure conda-build can tidy up this compiler cache tree +test -d gopath && chmod -R u+wX gopath -sh install.sh +mkdir -p $PREFIX/bin/data $PREFIX/bin/help +install -m 644 data/* $PREFIX/bin/data +install -m 644 help/* $PREFIX/bin/help -# clean up -rm -rf eutils cmd -rm -rf *.log *.go *.yaml setup.sh install.sh *.gz *.pdf -rm -rf idx-* index-* pm-* custom* xy-* CA.pm cacert.pem +install -m 755 bin/* $PREFIX/bin +echo "Check for additional scripts to be installed to .../bin" +ls diff --git a/recipes/entrez-direct/meta.yaml b/recipes/entrez-direct/meta.yaml index 9c509fc7a21c3..f4f4fc137f9bd 100644 --- a/recipes/entrez-direct/meta.yaml +++ b/recipes/entrez-direct/meta.yaml @@ -1,21 +1,24 @@ -{% set version = "16.2" %} -{% set date = "20211103" %} -{% set sha256 = "42124ac5aa9aed2bb399b064ad4dfe418b9facb6f61eef95ac7e92e7cc410dd3" %} +{% set version = "21.6" %} +{% set date = "20240308" %} +{% set sha256 = "805e34f2705905a7aed49b8bcd1ed6a1a6c2acf1f7ea249349cbbce30cac30bd" %} package: name: entrez-direct version: {{ version }} build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage("entrez-direct", max_pin="x") }} source: - url: https://raw.githubusercontent.com/biostars/conda-ready-entrez-direct/main/dist/edirect-16.2.20211103.tar.gz + url: https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/{{ version }}.{{ date }}/edirect.tar.gz sha256: {{ sha256 }} + patches: + - aarch64.patch requirements: build: - # The installer script downloads statically compiled binaries, so this is effectively just avoiding linter errors - {{ compiler('go') }} run: - wget @@ -29,13 +32,17 @@ test: - esearch --help - elink --help - esummary --help + - rchive -version + - transmute -version - xtract -version about: - home: ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/{{ version }}.{{ date }}/README + home: https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/{{ version }}.{{ date }}/README license: PUBLIC DOMAIN summary: Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process. extra: + additional-platforms: + - linux-aarch64 container: extended-base: True diff --git a/recipes/entrez-direct/xtract.patch b/recipes/entrez-direct/xtract.patch deleted file mode 100644 index 5a9c413eb66a8..0000000000000 --- a/recipes/entrez-direct/xtract.patch +++ /dev/null @@ -1,30 +0,0 @@ ---- setup.sh 2019-10-18 19:50:47.000000000 +0200 -+++ setup.sh.new 2020-02-03 08:32:53.591369832 +0100 -@@ -62,7 +62,8 @@ - - if [ -f xtract."$platform" ] - then -- chmod +x xtract."$platform" -+ mv xtract."$osname" xtract -+ chmod +x xtract - else - echo "Unable to download xtract executable." - fi -@@ -113,17 +114,4 @@ - | tee $advice - fi - --if [ -z "$prfx" ] --then --echo "" --echo "or manually edit the PATH variable assignment in your .bash_profile file." --echo "" --echo "Would you like to do that automatically now? [y/N]" --read response --case "$response" in -- [Yy]* ) . $advice; echo "OK, done." ;; -- [Nn]* | '' ) echo "Holding off, then." ;; -- * ) echo "Conservatively taking that as a no." ;; --esac --fi - rm $advice From 77bb4fb1f79d19cec30ae2ef779aebbfe7e3c644 Mon Sep 17 00:00:00 2001 From: John Lees Date: Wed, 13 Mar 2024 10:37:31 +0000 Subject: [PATCH 0917/1813] Bump poppunk to v2.6.5 (#46391) --- recipes/poppunk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index fe463f0193781..e596450103070 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.6.4" %} +{% set version = "2.6.5" %} {% set name = "PopPUNK" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 3cbedaea29807752e008f627d916d035a2c75522de19ea5a0b9c447d558f0e70 + sha256: d587b77c6b38e73035f9bd1b5cfcea9a048714112391a77139bb52e0a160b968 build: number: 0 From c936ef6f7f84ed5f1803de7c1ac3cd93fc0326d2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Mar 2024 06:58:33 -0400 Subject: [PATCH 0918/1813] Update virusrecom to 1.1.4 (#46389) --- recipes/virusrecom/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/virusrecom/meta.yaml b/recipes/virusrecom/meta.yaml index 6e9352ffa5415..0eba5822dff3e 100644 --- a/recipes/virusrecom/meta.yaml +++ b/recipes/virusrecom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virusrecom" %} -{% set version = "1.1.3.1" %} +{% set version = "1.1.4" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3fda39fc84b7a0ffccdfcdb309c2f8bb5e617d7dfc0c5b0cb0fc4a3d245c43b4 + sha256: 904a7da6c681041063e20ab39424ec0dc73fbdfedbfe0d89cbac5e65966b420f build: number: 0 From 9d4f294a1e005696f2bea9b992e79755e1f04490 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:35:09 -0400 Subject: [PATCH 0919/1813] Update ampcombi to 0.2.1 (#46394) * Update ampcombi to 0.2.1 * Update meta.yaml * Apply suggestions from code review * Update recipes/ampcombi/meta.yaml --------- Co-authored-by: James A. Fellows Yates --- recipes/ampcombi/meta.yaml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/recipes/ampcombi/meta.yaml b/recipes/ampcombi/meta.yaml index dd27f1ed0b8e9..58b3df97bdaef 100644 --- a/recipes/ampcombi/meta.yaml +++ b/recipes/ampcombi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "AMPcombi" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 96ddff5067279d3da05a662d627e793b040764560c6b6a6464bfe01a0768a27b + sha256: da699d66190e654b6c9ca333228678fd759f4ce8e84b8022c24417cf5a300c86 build: noarch: python @@ -22,19 +22,20 @@ requirements: host: - pandas - pip - - python >=3.9 + - python ==3.11 run: - - pandas + - pandas ==1.5.2 - requests - parsedatetime - subprocess32 - - biopython + - biopython ==1.80 - backports.tempfile - contextlib2 - - diamond - openpyxl - jsonschema - - python >=3.9 + - python ==3.11 + - diamond ==2.0.15 + - mmseqs2 ==15.6f452 test: imports: From 8302409e364fbe37503e152f794ad983cf2abbd3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Mar 2024 10:46:59 -0400 Subject: [PATCH 0920/1813] Update hitac to 2.2.2 (#46398) --- recipes/hitac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hitac/meta.yaml b/recipes/hitac/meta.yaml index 3a7e214569046..2c881eb7aac3f 100644 --- a/recipes/hitac/meta.yaml +++ b/recipes/hitac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hitac" %} -{% set version = "2.2.1" %} +{% set version = "2.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 3015bd17fee7f026ddf08708bf8a935d7a73108bc2cc8e9e9275fdf6b823298c + sha256: 22e69ba328f4d48b6f1dd6c394f37fdc429317a5a810a41c91e8e03454f8db09 build: noarch: python From 30c93d2a179243a81a692c4366705d3cffd59dec Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Wed, 13 Mar 2024 16:13:16 +0100 Subject: [PATCH 0921/1813] bump minimap2 so it's built and posted (#46401) Co-authored-by: Devon Ryan --- recipes/minimap2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/minimap2/meta.yaml b/recipes/minimap2/meta.yaml index 5a16eeea80c0a..6a9b301cd30f3 100644 --- a/recipes/minimap2/meta.yaml +++ b/recipes/minimap2/meta.yaml @@ -9,7 +9,7 @@ source: sha256: ca9ceb07e3b388858ebc2d7d91a6c74e996659402d16aa759ecedd63588b1ef7 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('minimap2', max_pin="x") }} From af0aa92e737288951f30f46e3696d8b3f8b80474 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Mar 2024 14:57:02 -0400 Subject: [PATCH 0922/1813] Update snakemake-executor-plugin-lsf to 0.2.2 (#46408) --- recipes/snakemake-executor-plugin-lsf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-lsf/meta.yaml b/recipes/snakemake-executor-plugin-lsf/meta.yaml index fef6a217b9517..c98403fa5b16f 100644 --- a/recipes/snakemake-executor-plugin-lsf/meta.yaml +++ b/recipes/snakemake-executor-plugin-lsf/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-lsf" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_lsf-{{ version }}.tar.gz - sha256: 2e03b98b29cf1469add3114046b5a1662e07879a8606914f4fe4c01f1fd53aea + sha256: 4d0cf9954ca95df71d9dce92416daf730539b11a0f2ea86319baaf41e58c60ff build: noarch: python From 9164b0af9247fdee8ef194ae6b121f4464acbca2 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Thu, 14 Mar 2024 10:43:42 +0100 Subject: [PATCH 0923/1813] Update recipe for metamaps (#45887) * Create new recipe for metamaps * Apply suggestions from code review * Update metamaps version Co-authored-by: James A. Fellows Yates * Update recipes/metamaps/meta.yaml * Fix Sha256 and link --------- Co-authored-by: James A. Fellows Yates --- recipes/metamaps/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/metamaps/meta.yaml b/recipes/metamaps/meta.yaml index 1f2146738044e..7f0573516b435 100644 --- a/recipes/metamaps/meta.yaml +++ b/recipes/metamaps/meta.yaml @@ -1,16 +1,18 @@ -{% set version = "0.1.98102e9" %} -{% set sha256 = "f73d80be084dc73128d4795e9d03abcd35be2ddc7ef81684fcadec154a28b7af" %} +{% set version = "0.1.633d2e0" %} +{% set sha256 = "9740c7882fe2ff39c0df9d44e85a725f73b531117ea265e2b45eeb1661d6a3e7" %} package: name: metamaps version: {{ version }} source: - url: https://github.com/DiltheyLab/MetaMaps/archive/98102e9e684efa6a9903d8abe93600132c101ad0.tar.gz + url: https://github.com/DiltheyLab/MetaMaps/archive/633d2e0ec1ffb4fd9111aca52a54d236ef5ef379.tar.gz sha256: {{ sha256 }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage("metamaps", max_pin=None) }} requirements: build: From bc1599bca457bcaba6c30077c0fcae89b4890f74 Mon Sep 17 00:00:00 2001 From: Kanglu123 <64641114+Kanglu123@users.noreply.github.com> Date: Thu, 14 Mar 2024 18:27:32 +0800 Subject: [PATCH 0924/1813] Update deepmei to version 1.6.24 (#46420) * Add files via upload * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh --- recipes/deepmei/meta.yaml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/deepmei/meta.yaml b/recipes/deepmei/meta.yaml index ab40e3175008d..5176e0a8ea618 100644 --- a/recipes/deepmei/meta.yaml +++ b/recipes/deepmei/meta.yaml @@ -1,16 +1,16 @@ package: name: deepmei - version: 1.0.0 + version: 1.6.24 source: - url: https://raw.githubusercontent.com/kanglu123/deepmei_v1.0.0/master/DeepMEI.without_models_and_files.tar.gz - sha256: 6af31abb690b3ba209d719a1e924baaab725760deb47a69319c171308d095269 + url: https://raw.githubusercontent.com/kanglu123/deepmei/deepmei-v1.6.24/deepmei_update_v1.6.24.2.tar.gz + sha256: 9a0fa0905776924969907cd71dfdf47e9e7afa8fc0ca277e30b2bf222efee3fd build: noarch: generic number: 0 run_exports: - {{ pin_subpackage('deepmei', max_pin="x.x") }} - + requirements: run: # List dependencies here. e.g.: @@ -26,10 +26,10 @@ requirements: test: commands: - - deepmeiv1 + - deepmei about: - home: https://github.com/Kanglu123/deepmei + home: https://github.com/Kanglu123/deepmei/tree/deepmei-v1.6.24 license: GPL-3.0 license_file: license.txt - summary: A pipeline to detect mobile elements insertion in human genome + summary: A tool to detect mobile elements insertion From b08916bb8228bdcc67d9f560a343e2c3ef87412d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 09:09:50 -0400 Subject: [PATCH 0925/1813] Update snakemake to 8.7.0 (#46404) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 330e389b6dcb9..fa78c30c8c0f8 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.6.0" %} +{% set version = "8.7.0" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: dafcd6e6aab257f6712ab7e9931164e7114a96a3b83cb0d97effd8db7b2d3295 + sha256: fbeb91045c984fad4e6e57b329ebc731bf9ec98eef29a772b79d440a51705078 build: number: 0 From a9b9bb4fa13c51e01adb2d08a2c966ba4dc72f97 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 14 Mar 2024 16:02:37 +0200 Subject: [PATCH 0926/1813] snakemake: add linux-aarch64 build (#46430) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * snakemake: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Update meta.yaml --------- Signed-off-by: Martin Tzvetanov Grigorov Co-authored-by: Felix Mölder Co-authored-by: Felix Mölder --- recipes/snakemake/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index fa78c30c8c0f8..415ca8e1a983a 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -53,6 +53,8 @@ about: files from input files. extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1093/bioinformatics/bts480 - biotools:Snakemake From 717b632510d1ca583d31fe2e3f9afba8d2a7334f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 10:48:40 -0400 Subject: [PATCH 0927/1813] Update taxmyphage to 0.2.9 (#46428) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index 9681cef1fff14..fac201dd375df 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.2.8" %} +{% set version = "0.2.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: 30e0194b4df6e8df8a3593729a0a6f19dd074e3d81d23c86f831f85356c8fd79 + sha256: 53208a3490d4c6ca0dab9b762ab0c9c609dcff2489926e3659277680fb4ef6b6 build: entry_points: From ad9aaeeb0d322bb6b99b7d00c1dd161ccd27aede Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 11:47:36 -0400 Subject: [PATCH 0928/1813] Update ena-webin-cli to 7.1.0 (#46437) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index 2046d32218378..728b408c42481 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "7.0.1" %} -{% set sha256 = "7adf27f5d333045a3a960b0cb6342e2facc082239ee815ba446d6c8f51492184" %} +{% set version = "7.1.0" %} +{% set sha256 = "934cd5517beaab3cd130abc31eb22c404868b7f10087067e271bca3cf9e87460" %} package: name: ena-webin-cli From a136d27eb2b855e86a9058c2f059341b54edaf1a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 11:53:55 -0400 Subject: [PATCH 0929/1813] Update pybarrnap to 0.5.0 (#46407) --- recipes/pybarrnap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybarrnap/meta.yaml b/recipes/pybarrnap/meta.yaml index 1f4e67ed04198..1e2657be3e50e 100644 --- a/recipes/pybarrnap/meta.yaml +++ b/recipes/pybarrnap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybarrnap" %} -{% set version = "0.4.1" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybarrnap-{{ version }}.tar.gz - sha256: d20c05a027f8b16a32855c5d63be0cff79150b1cb5f642037f31faf02a721679 + sha256: 9578c1677c60dfe7f12bccfd1613048918068289b0dc04b3d0396e699fd09073 build: number: 0 From fe55ea0d7c6a1c4d73d67ca2c90d7b9b79bf0300 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 11:54:02 -0400 Subject: [PATCH 0930/1813] Update skyline2isocor to 0.3.0 (#46405) --- recipes/skyline2isocor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skyline2isocor/meta.yaml b/recipes/skyline2isocor/meta.yaml index ce4c92b00b71e..738ece2929b3a 100644 --- a/recipes/skyline2isocor/meta.yaml +++ b/recipes/skyline2isocor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skyline2isocor" %} -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/skyline2isocor-{{ version }}.tar.gz - sha256: 7f8e122e4ffe2cb66d02fe1d5ee06d97846d120ffb4987ed46075f0267784796 + sha256: 220ed8f18f94c53f9349ceb62379633e373775aed7c39be6dfe5bbe19a7babdd build: entry_points: From 7ddb4a055c1d98a6408a7005b2f22a6804df4ef4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 11:54:21 -0400 Subject: [PATCH 0931/1813] Update influx_si to 7.0.3 (#46395) --- recipes/influx_si/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/influx_si/meta.yaml b/recipes/influx_si/meta.yaml index e8a9540f95912..6a7c84a478a97 100644 --- a/recipes/influx_si/meta.yaml +++ b/recipes/influx_si/meta.yaml @@ -1,5 +1,5 @@ {% set name = "influx_si" %} -{% set version = "7.0.2" %} +{% set version = "7.0.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "c76482e538363b1d158da78f26b21ead699e2e5d0cea3391173463eef76329c9" + sha256: "0685631a20ab422ae558fedd4184b2256fa4289f660227b1729ec71d0306116e" build: number: 0 From 15413eb7320d55099d289e5d2def84272eba7f16 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 11:54:29 -0400 Subject: [PATCH 0932/1813] Update dxpy to 0.371.0 (#46397) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 163150722513c..ee21bce95daa2 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.370.2" %} +{% set version = "0.371.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 7cb494300e8ae195ff0551708838a2fdaf5f5f68e4575e9014e9749e7186fbc6 + sha256: d264d06c9101877e5d185c9b3165a19c0d8c5af4bdaf1c42530ad316c53188ae build: number: 0 From 199f027eef3cff9639dfa74bc44164ce02712000 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Myl=C3=A8ne=20Mariana=20Gonzales=20Andr=C3=A9?= <103585173+mari-ga@users.noreply.github.com> Date: Thu, 14 Mar 2024 17:15:23 +0100 Subject: [PATCH 0933/1813] Add vireo (#46399) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * changes to cellhashr * cellhashr fixes * deleted word in bash * changes for linting * fixes cellhashr * minor fix * fixes run_exports and summary * sha code update * stable sha256 added * fix link to get right SHA * change sha * out incompatible packages * fixes to bash * test cellhashr * fix bash * out first line build sh * generated with grayskull vireo * out cellhashr from branch * fix name conflict * run exports added * fix for test * changes to pip name * updated subpackage name * fix subpackage * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/vireosnp/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/vireosnp/meta.yaml diff --git a/recipes/vireosnp/meta.yaml b/recipes/vireosnp/meta.yaml new file mode 100644 index 0000000000000..9e68523d7c8a4 --- /dev/null +++ b/recipes/vireosnp/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "vireoSNP" %} +{% set version = "0.5.8" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/vireoSNP-{{ version }}.tar.gz + sha256: f83f00a2d398f08735fc3b5cd9326027dfe89094c746eb53a03c7f0393788c65 + +build: + entry_points: + - vireo = vireoSNP.vireo:main + - GTbarcode = vireoSNP.GTbarcode:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('vireosnp', max_pin="x.x.x") }} + +requirements: + host: + - python + - pip + run: + - python + - numpy >=1.9.0 + - scipy >=1.4.0 + - matplotlib-base + +test: + imports: + - vireoSNP + commands: + - pip check + - vireo --help + - GTbarcode --help + requires: + - pip + +about: + home: https://github.com/huangyh09/vireoSNP + summary: vireoSNP - donor deconvolution for multiplexed scRNA-seq data + license: Apache-2.0 + license_file: LICENSE + doc_url: https://vireosnp.readthedocs.io/en/latest/ From 3c7d3d53f0be272a06a98fbe2ccb93dea12a4af7 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 14 Mar 2024 18:55:33 +0200 Subject: [PATCH 0934/1813] mafft: add linux-aarch64 build (#46431) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/mafft/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/mafft/meta.yaml b/recipes/mafft/meta.yaml index 9f79b00a30dc4..c9d6d09e82b29 100644 --- a/recipes/mafft/meta.yaml +++ b/recipes/mafft/meta.yaml @@ -11,7 +11,7 @@ source: sha256: "fbd94516539c3401243d80f0c33ee247362120b0efc92b31260b2d5db484b2a6" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -33,6 +33,8 @@ about: summary: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1093/nar/gkf436 - usegalaxy-eu:rbc_mafft From 69a3be8e990b5c5947c6682e66b6b9efed61accb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 13:24:22 -0400 Subject: [PATCH 0935/1813] Update cutadapt to 4.7 (#46442) * Update cutadapt to 4.7 * add license lines * revert changes according to suggestions * Update meta.yaml --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Marcel Martin --- recipes/cutadapt/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/cutadapt/meta.yaml b/recipes/cutadapt/meta.yaml index a6b4c6ec5aa58..bb66d16ea076c 100644 --- a/recipes/cutadapt/meta.yaml +++ b/recipes/cutadapt/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "4.6" %} +{% set version = "4.7" %} package: name: cutadapt version: {{ version }} source: - url: https://files.pythonhosted.org/packages/35/b4/f1a7401c3503c17998fb9547b04353217a18323d5d85a3b957f1049ab800/cutadapt-4.6.tar.gz - sha256: 924116f34569248035b16f58e73458ed4c0004e44823b80b07f4ab419272f591 + url: https://files.pythonhosted.org/packages/92/0f/acf2c1055b31c0cf9edc4a46dd6b900905989d78602aef62293b52057fcb/cutadapt-4.7.tar.gz + sha256: 8738a35b363eaf615665a4e7d1b4beb385cd93fb7ffdcf82cd4ab6457acc879b build: - number: 1 - script: "{{ PYTHON }} -m pip install . --no-deps -vv" - skip: True # [py27 or py36] + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + skip: True # [py < 38] run_exports: - {{ pin_subpackage("cutadapt", max_pin="x") }} @@ -36,7 +36,10 @@ test: about: home: https://cutadapt.readthedocs.io/ + dev_url: https://github.com/marcelm/cutadapt license: MIT + license_family: MIT + license_file: LICENSE summary: Trim adapters from high-throughput sequencing reads extra: @@ -45,3 +48,4 @@ extra: identifiers: - biotools:cutadapt - doi:10.14806/ej.17.1.200 + - usegalaxy-eu:cutadapt From 04e0eb94b26562ae59edbf52f137d2effbc21142 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 14 Mar 2024 19:31:54 +0200 Subject: [PATCH 0936/1813] vsearch: add linux-aarch64 build (#46435) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/vsearch/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index d453c4b0d1b98..8a16a497c8ed7 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('vsearch', max_pin="x") }} @@ -43,6 +43,8 @@ about: summary: A versatile open source tool for metagenomics (USEARCH alternative) extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:vsearch - doi:10.7717/peerj.2584 From ff1761e6dd4502c6bf0211d8e0812277609ba4ac Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 14 Mar 2024 19:32:35 +0200 Subject: [PATCH 0937/1813] dnaio: add linux-aarch64 build (#46429) Needed by `cutadapt`: https://github.com/bioconda/bioconda-recipes/pull/46424 Signed-off-by: Martin Tzvetanov Grigorov --- recipes/dnaio/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/dnaio/meta.yaml b/recipes/dnaio/meta.yaml index 6b39d3c44a898..dc4afde759949 100644 --- a/recipes/dnaio/meta.yaml +++ b/recipes/dnaio/meta.yaml @@ -9,7 +9,7 @@ source: sha256: d0528c23516fe4e947970bdef33c423f0a30ab3b083bd4f6f049fd66d8cef803 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps -vv" skip: True # [py27] run_exports: @@ -38,5 +38,7 @@ about: summary: 'Read and write FASTA and FASTQ files efficiently' extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - marcelm From 7ed325a74d8cface4fab4709c1ff5030eac0ba58 Mon Sep 17 00:00:00 2001 From: Chase Mateusiak Date: Thu, 14 Mar 2024 15:33:23 -0400 Subject: [PATCH 0938/1813] adding pyranges as a dep; incrementing build number (#46416) --- recipes/callingcardstools/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/callingcardstools/meta.yaml b/recipes/callingcardstools/meta.yaml index dc887ec16da56..211fc5825f7e1 100644 --- a/recipes/callingcardstools/meta.yaml +++ b/recipes/callingcardstools/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - callingcardstools = callingcardstools:__main__.main script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" @@ -31,6 +31,7 @@ requirements: - pysam - python >=3.8 - scipy >=1.11.4 + - pyranges >=0.0.129 test: imports: From a5660571875a47cd7841a284a56718408aa09d94 Mon Sep 17 00:00:00 2001 From: nickjcroucher Date: Thu, 14 Mar 2024 20:11:36 +0000 Subject: [PATCH 0939/1813] Update gubbins (#46410) * Update python version constraints * Reset build number * Limits to python version * Change otool version for osx --- recipes/gubbins/build.sh | 8 ++++++++ recipes/gubbins/meta.yaml | 10 +++++----- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/recipes/gubbins/build.sh b/recipes/gubbins/build.sh index e0713f9972a8e..109fbbc99f4dd 100644 --- a/recipes/gubbins/build.sh +++ b/recipes/gubbins/build.sh @@ -3,6 +3,14 @@ export CFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" export CPATH=${PREFIX}/include +if [[ $target_platform == osx-* ]]; then + for toolname in "otool" "install_name_tool"; do + tool=$(find "${BUILD_PREFIX}/bin/" -name "*apple*-$toolname") + mv "${tool}" "${tool}.bak" + ln -s "/Library/Developer/CommandLineTools/usr/bin/${toolname}" "$tool" + done +fi + autoreconf -i ./configure --prefix=$PREFIX make diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml index 41884170f7d23..ac2bc3d57f6d7 100644 --- a/recipes/gubbins/meta.yaml +++ b/recipes/gubbins/meta.yaml @@ -1,13 +1,13 @@ {% set name = "gubbins" %} -{% set version = "3.3.3" %} -{% set sha256 = "b1d878130a6f07ff133efa55f0d6ed2ec3bcfa64029352ce5050c6a162b9a0b2" %} +{% set version = "3.3.4" %} +{% set sha256 = "4176530be756a8b89ad533ca593d14d24742242199dede8469c53d509f229f21" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 0 skip: True # [py < 38] run_exports: - {{ pin_subpackage('gubbins', max_pin="x") }} @@ -28,7 +28,7 @@ requirements: host: - perl - zlib - - python >=3.8 + - python >=3.8,<3.11 - scipy - setuptools - dendropy @@ -36,7 +36,7 @@ requirements: - numpy <=1.23.0 - numba run: - - python >=3.8 + - python >=3.8,<3.11 - scipy - dendropy - biopython From ab8a2725c47d7e04cf95d3cb4e0068a35aab8cb0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 16:15:34 -0400 Subject: [PATCH 0940/1813] Update segmetrics to 1.5 (#46421) --- recipes/segmetrics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/segmetrics/meta.yaml b/recipes/segmetrics/meta.yaml index 085a15459bbea..bc1fdeceb7031 100644 --- a/recipes/segmetrics/meta.yaml +++ b/recipes/segmetrics/meta.yaml @@ -1,5 +1,5 @@ {% set name = "segmetrics" %} -{% set version = "1.4.1" %} +{% set version = "1.5" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/BMCV/segmetrics/archive/refs/tags/{{ version }}.zip" - sha256: a9c2eec155cc3cc3028fed4e9cf97d08fe1ef666100bb50f251f2b63b8377616 + sha256: 3169055e6d7fdc269d7ce0d32c1f5871752001a0e03f13a25de67d52a1b4e386 build: number: 0 From 3a41450224b13a3a9e4efbd7ed527c32880683bc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 17:04:01 -0400 Subject: [PATCH 0941/1813] Update callingcardstools to 1.5.0 (#46449) --- recipes/callingcardstools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/callingcardstools/meta.yaml b/recipes/callingcardstools/meta.yaml index 211fc5825f7e1..9de7e12cdb16d 100644 --- a/recipes/callingcardstools/meta.yaml +++ b/recipes/callingcardstools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "callingcardstools" %} -{% set version = "1.4.1" %} +{% set version = "1.5.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b5e312e790fc5f88f979885ee080284a67e7142308350dcd7ca0566ec4ffc8d1 + sha256: 0606a0f51c62a7c387350f35f3cb41cd74d0c42b6f03a23e79089239de7339c4 build: noarch: python - number: 1 + number: 0 entry_points: - callingcardstools = callingcardstools:__main__.main script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" From 547f006cd316d90f8c85221a31a6230a232e9df6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 17:10:13 -0400 Subject: [PATCH 0942/1813] Update orthoflow to 0.3.4 (#46426) * Update orthoflow to 0.3.4 * add missing deps --------- Co-authored-by: mencian --- recipes/orthoflow/meta.yaml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/recipes/orthoflow/meta.yaml b/recipes/orthoflow/meta.yaml index e693187f59ef0..be8b066f348c6 100644 --- a/recipes/orthoflow/meta.yaml +++ b/recipes/orthoflow/meta.yaml @@ -1,5 +1,5 @@ {% set name = "orthoflow" %} -{% set version = "0.3.1" %} +{% set version = "0.3.4" %} package: name: {{ name|lower }} @@ -7,25 +7,24 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/orthoflow-{{ version }}.tar.gz - sha256: fb7b14dcc52d3d4ce3ef39cf50a2bf68a43f5cd2b46898b3b50a054b78fc91c8 + sha256: 063bff7c0f5e4a62e637f472ce27b95a6ccd8709fcf381b8b735bfd7df3a55e6 build: entry_points: - orthoflow = orthoflow.main:app noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv number: 0 run_exports: - - {{ pin_subpackage(name, max_pin="x") }} + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: - - python - - setuptools + - python >=3.8,<3.12 - poetry-core >=1.0.0 - pip run: - - python + - python >=3.8,<3.12 - snakemake-minimal >=7.0.0 - pandas >=1.2.5,<2.0.0 - typer >=0.4.1 @@ -36,8 +35,9 @@ requirements: - appdirs >=1.4.4 - joblib >=1.2.0 - toml >=0.10.2 - - phytest >=1.2.0 + - phytest >=1.4.1 - rich >=13.3.3 + - pulp 2.7.0 test: imports: @@ -49,6 +49,7 @@ about: home: https://github.com/rbturnbull/orthoflow summary: Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes. license: Apache-2.0 + license_family: APACHE license_file: LICENSE dev_url: https://github.com/rbturnbull/orthoflow doc_url: https://rbturnbull.github.io/orthoflow/ From f41fdb79e8eead288e7df8c4c9f8f9af5b7a896f Mon Sep 17 00:00:00 2001 From: mjohnpayne Date: Fri, 15 Mar 2024 08:11:51 +1100 Subject: [PATCH 0943/1813] Add campygstyper (#46417) * Create meta.yaml * add campygstyper --- recipes/campygstyper/meta.yaml | 35 ++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 recipes/campygstyper/meta.yaml diff --git a/recipes/campygstyper/meta.yaml b/recipes/campygstyper/meta.yaml new file mode 100644 index 0000000000000..0d869745829a8 --- /dev/null +++ b/recipes/campygstyper/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.1.1" %} +{% set name = "campygstyper" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/LanLab/{{ name }}/archive/v{{ version }}.tar.gz + sha256: 125787f7db92b8d787e47eeac710b66c6bc9e71a043dbc68de2427af09546e37 + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage('campygstyper', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - fastani >=1.3 + +about: + home: https://github.com/LanLab/campygstyper + license: GPL-3.0-or-later + license_file: LICENSE + summary: Accurate assignment of ANI genomic species to Campylobacter genomes. + +test: + commands: + - campygstyper --help From 638b60cfac204ab7d236d1acc7cab6e9386a3f22 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 17:32:55 -0400 Subject: [PATCH 0944/1813] Update morpheus to 288 (#46412) * Update morpheus to 288 * add run_exports --------- Co-authored-by: mencian --- recipes/morpheus/meta.yaml | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/recipes/morpheus/meta.yaml b/recipes/morpheus/meta.yaml index 258c57cd1367e..f4230238a4989 100644 --- a/recipes/morpheus/meta.yaml +++ b/recipes/morpheus/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "287" %} -{% set sha256 = "26757d63e44f8cd3888145edd4ddd7376e1502599672df768f3a448cbee88b5d" %} +{% set version = "288" %} +{% set sha256 = "05f2f502e591d349006eabd23f4c6a3933608d8ad1a2cfa898a46afd3245268a" %} package: name: morpheus @@ -10,9 +10,11 @@ source: sha256: '{{ sha256 }}' build: - number: 1 - skip: true # [osx] + number: 0 + skip: True # [osx] script: mkdir -p $PREFIX/bin && cp * $PREFIX/bin && cd $PREFIX/bin && ln -s ./morpheus_mzml_mono_cl.exe ./morpheus && chmod +x $PREFIX/bin/morpheus* + run_exports: + - {{ pin_subpackage('morpheus', max_pin=None) }} requirements: run: @@ -28,9 +30,12 @@ about: license_family: MIT license_file: MIT_License.CommandLine.txt summary: mass spectrometry–based proteomics database search algorithm - + doc_url: https://cwenger.github.io/Morpheus/ + dev_url: https://github.com/cwenger/Morpheus/ + extra: identifiers: - doi:10.1021/pr301024c + - biotools:morpheus skip-lints: - should_be_noarch_generic From bab54c04941a9e1623015df9d6410b2c42d61911 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 14 Mar 2024 17:21:43 -0500 Subject: [PATCH 0945/1813] Update iqtree to 2.3.0 (#46451) --- recipes/iqtree/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/iqtree/meta.yaml b/recipes/iqtree/meta.yaml index 546ddf58b9357..3f9a392ea0926 100644 --- a/recipes/iqtree/meta.yaml +++ b/recipes/iqtree/meta.yaml @@ -1,6 +1,6 @@ {% set name = "IQTREE" %} -{% set version = "2.2.6" %} -{% set sha256 = "8026bf089a135f4586ebca43fff9af6d4718a936f262b5ea11648b8947782c42" %} +{% set version = "2.3.0" %} +{% set sha256 = "d55af7fda5a4bbe0bdda7a0e00aa5003bcfe78c771a5f2210b547bf7c7281d63" %} package: name: {{ name|lower }} @@ -24,7 +24,7 @@ requirements: - make - cmake - llvm-openmp # [osx] - - ld64 # [osx] + - ld64 # [osx] host: - boost-cpp - eigen @@ -42,6 +42,7 @@ about: license_family: GPL2 license_file: LICENSE summary: "Efficient phylogenomic software by maximum likelihood." + doc_url: http://www.iqtree.org/doc/ extra: identifiers: @@ -49,4 +50,5 @@ extra: - doi:10.1093/molbev/msu300 - doi:10.1038/nmeth.4285 - doi:10.1093/molbev/msx281 + - doi:10.1093/sysbio/syae008 - usegalaxy-eu:{{ name|lower }} From 6109de5e743058cef6cfc0f337924ca8d36f4b7a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 18:22:56 -0400 Subject: [PATCH 0946/1813] Update msmetaenhancer to 0.4.0 (#46402) * Update msmetaenhancer to 0.4.0 * add run_exports --------- Co-authored-by: mencian --- recipes/msmetaenhancer/meta.yaml | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/recipes/msmetaenhancer/meta.yaml b/recipes/msmetaenhancer/meta.yaml index f3d1f4ad42681..a241ca1e81132 100644 --- a/recipes/msmetaenhancer/meta.yaml +++ b/recipes/msmetaenhancer/meta.yaml @@ -1,22 +1,25 @@ -{% set name = "MSMetaEnhancer" %} -{% set version = "0.3.0" %} +{% set name = "msmetaenhancer" %} +{% set version = "0.4.0" %} package: name: {{ name|lower }} version: {{ version }} source: - url: "https://github.com/RECETOX/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 7d889be548db18ec1e34c04947b8f8c7d9660241d8142bdc9842052396475ba8 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/msmetaenhancer-{{ version }}.tar.gz + sha256: e422a3849a486613b08d04801c873fa369b170361b4e27c06c2531023a47823b build: - number: 1 + number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('msmetaenhancer', max_pin="x.x") }} requirements: host: - python >=3.9 + - poetry-core - pip run: - python >=3.9 @@ -27,12 +30,13 @@ requirements: - aiohttp - asyncstdlib - frozendict + - twine - tabulate - rdkit - multidict - aiocircuitbreaker - openpyxl - + test: imports: - MSMetaEnhancer @@ -40,6 +44,7 @@ test: about: home: https://github.com/RECETOX/MSMetaEnhancer license: MIT + license_family: MIT license_file: LICENSE summary: "MSMetaEnhancer is a Python tool that adds more annotations (e.g. SMILES, InChI, CAS number) to MSP files." dev_url: "https://github.com/RECETOX/MSMetaEnhancer" @@ -49,3 +54,6 @@ extra: recipe-maintainers: - xtrojak - martenson + identifiers: + - biotools:msmetaenhancer + - doi:10.21105/joss.04494 From 85e2a9493f9c0548c0b05fc557fc773ee5f53532 Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Thu, 14 Mar 2024 18:27:10 -0400 Subject: [PATCH 0947/1813] sistr v1.1.2 new conda recipe (#46448) --- recipes/sistr_cmd/build.sh | 2 ++ recipes/sistr_cmd/meta.yaml | 52 ++++++++++++++++++++++++++----------- 2 files changed, 39 insertions(+), 15 deletions(-) create mode 100644 recipes/sistr_cmd/build.sh diff --git a/recipes/sistr_cmd/build.sh b/recipes/sistr_cmd/build.sh new file mode 100644 index 0000000000000..87f4375bf2c85 --- /dev/null +++ b/recipes/sistr_cmd/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +python -m pip install . --no-deps --no-build-isolation --ignore-installed --no-cache-dir -vvv \ No newline at end of file diff --git a/recipes/sistr_cmd/meta.yaml b/recipes/sistr_cmd/meta.yaml index b87ccfaeab3f3..bec537bcae08d 100644 --- a/recipes/sistr_cmd/meta.yaml +++ b/recipes/sistr_cmd/meta.yaml @@ -1,33 +1,47 @@ {% set name = "sistr_cmd" %} -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: bf6f076b2bf4b7df78ff86bc905f11f19f982bddc812effb1ae373de86d4ae6f + #url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + #sha256: f68de3f90c2d744db1f282db82f9e4094626c1448a5dbf834ff853c760975bb5 + url: https://github.com/phac-nml/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 5acffbaeb345bb6bdea4fae3317e651c254b114b37762eeb284c5bfa928329a2 + build: + number: 0 noarch: python - number: 3 - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + #script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --ignore-installed --no-cache-dir -vvv + entry_points: + - sistr=sistr.sistr_cmd:main + - sistr_init=sistr.sistr_cmd:setup_sistr_dbs requirements: host: - - python + - python >=3.4 - pip + - setuptools ==58.2.0 + - pandas >=0.22,<3 + - pycurl + - scipy >=1.1.0,<2 + - pytables >=3.3.0 + - numpy run: - - python - - numpy >=1.11.1,<1.23.5 - - pandas >=0.18.1,<=1.0.5 + - python >=3.4 + - {{ pin_compatible('numpy', max_pin="x") }} + - pandas >=0.22,<3 - pytables >=3.3.0 - - pycurl >=7.43.0,<8 - - scipy >=1.1.0,<2 - - blast + - {{ pin_compatible('scipy', max_pin="x.x") }} + - {{ pin_compatible('pycurl') }} + - blast >=2.9.0 - mafft - - mash + - mash >=2.0 - python-dateutil test: @@ -36,8 +50,16 @@ test: - sistr -V about: - home: https://github.com/peterk87/sistr_cmd/ + home: https://github.com/phac-nml/sistr_cmd/ license: Apache-2.0 license_family: APACHE license_file: LICENSE - summary: "Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction" \ No newline at end of file + summary: "Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction" + dev_url: https://github.com/phac-nml/sistr_cmd + +extra: + identifiers: + - usegalaxy-eu:sistr_cmd + - doi:10.1371/journal.pone.0147101 + - biotools:SISTR + From f463d48549370c8b35d5619c043dd97ce723f901 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 18:38:01 -0400 Subject: [PATCH 0948/1813] Update sanntis to 0.9.3.5 (#46422) --- recipes/sanntis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sanntis/meta.yaml b/recipes/sanntis/meta.yaml index 8924ab66247f5..72516e12f2345 100644 --- a/recipes/sanntis/meta.yaml +++ b/recipes/sanntis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sanntis" %} -{% set version = "0.9.3.4" %} -{% set sha256 = "a5b1fad410981e330827949699f29dd9a521bafbbef0ea2859ae33bd3add024e" %} +{% set version = "0.9.3.5" %} +{% set sha256 = "6e6753afb557fd4c1a5bb63059bfe9ce68bcdaf64a41162494cb5ebbef16ab18" %} package: name: {{ name }} From f8ce0871fc19b2482dfd517cd5f19f2e4f90520f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 18:38:19 -0400 Subject: [PATCH 0949/1813] Update callingcardstools to 1.5.1 (#46452) --- recipes/callingcardstools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/callingcardstools/meta.yaml b/recipes/callingcardstools/meta.yaml index 9de7e12cdb16d..08159508bcc91 100644 --- a/recipes/callingcardstools/meta.yaml +++ b/recipes/callingcardstools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "callingcardstools" %} -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 0606a0f51c62a7c387350f35f3cb41cd74d0c42b6f03a23e79089239de7339c4 + sha256: 05d19fa9a41c086413fd4067c69170bd9f7cdfb786cf40d5217b48926854d3ec build: noarch: python From 096252e231d27d25fd0c1b1b0df6bda2bb03131b Mon Sep 17 00:00:00 2001 From: Ryan Morrison <54183277+ryanmorrison22@users.noreply.github.com> Date: Thu, 14 Mar 2024 22:40:43 +0000 Subject: [PATCH 0950/1813] Add BioCamLib (#46309) Co-authored-by: Ryan Morrison --- recipes/biocamlib/build.sh | 17 ++++++++++++++ recipes/biocamlib/meta.yaml | 47 +++++++++++++++++++++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 recipes/biocamlib/build.sh create mode 100644 recipes/biocamlib/meta.yaml diff --git a/recipes/biocamlib/build.sh b/recipes/biocamlib/build.sh new file mode 100644 index 0000000000000..1851efa249a27 --- /dev/null +++ b/recipes/biocamlib/build.sh @@ -0,0 +1,17 @@ +#!/bin/bash +if [ "$(uname)" == "Darwin" ]; then + echo "Installing BiOCamLib for OSX." +else + echo "Installing BiOCamLib for Linux" +fi + +mkdir -p $PREFIX/bin +cp $SRC_DIR/FASTools $PREFIX/bin +cp $SRC_DIR/Parallel $PREFIX/bin +cp $SRC_DIR/Octopus $PREFIX/bin +cp $SRC_DIR/RC $PREFIX/bin + +chmod +x $PREFIX/bin/FASTools +chmod +x $PREFIX/bin/Parallel +chmod +x $PREFIX/bin/Octopus +chmod +x $PREFIX/bin/RC \ No newline at end of file diff --git a/recipes/biocamlib/meta.yaml b/recipes/biocamlib/meta.yaml new file mode 100644 index 0000000000000..5c9bd52dd6bc1 --- /dev/null +++ b/recipes/biocamlib/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "biocamlib" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + - url: https://github.com/PaoloRibeca/BiOCamLib/releases/download/v{{ version }}/BiOCamLib-{{ version }}-Linux_x86-64.tar.xz # [linux] + sha256: bd08b1fe1949cb2faa98b46b40a99c84f0f5581515e337bab50111b11d9c7f12 # [linux] + - url: https://github.com/PaoloRibeca/BiOCamLib/releases/download/v{{ version }}/BiOCamLib-{{ version }}-MacOS_x86-64.tar.xz # [osx] + sha256: e55766df1e0af12f825ab1fe244841b70b8ccce9c764b60acc56d4386d3ce9bb # [osx] + +build: + run_exports: + {{ pin_subpackage(name, max_pin="x") }} + number: 0 + skip: true # [win] + +test: + commands: + - Parallel -V + - FASTools -V + - Octopus -V + - RC -V + +about: + home: https://github.com/PaoloRibeca/BiOCamLib + license: GPL-3.0-only + license_file: LICENSE + summary: 'An OCaml foundation upon which a number of the bioinformatics tools are built.' + description: | + BiOCamLib is an OCaml foundation upon which a number of the bioinformatics tools are built, + including KPop . It consists of four tools: + 1. RC, which can efficiently compute the reverse complement of sequences. + 2. Octopus, which is a high-throughput program to compute the transitive closure of strings. + 3. Parallel, which allows the splits and processes an input file chunk-wise using a reader/workers/writer model. + 4. FASTools, which is a Swiss-knife tool for the manipulation of FASTA/FASTQ files. + + dev_url: https://github.com/PaoloRibeca/BiOCamLib + +extra: + recipe-maintainers: + - PaoloRibeca + - ryanmorrison22 + skip-lints: + - should_be_noarch_generic From d0371a0776864302ed2b6d183b4fc71df4d4020d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 19:00:53 -0400 Subject: [PATCH 0951/1813] Update ostir to 1.1.2 (#46443) * Update ostir to 1.1.2 * Adds Version Pinning (#46445) Updates Bioconda recipe to include the pinning introduced since OSTIR was last updated. At this time OSTIR does not comply with SimVar * bump minimum python version * remove LICENSE; it is packaged along with pypi source * revert to x.x.x --------- Co-authored-by: Cameron Roots <38054423+croots@users.noreply.github.com> Co-authored-by: mencian --- recipes/ostir/LICENSE | 674 ---------------------------------------- recipes/ostir/meta.yaml | 16 +- 2 files changed, 10 insertions(+), 680 deletions(-) delete mode 100644 recipes/ostir/LICENSE diff --git a/recipes/ostir/LICENSE b/recipes/ostir/LICENSE deleted file mode 100644 index 02fefceb563f1..0000000000000 --- a/recipes/ostir/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. - - If the disclaimer of warranty and limitation of liability provided -above cannot be given local legal effect according to their terms, -reviewing courts shall apply local law that most closely approximates -an absolute waiver of all civil liability in connection with the -Program, unless a warranty or assumption of liability accompanies a -copy of the Program in return for a fee. - - END OF TERMS AND CONDITIONS - - How to Apply These Terms to Your New Programs - - If you develop a new program, and you want it to be of the greatest -possible use to the public, the best way to achieve this is to make it -free software which everyone can redistribute and change under these terms. - - To do so, attach the following notices to the program. It is safest -to attach them to the start of each source file to most effectively -state the exclusion of warranty; and each file should have at least -the "copyright" line and a pointer to where the full notice is found. - - OSTIR: Open Source Translation Initiation Rates - Copyright (C) 2021 Cameron Roots, Jeffrey Barrick - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/recipes/ostir/meta.yaml b/recipes/ostir/meta.yaml index d826cf029e5fa..14914da27c56f 100644 --- a/recipes/ostir/meta.yaml +++ b/recipes/ostir/meta.yaml @@ -1,5 +1,5 @@ {% set name = "OSTIR" %} -{% set version = "1.1.0" %} +{% set version = "1.1.2" %} package: name: "{{ name|lower }}" @@ -7,21 +7,23 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 05df18370a371ea1fa5260d1eeeebf015368363b4174ee1005b3047c697489b4 + sha256: 9ca8941245ed0265e87e68c4b09adc599324d8f9e10e19e377262680288c7771 build: number: 0 entry_points: - ostir = ostir.ostir:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('ostir', max_pin="x.x.x") }} requirements: host: - pip - - python >=3.7 + - python >=3.8 run: - - python >=3.7 + - python >=3.8 - viennarna >=2.4.18 - numpy >=1.20.1 @@ -34,10 +36,12 @@ test: about: home: "https://github.com/barricklab/ostir" - license: "GNU General Public v3 or later (GPLv3+)" + license: "GPL-3.0-or-later" license_family: GPL3 license_file: "LICENSE" summary: "Open Source Transcription Initiation Rates" + doc_url: "https://github.com/barricklab/ostir/wiki" + dev_url: "https://github.com/barricklab/ostir" extra: recipe-maintainers: From e69ce97339edbc3475d0fef0b844c9dd0d726f8c Mon Sep 17 00:00:00 2001 From: Reid Wagner <74672860+reid-wagner@users.noreply.github.com> Date: Thu, 14 Mar 2024 18:41:13 -0500 Subject: [PATCH 0952/1813] Add libraries necessary for database splitting. (#46453) --- recipes/fragpipe/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/fragpipe/meta.yaml b/recipes/fragpipe/meta.yaml index a093ff8dc5456..26d268719fd09 100644 --- a/recipes/fragpipe/meta.yaml +++ b/recipes/fragpipe/meta.yaml @@ -12,7 +12,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('fragpipe', max_pin="x.x") }} @@ -31,6 +31,8 @@ requirements: - python =3.9 - msfragger >=4.0 - ionquant >=1.10.12 + - easypqp >=0.1.34 + - lxml test: commands: From 7f3f1d821a422c81f6c87f5c36510a2978607891 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 21:55:24 -0400 Subject: [PATCH 0953/1813] Update parsnp to 2.0.4 (#46454) --- recipes/parsnp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index 80b3d3aff5598..33ba8ff6a4f39 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.3" %} +{% set version = "2.0.4" %} package: name: parsnp @@ -6,7 +6,7 @@ package: source: url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" - sha256: 8e0c71662f69fc77eeb10a8c4687ff75dfb9d37daf7fca1a4ca410b1c1b1f7cb + sha256: 04993dcb60034d3c9188fbbbbd6c8209760d1e0d0b0b3efc6458479965ea31b0 build: number: 0 From 0e422d1d5c473c9793a2e69560ff4a4891728c40 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 21:55:31 -0400 Subject: [PATCH 0954/1813] Update lamassemble to 1.7.2 (#46456) --- recipes/lamassemble/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/lamassemble/meta.yaml b/recipes/lamassemble/meta.yaml index b9864b9b87ac8..dc72a38790941 100644 --- a/recipes/lamassemble/meta.yaml +++ b/recipes/lamassemble/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.7.1" %} +{% set version = "1.7.2" %} package: name: lamassemble @@ -6,7 +6,7 @@ package: source: url: https://gitlab.com/mcfrith/lamassemble/-/archive/{{ version }}/lamassemble-{{ version }}.tar.gz - sha256: 74c3965c33d1e8807ff4d7b90b55630e1bf7a2485e1d58615b1ed377958ad6c6 + sha256: 786f509c4b4b61521ff4d6bbe589acd7fdd49969bf190db345d501a823a91a75 build: number: 0 From 2bd71881d42ba556289cb0c5bebc98d7524283a2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Mar 2024 23:13:51 -0400 Subject: [PATCH 0955/1813] Update sage-proteomics to 0.14.7 (#46455) --- recipes/sage-proteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sage-proteomics/meta.yaml b/recipes/sage-proteomics/meta.yaml index c6e19501ae077..2e26967970fd3 100644 --- a/recipes/sage-proteomics/meta.yaml +++ b/recipes/sage-proteomics/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sage-proteomics" %} -{% set version = "0.14.6" %} -{% set sha256 = "5df02517d7c3e4f99785177d595c3106db8df6e443618837bab840c664886f54" %} +{% set version = "0.14.7" %} +{% set sha256 = "894b59429a67dc22592fc65fca547ee6d67f8bada71d09f7c1a81524b65fe6da" %} package: name: {{ name }} From 87cf07c7c882ea5563e2a7900a583790a0b43cc1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 15 Mar 2024 04:38:26 -0400 Subject: [PATCH 0956/1813] Update phables to 1.3.1 (#46460) --- recipes/phables/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phables/meta.yaml b/recipes/phables/meta.yaml index c2f2754b2359c..eb65405a8a2a0 100644 --- a/recipes/phables/meta.yaml +++ b/recipes/phables/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phables" %} -{% set version = "1.3.0" %} +{% set version = "1.3.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/Vini2/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: bded81ddbfdce0b5143da3ebf51e56b1fe61f3b23c282433940c0e357014e642 + sha256: 75509327984bdf0b8d28ea84c188800ec8054ef6af08ae4b47b142b40065fbc0 build: number: 0 From 4dbae67ff0491442313bd289ea06d7dc571ec2e3 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Fri, 15 Mar 2024 10:46:32 -0600 Subject: [PATCH 0957/1813] pin tabix version in snippy (#46458) * pin tabix version in snippy * fix tabix typo --- recipes/snippy/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/snippy/meta.yaml b/recipes/snippy/meta.yaml index f20c442102beb..42b89cd854fde 100644 --- a/recipes/snippy/meta.yaml +++ b/recipes/snippy/meta.yaml @@ -12,8 +12,10 @@ source: sha256: '{{ sha256 }}' build: - number: 3 + number: 4 noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: run: @@ -26,6 +28,7 @@ requirements: - parallel >=20170422 - freebayes >=1.3.1 - vcflib >=1.0.0_rc3,<=1.0.2 # crashes with v1.0.3 and later + - tabixpp 1.1.0 # vcflib requires libtabixpp.so.0, no longer available as of 1.1.2 - snpeff >=4.3,<=5.0 # crashes with v5.1 - vt >=0.5772 - snp-sites >=2.4 From 5eeac55d9b7dff133bac0fa150937db24e51b2ee Mon Sep 17 00:00:00 2001 From: Isuru Fernando Date: Fri, 15 Mar 2024 12:03:07 -0500 Subject: [PATCH 0958/1813] Add azimuth and dependencies (#45914) * Add azimuth and dependencies * Use github archives and add run_exports * fix run_exports * rename to have r- prefix * SPDX --- recipes/r-azimuth/meta.yaml | 86 +++++++++++++++++++++++++++++++++ recipes/r-presto/meta.yaml | 54 +++++++++++++++++++++ recipes/r-seurat-data/meta.yaml | 42 ++++++++++++++++ recipes/r-seurat-disk/meta.yaml | 59 ++++++++++++++++++++++ 4 files changed, 241 insertions(+) create mode 100644 recipes/r-azimuth/meta.yaml create mode 100644 recipes/r-presto/meta.yaml create mode 100644 recipes/r-seurat-data/meta.yaml create mode 100644 recipes/r-seurat-disk/meta.yaml diff --git a/recipes/r-azimuth/meta.yaml b/recipes/r-azimuth/meta.yaml new file mode 100644 index 0000000000000..ee0ab9c9b5eb4 --- /dev/null +++ b/recipes/r-azimuth/meta.yaml @@ -0,0 +1,86 @@ +{% set version = '0.4.6' %} +package: + name: r-azimuth + version: {{ version|replace("-", "_") }} +source: + url: https://github.com/satijalab/azimuth/archive/refs/tags/v{{ version }}.tar.gz + sha256: 14f2c307590dec6184702be4042f62def674b91f75af5153a6ae0d89277f5fd2 +build: + script: $R CMD INSTALL --build . + run_exports: + - {{ pin_subpackage("r-azimuth", max_pin="x.x.x") }} + number: 0 + rpaths: + - lib/R/lib/ +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - r-base + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - 'r-dt >=0.15' + - 'r-matrix >=1.2.18' + - 'r-rcpp >=1.0.7' + - 'r-seurat >=4.0.0' + - 'r-seurat-data ==0.2.1' + - 'r-seurat-disk ==0.0.0.9021' + - 'r-seuratobject' + - 'r-future >=1.19.1' + - 'r-ggplot2 >=3.3.2' + - 'bioconductor-glmgampoi >=1.0.0' + - 'r-googlesheets4 >=0.2.0' + - 'r-hdf5r >=1.3.2' + - 'r-htmltools >=0.5.0' + - 'r-httr >=1.4.2' + - 'r-jsonlite >=1.7.0' + - 'r-patchwork >=1.0.1' + - 'r-plotly' + - 'r-presto ==1.0.0' + - 'r-rlang >=0.4.8' + - 'r-scales >=1.1.1' + - 'r-shiny >=1.5.0' + - 'r-shinybs >=0.61' + - 'r-shinydashboard >=0.7.1' + - 'r-shinyjs >=2.0.0' + - 'r-stringr >=1.4.0' + - 'r-withr >=2.3.0' + run: + - r-base + - 'r-dt >=0.15' + - 'r-matrix >=1.2.18' + - 'r-rcpp >=1.0.7' + - 'r-seurat >=4.0.0' + - 'r-seurat-data ==0.2.1' + - 'r-seurat-disk ==0.0.0.9021' + - 'r-seuratobject' + - 'r-future >=1.19.1' + - 'r-ggplot2 >=3.3.2' + - 'bioconductor-glmgampoi >=1.0.0' + - 'r-googlesheets4 >=0.2.0' + - 'r-hdf5r >=1.3.2' + - 'r-htmltools >=0.5.0' + - 'r-httr >=1.4.2' + - 'r-jsonlite >=1.7.0' + - 'r-patchwork >=1.0.1' + - 'r-plotly' + - 'r-presto ==1.0.0' + - 'r-rlang >=0.4.8' + - 'r-scales >=1.1.1' + - 'r-shiny >=1.5.0' + - 'r-shinybs >=0.61' + - 'r-shinydashboard >=0.7.1' + - 'r-shinyjs >=2.0.0' + - 'r-stringr >=1.4.0' + - 'r-withr >=2.3.0' +test: + commands: + - '$R -e "library(''Azimuth'')"' +about: + home: https://github.com/satijalab/azimuth + license: GPL-3.0-only + summary: Azimuth is a Shiny app demonstrating a query-reference mapping algorithm for single-cell data. + license_family: GPL3 + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - LICENSE diff --git a/recipes/r-presto/meta.yaml b/recipes/r-presto/meta.yaml new file mode 100644 index 0000000000000..5cf1e0652e250 --- /dev/null +++ b/recipes/r-presto/meta.yaml @@ -0,0 +1,54 @@ +{% set version = '1.0.0' %} +package: + name: r-presto + version: {{ version|replace("-", "_") }} +source: + url: https://github.com/immunogenomics/presto/archive/31dc97fed5e2e7fc323ae4af62f72181cc51d9a3.tar.gz + sha256: 720ef58aba219af03344e0ae0408fc48feda50e6b7f7f4af2251eb24ce1bfb88 +build: + script: $R CMD INSTALL --build . + run_exports: + - {{ pin_subpackage("r-presto", max_pin="x.x.x") }} + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, testthat, Seurat, SingleCellExperiment, SummarizedExperiment, broom, BiocStyle, DESeq2 +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - r-base + - r-matrix + - r-rcpp + - r-rcpparmadillo + - r-data.table + - r-dplyr + - r-purrr + - r-rlang + - r-tibble + - r-tidyr + run: + - r-base + - r-matrix + - r-rcpp + - r-rcpparmadillo + - r-data.table + - r-dplyr + - r-purrr + - r-rlang + - r-tibble + - r-tidyr +test: + commands: + - $R -e "library('presto')" +about: + home: https://github.com/immunogenomics/presto + license: GPL-3.0-only + summary: Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces + to dense and sparse matrices, as well as genomics analysis frameworks Seurat and + SingleCellExperiment. + license_family: GPL3 + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/r-seurat-data/meta.yaml b/recipes/r-seurat-data/meta.yaml new file mode 100644 index 0000000000000..da945540fea2a --- /dev/null +++ b/recipes/r-seurat-data/meta.yaml @@ -0,0 +1,42 @@ +{% set version = '0.2.1' %} +package: + name: r-seurat-data + version: {{ version|replace("-", "_") }} +source: + url: https://github.com/satijalab/seurat-data/archive/refs/tags/v{{ version }}.tar.gz + sha256: 134b0dbc113e3533494461646c8362189b2bdf8940050de3561bcd488d905438 +build: + script: $R CMD INSTALL --build . + run_exports: + - {{ pin_subpackage("r-seurat-data", max_pin="x.x.x") }} + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + host: + - r-base + - r-cli + - r-crayon + - r-rappdirs + run: + - r-base + - r-cli + - r-crayon + - r-rappdirs +test: + commands: + - $R -e "library('SeuratData')" +about: + home: http://www.satijalab.org/seurat + dev_url: https://github.com/satijalab/seurat-data + license: GPL-3.0-only + summary: Single cell RNA sequencing datasets can be large, consisting of matrices that contain + expression data for several thousand features across several thousand cells. This + package is designed to easily install, manage, and learn about various single-cell + datasets, provided Seurat objects and distributed as independent packages. + license_family: GPL3 + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - LICENSE diff --git a/recipes/r-seurat-disk/meta.yaml b/recipes/r-seurat-disk/meta.yaml new file mode 100644 index 0000000000000..6cda8484ac46d --- /dev/null +++ b/recipes/r-seurat-disk/meta.yaml @@ -0,0 +1,59 @@ +{% set version = '0.0.0.9021' %} +package: + name: r-seurat-disk + version: {{ version|replace("-", "_") }} +source: + url: https://github.com/mojaveazure/seurat-disk/archive/877d4e18ab38c686f5db54f8cd290274ccdbe295.tar.gz + sha256: d2d6b6604e8a1f6de90956d0401d34b51b07b30671a445d0e06876f2dec999ac +build: + script: $R CMD INSTALL --build . + run_exports: + - {{ pin_subpackage("r-seurat-disk", max_pin="x.x.x.x") }} + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + host: + - r-base + - r-matrix >=1.2.18 + - r-r6 >=2.4.1 + - r-seurat >=3.2.0 + - r-seuratobject >=4.0.0 + - r-cli >=2.0.1 + - r-crayon >=1.3.4 + - r-hdf5r >=1.3.0 + - r-rlang >=0.4.4 + - r-stringi >=1.4.6 + - r-withr >=2.1.2 + run: + - r-base + - r-matrix >=1.2.18 + - r-r6 >=2.4.1 + - r-seurat >=3.2.0 + - r-seuratobject >=4.0.0 + - r-cli >=2.0.1 + - r-crayon >=1.3.4 + - r-hdf5r >=1.3.0 + - r-rlang >=0.4.4 + - r-stringi >=1.4.6 + - r-withr >=2.1.2 +test: + commands: + - '$R -e "library(''SeuratDisk'')"' +about: + home: https://mojaveazure.github.io/seurat-disk/ + dev_url: https://github.com/mojaveazure/seurat-disk + license: GPL-3.0-only + summary: The h5Seurat file format is specifically designed for the storage and analysis of + multi-modal single-cell and spatially-resolved expression experiments, for example, + from CITE-seq or 10X Visium technologies. It holds all molecular information and + associated metadata, including (for example) nearest-neighbor graphs, dimensional + reduction information, spatial coordinates and image data, and cluster labels. We + also support rapid and on-disk conversion between h5Seurat and AnnData objects, + with the goal of enhancing interoperability between Seurat and Scanpy. + license_family: GPL3 + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - LICENSE From 0d70054b70bf285289a22a1de708c744c0fdab15 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 15 Mar 2024 13:27:34 -0400 Subject: [PATCH 0959/1813] Update busco to 5.7.0 (#46490) * Update busco to 5.7.0 * Constrain biopython; add patch --------- Co-authored-by: Matthew Berkeley <42berkeley@cua.edu> --- .../busco/0001-Set-conda-distribution.patch | 23 +++++++++++++++++++ recipes/busco/meta.yaml | 8 +++---- 2 files changed, 27 insertions(+), 4 deletions(-) create mode 100644 recipes/busco/0001-Set-conda-distribution.patch diff --git a/recipes/busco/0001-Set-conda-distribution.patch b/recipes/busco/0001-Set-conda-distribution.patch new file mode 100644 index 0000000000000..b8a0ac5f2531e --- /dev/null +++ b/recipes/busco/0001-Set-conda-distribution.patch @@ -0,0 +1,23 @@ +--- a/src/busco/run_BUSCO.py ++++ b/src/busco/run_BUSCO.py +@@ -121,18 +121,12 @@ class BuscoMaster: + logger.debug("File upload failed. Status code: {}".format(response.status)) + + def get_dist_info(self): +- if ( # todo: fix +- "conda" in __file__ +- and os.environ("CONDA_DEFAULT_ENV") +- and os.environ("CONDA_PREFIX") +- ): +- self.run_data["distribution"] = "conda" +- elif os.path.exists("/.dockerenv"): ++ if os.path.exists("/.dockerenv"): + self.run_data["distribution"] = "docker" + elif os.path.exists("/.singularity.d"): + self.run_data["distribution"] = "singularity" + else: +- self.run_data["distribution"] = "manual" ++ self.run_data["distribution"] = "conda" + + def get_download_url(self): + if self.config.getboolean("busco_run", "offline"): diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml index 515c990c241e1..a6261567bb48f 100644 --- a/recipes/busco/meta.yaml +++ b/recipes/busco/meta.yaml @@ -1,6 +1,6 @@ {% set name = "busco" %} -{% set version = "5.6.1" %} -{% set sha256 = "1129d8dd1779455b77c47a926650e1974aaca58eeb9e6b3b6e4a706154ab2da8" %} +{% set version = "5.7.0" %} +{% set sha256 = "dbd9e07a5fb42583bd6ddbbfe06c420d5317a6f3698e6f4be0f53baa6c3ccc5e" %} package: name: busco @@ -26,7 +26,7 @@ requirements: - blast >=2.10.1 # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0 - hmmer >=3.1b2 # sepp needs this version - augustus >=3.3 - - biopython + - biopython >=1.79 - prodigal - sepp >=4.3.10 - dendropy <4.6.0 # necessary temporarily until SEPP updates their codebase or recipe @@ -41,7 +41,7 @@ requirements: - blast >=2.10.1 # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0 - hmmer >=3.1b2 # sepp needs this version - augustus >=3.3 - - biopython + - biopython >=1.79 - r-base - r-ggplot2 >=2.2.1 - prodigal From 98196d74c913fd34b91d7e290230ea83633a3411 Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Fri, 15 Mar 2024 19:28:45 +0000 Subject: [PATCH 0960/1813] Update csvtk to v0.30.0 (#46464) --- recipes/csvtk/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/csvtk/meta.yaml b/recipes/csvtk/meta.yaml index f81d3b38c5053..02ffed6b4f62e 100644 --- a/recipes/csvtk/meta.yaml +++ b/recipes/csvtk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.29.0" %} +{% set version = "0.30.0" %} package: name: csvtk @@ -11,9 +11,9 @@ build: source: - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx] - md5: 055172fe0ce888cdbbe11c3c03846aa4 # [osx] + md5: c415255e265ba0cd547806fdbda05652 # [osx] - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux] - md5: ac796feaa66514b0b5eb9b21df81c22b # [linux] + md5: 8f5877d4fbea89609d64bd2679956476 # [linux] test: commands: From f166df2cbe12844a66280a250feb19a1ba1c3ddb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 15 Mar 2024 15:53:51 -0400 Subject: [PATCH 0961/1813] Update bactopia-variants to 1.0.2 (#46493) * Update bactopia-variants to 1.0.2 * Update meta.yaml * add run_exports --------- Co-authored-by: Robert A. Petit III --- recipes/bactopia-variants/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/bactopia-variants/meta.yaml b/recipes/bactopia-variants/meta.yaml index fa794e76b8c6d..cb6e67163305d 100644 --- a/recipes/bactopia-variants/meta.yaml +++ b/recipes/bactopia-variants/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: bactopia-variants @@ -7,10 +7,12 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage("bactopia-variants", max_pin="x") }} source: url: https://github.com/bactopia/bactopia-variants/archive/v{{version}}.tar.gz - sha256: 4a18e88b7b01790620911762cf8e7d38d1c74ad94044b5ebdd23b9a246a96562 + sha256: 0adcc2cbdbcdd851f604243e88a9bb687baf00c533152899399da1f4ef759ae9 requirements: run: @@ -25,6 +27,7 @@ requirements: - sed - vcf-annotator >=0.7 - vcflib >=1.0.0_rc3,<=1.0.2 # Snippy crashes with v1.0.3 and later + - tabixpp 1.1.0 # vcflib requires libtabixpp.so.0, no longer available as of 1.1.2 test: commands: From d4b4e5395dba8259877bd71b227cd668bde8e41f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 15 Mar 2024 17:02:17 -0400 Subject: [PATCH 0962/1813] Update clair3-illumina to 1.0.6 (#46494) --- recipes/clair3-illumina/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clair3-illumina/meta.yaml b/recipes/clair3-illumina/meta.yaml index 0f7f70a0be418..468c6582e9270 100644 --- a/recipes/clair3-illumina/meta.yaml +++ b/recipes/clair3-illumina/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clair3-illumina" %} -{% set version = "1.0.5" %} +{% set version = "1.0.6" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/HKU-BAL/Clair3/archive/refs/tags/v{{ version }}.zip - sha256: 515129dace446d48a58e7f156d40ce09eb8ef15484661e0b7ff53fe83e5ac40a + sha256: 30821ae909e4d28d5ca01594873b7977690cc2e63f5777b5d6799ec86660e370 build: number: 0 From d1b59bd879bfb85edbff9c66d81182645056e00c Mon Sep 17 00:00:00 2001 From: zhenxian <920596906@qq.com> Date: Sat, 16 Mar 2024 14:52:00 +0800 Subject: [PATCH 0963/1813] Update clair3 to v1.0.6 (#46487) * Update clair3 to v1.0.6 * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/clair3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clair3/meta.yaml b/recipes/clair3/meta.yaml index 057a47b092a51..038a1a59b7bf1 100644 --- a/recipes/clair3/meta.yaml +++ b/recipes/clair3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clair3" %} -{% set version = "1.0.5" %} +{% set version = "1.0.6" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: http://www.bio8.cs.hku.hk/clair3/bioconda/Clair3_v{{ version }}.zip - sha256: 05ba9b4de25753ef1f20f0199521672d6d5a4f986d1b2b5d7dc77e5c4bcd3b9a + sha256: 771cc626460bfe1acf9bc535e2d44110e4076622ed900a6867861bb324687b7e build: number: 0 From 2a5501c7be1542fcbf0adc268fb9ac14fcbd0376 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sat, 16 Mar 2024 08:47:00 +0100 Subject: [PATCH 0964/1813] Add revoluzer 0.1.5 (#46403) * revoluzer 0.1.3 * bump to 0.1.4 * fix sha * 0.1.5 --- recipes/revoluzer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/revoluzer/meta.yaml b/recipes/revoluzer/meta.yaml index 1bb05b1981a8b..b9254298cc1b7 100644 --- a/recipes/revoluzer/meta.yaml +++ b/recipes/revoluzer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "revoluzer" %} -{% set version = "0.1.2" %} +{% set version = "0.1.5" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/Bernt/{{ name }}/-/archive/{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: f2957266157797c4fe2338e07ea756ad8fc688efe90b6b48a83744a0b82c986a + sha256: 80d46c701dc1614cfe63b0b7aea2973d33c2ee56ed637a1fe92df30d9305c144 build: number: 0 From 0d8421ec8f092d3930fa760b0d80533e48b068fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Mar 2024 03:47:27 -0400 Subject: [PATCH 0965/1813] Update ont-modkit to 0.2.6 (#46502) --- recipes/ont-modkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml index 8b366795bee15..de4665f2e5551 100644 --- a/recipes/ont-modkit/meta.yaml +++ b/recipes/ont-modkit/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.5" %} -{% set sha256 = "06bb7a0ad3de72c8b2865975bd793654bb9e88f4aa5db1ce46611c024fae5d6f" %} +{% set version = "0.2.6" %} +{% set sha256 = "ca5e864582eb1e3a1277a7ea11745ae9d2b83ff4e5d1efc394b7b81e23aa9ec3" %} package: name: ont-modkit From a895ba80197a07cff12a8307cde047342f37b195 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Sat, 16 Mar 2024 00:47:42 -0700 Subject: [PATCH 0966/1813] Falco update (#46500) * Update falco: new version 1.2.2 * Update falco: adding run_exports which was forgotten --- recipes/falco/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/falco/meta.yaml b/recipes/falco/meta.yaml index 2c839a9280689..766c20816dbf0 100644 --- a/recipes/falco/meta.yaml +++ b/recipes/falco/meta.yaml @@ -1,15 +1,19 @@ -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: falco version: {{ version }} build: - number: 5 + number: 0 + run_exports: + # falco is currently not intended to be stable between minor versions (x.x). + - {{ pin_subpackage('falco', max_pin="x.x") }} + source: url: https://github.com/smithlabcode/falco/releases/download/v{{ version }}/falco-{{ version }}.tar.gz - sha256: 33de8aafac45c7aea055ed7ab837d0a39d12dcf782816cea8a6c648acb911057 + sha256: 09cfb96eb4292ba0ca48713634e9da48fbe07e57a4ae8f24f356583ed6b1028b requirements: build: From 33891b6743baf7d0841a42f5aea2e8a7d9ee8b45 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Mar 2024 03:48:03 -0400 Subject: [PATCH 0967/1813] Update snakemake to 8.8.0 (#46489) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 415ca8e1a983a..62c423e0f7660 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.7.0" %} +{% set version = "8.8.0" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: fbeb91045c984fad4e6e57b329ebc731bf9ec98eef29a772b79d440a51705078 + sha256: d676ea965a2bef00f7b3b5e1707482f2728e52abc5c85c2600e614e3a405bb1a build: number: 0 From 27d1630fe60b226ad655ece4c0a184f1b84b281a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Mar 2024 03:48:09 -0400 Subject: [PATCH 0968/1813] Update mhcflurry to 2.1.1 (#46496) --- recipes/mhcflurry/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mhcflurry/meta.yaml b/recipes/mhcflurry/meta.yaml index b69f1d8f20efe..e1fa36f02ca62 100644 --- a/recipes/mhcflurry/meta.yaml +++ b/recipes/mhcflurry/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mhcflurry" %} -{% set version = "2.1.0" %} +{% set version = "2.1.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a4129922db5b662e248e066e73e12be74c3d08c7c0a9f1de4776b7e5aafa42bb + sha256: 5907a489ffe7e459295b08849428677fc738fcb19716628e4e3d06f247131ff8 build: number: 0 From 73ae9a1324e3a01f321eb1af7903ce013b798272 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Mar 2024 03:48:18 -0400 Subject: [PATCH 0969/1813] Update sequali to 0.5.0 (#46492) --- recipes/sequali/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index 8aeec56e9acfe..57275892e7239 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.4.1" %} +{% set version = "0.5.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: cc62e1641d85fc14eaa70418f0e32cac2b0639374d8b1eba9e9d95388daab369 + sha256: b21cc15395091da6f094b102e0285c595e7727f1db5ff59b8bcb08cc0b236d29 build: number: 0 From 5fc2e7b2c9cf2fd7d80dd428705221da4095cda0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Mar 2024 03:49:31 -0400 Subject: [PATCH 0970/1813] Update ms2rescore to 3.0.2 (#46486) --- recipes/ms2rescore/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index c9fd49da47b4d..c561cb34e5e8d 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms2rescore" %} -{% set version = "3.0.1" %} +{% set version = "3.0.2" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz - sha256: c016f64d76cc0fc6d3ed691d1d8350d2d6e52da5e84e4fc258f4445264a4b9ad + sha256: 6049cdf2afdd70244552a47ee369ca89ff3a851440f56e181b01e5f9691fbc12 build: - number: 2 + number: 0 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} From f15b722391f22e00e41f9e86246f218183d54a6c Mon Sep 17 00:00:00 2001 From: sunqian2002 <50086972+huazhong28@users.noreply.github.com> Date: Sat, 16 Mar 2024 15:51:28 +0800 Subject: [PATCH 0971/1813] linux-aarch64 build for pybedtools (#46467) --- recipes/pybedtools/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/pybedtools/meta.yaml b/recipes/pybedtools/meta.yaml index 49e64af7bf5c7..a983e247c6501 100644 --- a/recipes/pybedtools/meta.yaml +++ b/recipes/pybedtools/meta.yaml @@ -8,7 +8,9 @@ source: build: skip: True # [py2k] - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage("pybedtools", max_pin="x.x.x") }} requirements: build: @@ -41,3 +43,5 @@ about: extra: identifiers: - biotools:pybedtools + additional-platforms: + - linux-aarch64 From 664a525c0b72e070f6ca23d61d81b3e997ba60aa Mon Sep 17 00:00:00 2001 From: sunqian2002 <50086972+huazhong28@users.noreply.github.com> Date: Sat, 16 Mar 2024 15:51:56 +0800 Subject: [PATCH 0972/1813] linux-aarch64 build for bgreat (#46472) * linux-aarch64 build for bgreat * linux-aarch64 build for bgreat * linux-aarch64 build for bgreat * linux-aarch64 build for bgreat --- recipes/bgreat/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/bgreat/meta.yaml b/recipes/bgreat/meta.yaml index 8962130ba8d8f..586688e1e95e1 100644 --- a/recipes/bgreat/meta.yaml +++ b/recipes/bgreat/meta.yaml @@ -10,7 +10,9 @@ source: sha256: bc60e755a3205b725834f37d7509062879415f03730b424cbac06b776eb977cc build: - number: 6 + number: 7 + run_exports: + - {{ pin_subpackage("bgreat", max_pin="x.x.x") }} skip: true # [osx] requirements: @@ -29,3 +31,7 @@ about: home: https://github.com/Malfoy/BGREAT2 license: AGPL-3.0 summary: BGREAT2 is a read mapping tool for NGS sequencing data that align reads on a de Bruijn graph. Preliminary version described at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1103-9 and used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336) + +extra: + additional-platforms: + - linux-aarch64 From ba39ca20161de717998a9d364606260d6747598d Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Sat, 16 Mar 2024 09:52:37 +0200 Subject: [PATCH 0973/1813] clustalw: add linux-aarch64 build (#46482) * clustalw: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Use newer config.guess and config.sub for clustalw The config.* files are taken from https://github.com/gcc-mirror/gcc/tree/master Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/clustalw/build.sh | 3 + recipes/clustalw/config.guess | 1700 +++++++++++++++++++++++++++++ recipes/clustalw/config.sub | 1885 +++++++++++++++++++++++++++++++++ recipes/clustalw/meta.yaml | 7 +- 4 files changed, 3594 insertions(+), 1 deletion(-) create mode 100644 recipes/clustalw/config.guess create mode 100644 recipes/clustalw/config.sub diff --git a/recipes/clustalw/build.sh b/recipes/clustalw/build.sh index d5c9f16d06afe..d7f3623f6c4d8 100644 --- a/recipes/clustalw/build.sh +++ b/recipes/clustalw/build.sh @@ -1,5 +1,8 @@ #!/bin/bash +# use newer config.guess and config.sub that support linux-aarch64 +cp ${RECIPE_DIR}/config.* . + mkdir -p ${PREFIX} ./configure --prefix=$PREFIX make install diff --git a/recipes/clustalw/config.guess b/recipes/clustalw/config.guess new file mode 100644 index 0000000000000..1972fda8eb05d --- /dev/null +++ b/recipes/clustalw/config.guess @@ -0,0 +1,1700 @@ +#! /bin/sh +# Attempt to guess a canonical system name. +# Copyright 1992-2021 Free Software Foundation, Inc. + +timestamp='2021-01-25' + +# This file is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, see . +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that +# program. This Exception is an additional permission under section 7 +# of the GNU General Public License, version 3 ("GPLv3"). +# +# Originally written by Per Bothner; maintained since 2000 by Ben Elliston. +# +# You can get the latest version of this script from: +# https://git.savannah.gnu.org/cgit/config.git/plain/config.guess +# +# Please send patches to . + + +me=$(echo "$0" | sed -e 's,.*/,,') + +usage="\ +Usage: $0 [OPTION] + +Output the configuration name of the system \`$me' is run on. + +Options: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.guess ($timestamp) + +Originally written by Per Bothner. +Copyright 1992-2021 Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit ;; + --version | -v ) + echo "$version" ; exit ;; + --help | --h* | -h ) + echo "$usage"; exit ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" >&2 + exit 1 ;; + * ) + break ;; + esac +done + +if test $# != 0; then + echo "$me: too many arguments$help" >&2 + exit 1 +fi + +# CC_FOR_BUILD -- compiler used by this script. Note that the use of a +# compiler to aid in system detection is discouraged as it requires +# temporary files to be created and, as you can see below, it is a +# headache to deal with in a portable fashion. + +# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still +# use `HOST_CC' if defined, but it is deprecated. + +# Portable tmp directory creation inspired by the Autoconf team. + +tmp= +# shellcheck disable=SC2172 +trap 'test -z "$tmp" || rm -fr "$tmp"' 0 1 2 13 15 + +set_cc_for_build() { + # prevent multiple calls if $tmp is already set + test "$tmp" && return 0 + : "${TMPDIR=/tmp}" + # shellcheck disable=SC2039 + { tmp=$( (umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null) && test -n "$tmp" && test -d "$tmp" ; } || + { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir "$tmp" 2>/dev/null) ; } || + { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir "$tmp" 2>/dev/null) && echo "Warning: creating insecure temp directory" >&2 ; } || + { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } + dummy=$tmp/dummy + case ${CC_FOR_BUILD-},${HOST_CC-},${CC-} in + ,,) echo "int x;" > "$dummy.c" + for driver in cc gcc c89 c99 ; do + if ($driver -c -o "$dummy.o" "$dummy.c") >/dev/null 2>&1 ; then + CC_FOR_BUILD="$driver" + break + fi + done + if test x"$CC_FOR_BUILD" = x ; then + CC_FOR_BUILD=no_compiler_found + fi + ;; + ,,*) CC_FOR_BUILD=$CC ;; + ,*,*) CC_FOR_BUILD=$HOST_CC ;; + esac +} + +# This is needed to find uname on a Pyramid OSx when run in the BSD universe. +# (ghazi@noc.rutgers.edu 1994-08-24) +if test -f /.attbin/uname ; then + PATH=$PATH:/.attbin ; export PATH +fi + +UNAME_MACHINE=$( (uname -m) 2>/dev/null) || UNAME_MACHINE=unknown +UNAME_RELEASE=$( (uname -r) 2>/dev/null) || UNAME_RELEASE=unknown +UNAME_SYSTEM=$( (uname -s) 2>/dev/null) || UNAME_SYSTEM=unknown +UNAME_VERSION=$( (uname -v) 2>/dev/null) || UNAME_VERSION=unknown + +case "$UNAME_SYSTEM" in +Linux|GNU|GNU/*) + LIBC=unknown + + set_cc_for_build + cat <<-EOF > "$dummy.c" + #include + #if defined(__UCLIBC__) + LIBC=uclibc + #elif defined(__dietlibc__) + LIBC=dietlibc + #elif defined(__GLIBC__) + LIBC=gnu + #else + #include + /* First heuristic to detect musl libc. */ + #ifdef __DEFINED_va_list + LIBC=musl + #endif + #endif + EOF + eval "$($CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^LIBC' | sed 's, ,,g')" + + # Second heuristic to detect musl libc. + if [ "$LIBC" = unknown ] && + command -v ldd >/dev/null && + ldd --version 2>&1 | grep -q ^musl; then + LIBC=musl + fi + + # If the system lacks a compiler, then just pick glibc. + # We could probably try harder. + if [ "$LIBC" = unknown ]; then + LIBC=gnu + fi + ;; +esac + +# Note: order is significant - the case branches are not exclusive. + +case "$UNAME_MACHINE:$UNAME_SYSTEM:$UNAME_RELEASE:$UNAME_VERSION" in + *:NetBSD:*:*) + # NetBSD (nbsd) targets should (where applicable) match one or + # more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*, + # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently + # switched to ELF, *-*-netbsd* would select the old + # object file format. This provides both forward + # compatibility and a consistent mechanism for selecting the + # object file format. + # + # Note: NetBSD doesn't particularly care about the vendor + # portion of the name. We always set it to "unknown". + UNAME_MACHINE_ARCH=$( (uname -p 2>/dev/null || \ + /sbin/sysctl -n hw.machine_arch 2>/dev/null || \ + /usr/sbin/sysctl -n hw.machine_arch 2>/dev/null || \ + echo unknown)) + case "$UNAME_MACHINE_ARCH" in + aarch64eb) machine=aarch64_be-unknown ;; + armeb) machine=armeb-unknown ;; + arm*) machine=arm-unknown ;; + sh3el) machine=shl-unknown ;; + sh3eb) machine=sh-unknown ;; + sh5el) machine=sh5le-unknown ;; + earmv*) + arch=$(echo "$UNAME_MACHINE_ARCH" | sed -e 's,^e\(armv[0-9]\).*$,\1,') + endian=$(echo "$UNAME_MACHINE_ARCH" | sed -ne 's,^.*\(eb\)$,\1,p') + machine="${arch}${endian}"-unknown + ;; + *) machine="$UNAME_MACHINE_ARCH"-unknown ;; + esac + # The Operating System including object format, if it has switched + # to ELF recently (or will in the future) and ABI. + case "$UNAME_MACHINE_ARCH" in + earm*) + os=netbsdelf + ;; + arm*|i386|m68k|ns32k|sh3*|sparc|vax) + set_cc_for_build + if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ELF__ + then + # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). + # Return netbsd for either. FIX? + os=netbsd + else + os=netbsdelf + fi + ;; + *) + os=netbsd + ;; + esac + # Determine ABI tags. + case "$UNAME_MACHINE_ARCH" in + earm*) + expr='s/^earmv[0-9]/-eabi/;s/eb$//' + abi=$(echo "$UNAME_MACHINE_ARCH" | sed -e "$expr") + ;; + esac + # The OS release + # Debian GNU/NetBSD machines have a different userland, and + # thus, need a distinct triplet. However, they do not need + # kernel version information, so it can be replaced with a + # suitable tag, in the style of linux-gnu. + case "$UNAME_VERSION" in + Debian*) + release='-gnu' + ;; + *) + release=$(echo "$UNAME_RELEASE" | sed -e 's/[-_].*//' | cut -d. -f1,2) + ;; + esac + # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: + # contains redundant information, the shorter form: + # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. + echo "$machine-${os}${release}${abi-}" + exit ;; + *:Bitrig:*:*) + UNAME_MACHINE_ARCH=$(arch | sed 's/Bitrig.//') + echo "$UNAME_MACHINE_ARCH"-unknown-bitrig"$UNAME_RELEASE" + exit ;; + *:OpenBSD:*:*) + UNAME_MACHINE_ARCH=$(arch | sed 's/OpenBSD.//') + echo "$UNAME_MACHINE_ARCH"-unknown-openbsd"$UNAME_RELEASE" + exit ;; + *:LibertyBSD:*:*) + UNAME_MACHINE_ARCH=$(arch | sed 's/^.*BSD\.//') + echo "$UNAME_MACHINE_ARCH"-unknown-libertybsd"$UNAME_RELEASE" + exit ;; + *:MidnightBSD:*:*) + echo "$UNAME_MACHINE"-unknown-midnightbsd"$UNAME_RELEASE" + exit ;; + *:ekkoBSD:*:*) + echo "$UNAME_MACHINE"-unknown-ekkobsd"$UNAME_RELEASE" + exit ;; + *:SolidBSD:*:*) + echo "$UNAME_MACHINE"-unknown-solidbsd"$UNAME_RELEASE" + exit ;; + *:OS108:*:*) + echo "$UNAME_MACHINE"-unknown-os108_"$UNAME_RELEASE" + exit ;; + macppc:MirBSD:*:*) + echo powerpc-unknown-mirbsd"$UNAME_RELEASE" + exit ;; + *:MirBSD:*:*) + echo "$UNAME_MACHINE"-unknown-mirbsd"$UNAME_RELEASE" + exit ;; + *:Sortix:*:*) + echo "$UNAME_MACHINE"-unknown-sortix + exit ;; + *:Twizzler:*:*) + echo "$UNAME_MACHINE"-unknown-twizzler + exit ;; + *:Redox:*:*) + echo "$UNAME_MACHINE"-unknown-redox + exit ;; + mips:OSF1:*.*) + echo mips-dec-osf1 + exit ;; + alpha:OSF1:*:*) + case $UNAME_RELEASE in + *4.0) + UNAME_RELEASE=$(/usr/sbin/sizer -v | awk '{print $3}') + ;; + *5.*) + UNAME_RELEASE=$(/usr/sbin/sizer -v | awk '{print $4}') + ;; + esac + # According to Compaq, /usr/sbin/psrinfo has been available on + # OSF/1 and Tru64 systems produced since 1995. I hope that + # covers most systems running today. This code pipes the CPU + # types through head -n 1, so we only detect the type of CPU 0. + ALPHA_CPU_TYPE=$(/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1) + case "$ALPHA_CPU_TYPE" in + "EV4 (21064)") + UNAME_MACHINE=alpha ;; + "EV4.5 (21064)") + UNAME_MACHINE=alpha ;; + "LCA4 (21066/21068)") + UNAME_MACHINE=alpha ;; + "EV5 (21164)") + UNAME_MACHINE=alphaev5 ;; + "EV5.6 (21164A)") + UNAME_MACHINE=alphaev56 ;; + "EV5.6 (21164PC)") + UNAME_MACHINE=alphapca56 ;; + "EV5.7 (21164PC)") + UNAME_MACHINE=alphapca57 ;; + "EV6 (21264)") + UNAME_MACHINE=alphaev6 ;; + "EV6.7 (21264A)") + UNAME_MACHINE=alphaev67 ;; + "EV6.8CB (21264C)") + UNAME_MACHINE=alphaev68 ;; + "EV6.8AL (21264B)") + UNAME_MACHINE=alphaev68 ;; + "EV6.8CX (21264D)") + UNAME_MACHINE=alphaev68 ;; + "EV6.9A (21264/EV69A)") + UNAME_MACHINE=alphaev69 ;; + "EV7 (21364)") + UNAME_MACHINE=alphaev7 ;; + "EV7.9 (21364A)") + UNAME_MACHINE=alphaev79 ;; + esac + # A Pn.n version is a patched version. + # A Vn.n version is a released version. + # A Tn.n version is a released field test version. + # A Xn.n version is an unreleased experimental baselevel. + # 1.2 uses "1.2" for uname -r. + echo "$UNAME_MACHINE"-dec-osf"$(echo "$UNAME_RELEASE" | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz)" + # Reset EXIT trap before exiting to avoid spurious non-zero exit code. + exitcode=$? + trap '' 0 + exit $exitcode ;; + Amiga*:UNIX_System_V:4.0:*) + echo m68k-unknown-sysv4 + exit ;; + *:[Aa]miga[Oo][Ss]:*:*) + echo "$UNAME_MACHINE"-unknown-amigaos + exit ;; + *:[Mm]orph[Oo][Ss]:*:*) + echo "$UNAME_MACHINE"-unknown-morphos + exit ;; + *:OS/390:*:*) + echo i370-ibm-openedition + exit ;; + *:z/VM:*:*) + echo s390-ibm-zvmoe + exit ;; + *:OS400:*:*) + echo powerpc-ibm-os400 + exit ;; + arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) + echo arm-acorn-riscix"$UNAME_RELEASE" + exit ;; + arm*:riscos:*:*|arm*:RISCOS:*:*) + echo arm-unknown-riscos + exit ;; + SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) + echo hppa1.1-hitachi-hiuxmpp + exit ;; + Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) + # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. + if test "$( (/bin/universe) 2>/dev/null)" = att ; then + echo pyramid-pyramid-sysv3 + else + echo pyramid-pyramid-bsd + fi + exit ;; + NILE*:*:*:dcosx) + echo pyramid-pyramid-svr4 + exit ;; + DRS?6000:unix:4.0:6*) + echo sparc-icl-nx6 + exit ;; + DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) + case $(/usr/bin/uname -p) in + sparc) echo sparc-icl-nx7; exit ;; + esac ;; + s390x:SunOS:*:*) + echo "$UNAME_MACHINE"-ibm-solaris2"$(echo "$UNAME_RELEASE" | sed -e 's/[^.]*//')" + exit ;; + sun4H:SunOS:5.*:*) + echo sparc-hal-solaris2"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) + echo sparc-sun-solaris2"$(echo "$UNAME_RELEASE" | sed -e 's/[^.]*//')" + exit ;; + i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*) + echo i386-pc-auroraux"$UNAME_RELEASE" + exit ;; + i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) + set_cc_for_build + SUN_ARCH=i386 + # If there is a compiler, see if it is configured for 64-bit objects. + # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. + # This test works for both compilers. + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + SUN_ARCH=x86_64 + fi + fi + echo "$SUN_ARCH"-pc-solaris2"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + sun4*:SunOS:6*:*) + # According to config.sub, this is the proper way to canonicalize + # SunOS6. Hard to guess exactly what SunOS6 will be like, but + # it's likely to be more like Solaris than SunOS4. + echo sparc-sun-solaris3"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + sun4*:SunOS:*:*) + case "$(/usr/bin/arch -k)" in + Series*|S4*) + UNAME_RELEASE=$(uname -v) + ;; + esac + # Japanese Language versions have a version number like `4.1.3-JL'. + echo sparc-sun-sunos"$(echo "$UNAME_RELEASE"|sed -e 's/-/_/')" + exit ;; + sun3*:SunOS:*:*) + echo m68k-sun-sunos"$UNAME_RELEASE" + exit ;; + sun*:*:4.2BSD:*) + UNAME_RELEASE=$( (sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null) + test "x$UNAME_RELEASE" = x && UNAME_RELEASE=3 + case "$(/bin/arch)" in + sun3) + echo m68k-sun-sunos"$UNAME_RELEASE" + ;; + sun4) + echo sparc-sun-sunos"$UNAME_RELEASE" + ;; + esac + exit ;; + aushp:SunOS:*:*) + echo sparc-auspex-sunos"$UNAME_RELEASE" + exit ;; + # The situation for MiNT is a little confusing. The machine name + # can be virtually everything (everything which is not + # "atarist" or "atariste" at least should have a processor + # > m68000). The system name ranges from "MiNT" over "FreeMiNT" + # to the lowercase version "mint" (or "freemint"). Finally + # the system name "TOS" denotes a system which is actually not + # MiNT. But MiNT is downward compatible to TOS, so this should + # be no problem. + atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint"$UNAME_RELEASE" + exit ;; + atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint"$UNAME_RELEASE" + exit ;; + *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) + echo m68k-atari-mint"$UNAME_RELEASE" + exit ;; + milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) + echo m68k-milan-mint"$UNAME_RELEASE" + exit ;; + hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) + echo m68k-hades-mint"$UNAME_RELEASE" + exit ;; + *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) + echo m68k-unknown-mint"$UNAME_RELEASE" + exit ;; + m68k:machten:*:*) + echo m68k-apple-machten"$UNAME_RELEASE" + exit ;; + powerpc:machten:*:*) + echo powerpc-apple-machten"$UNAME_RELEASE" + exit ;; + RISC*:Mach:*:*) + echo mips-dec-mach_bsd4.3 + exit ;; + RISC*:ULTRIX:*:*) + echo mips-dec-ultrix"$UNAME_RELEASE" + exit ;; + VAX*:ULTRIX*:*:*) + echo vax-dec-ultrix"$UNAME_RELEASE" + exit ;; + 2020:CLIX:*:* | 2430:CLIX:*:*) + echo clipper-intergraph-clix"$UNAME_RELEASE" + exit ;; + mips:*:*:UMIPS | mips:*:*:RISCos) + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" +#ifdef __cplusplus +#include /* for printf() prototype */ + int main (int argc, char *argv[]) { +#else + int main (argc, argv) int argc; char *argv[]; { +#endif + #if defined (host_mips) && defined (MIPSEB) + #if defined (SYSTYPE_SYSV) + printf ("mips-mips-riscos%ssysv\\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_SVR4) + printf ("mips-mips-riscos%ssvr4\\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) + printf ("mips-mips-riscos%sbsd\\n", argv[1]); exit (0); + #endif + #endif + exit (-1); + } +EOF + $CC_FOR_BUILD -o "$dummy" "$dummy.c" && + dummyarg=$(echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p') && + SYSTEM_NAME=$("$dummy" "$dummyarg") && + { echo "$SYSTEM_NAME"; exit; } + echo mips-mips-riscos"$UNAME_RELEASE" + exit ;; + Motorola:PowerMAX_OS:*:*) + echo powerpc-motorola-powermax + exit ;; + Motorola:*:4.3:PL8-*) + echo powerpc-harris-powermax + exit ;; + Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) + echo powerpc-harris-powermax + exit ;; + Night_Hawk:Power_UNIX:*:*) + echo powerpc-harris-powerunix + exit ;; + m88k:CX/UX:7*:*) + echo m88k-harris-cxux7 + exit ;; + m88k:*:4*:R4*) + echo m88k-motorola-sysv4 + exit ;; + m88k:*:3*:R3*) + echo m88k-motorola-sysv3 + exit ;; + AViiON:dgux:*:*) + # DG/UX returns AViiON for all architectures + UNAME_PROCESSOR=$(/usr/bin/uname -p) + if test "$UNAME_PROCESSOR" = mc88100 || test "$UNAME_PROCESSOR" = mc88110 + then + if test "$TARGET_BINARY_INTERFACE"x = m88kdguxelfx || \ + test "$TARGET_BINARY_INTERFACE"x = x + then + echo m88k-dg-dgux"$UNAME_RELEASE" + else + echo m88k-dg-dguxbcs"$UNAME_RELEASE" + fi + else + echo i586-dg-dgux"$UNAME_RELEASE" + fi + exit ;; + M88*:DolphinOS:*:*) # DolphinOS (SVR3) + echo m88k-dolphin-sysv3 + exit ;; + M88*:*:R3*:*) + # Delta 88k system running SVR3 + echo m88k-motorola-sysv3 + exit ;; + XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) + echo m88k-tektronix-sysv3 + exit ;; + Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) + echo m68k-tektronix-bsd + exit ;; + *:IRIX*:*:*) + echo mips-sgi-irix"$(echo "$UNAME_RELEASE"|sed -e 's/-/_/g')" + exit ;; + ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. + echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id + exit ;; # Note that: echo "'$(uname -s)'" gives 'AIX ' + i*86:AIX:*:*) + echo i386-ibm-aix + exit ;; + ia64:AIX:*:*) + if test -x /usr/bin/oslevel ; then + IBM_REV=$(/usr/bin/oslevel) + else + IBM_REV="$UNAME_VERSION.$UNAME_RELEASE" + fi + echo "$UNAME_MACHINE"-ibm-aix"$IBM_REV" + exit ;; + *:AIX:2:3) + if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" + #include + + main() + { + if (!__power_pc()) + exit(1); + puts("powerpc-ibm-aix3.2.5"); + exit(0); + } +EOF + if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=$("$dummy") + then + echo "$SYSTEM_NAME" + else + echo rs6000-ibm-aix3.2.5 + fi + elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then + echo rs6000-ibm-aix3.2.4 + else + echo rs6000-ibm-aix3.2 + fi + exit ;; + *:AIX:*:[4567]) + IBM_CPU_ID=$(/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }') + if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then + IBM_ARCH=rs6000 + else + IBM_ARCH=powerpc + fi + if test -x /usr/bin/lslpp ; then + IBM_REV=$(/usr/bin/lslpp -Lqc bos.rte.libc | + awk -F: '{ print $3 }' | sed s/[0-9]*$/0/) + else + IBM_REV="$UNAME_VERSION.$UNAME_RELEASE" + fi + echo "$IBM_ARCH"-ibm-aix"$IBM_REV" + exit ;; + *:AIX:*:*) + echo rs6000-ibm-aix + exit ;; + ibmrt:4.4BSD:*|romp-ibm:4.4BSD:*) + echo romp-ibm-bsd4.4 + exit ;; + ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and + echo romp-ibm-bsd"$UNAME_RELEASE" # 4.3 with uname added to + exit ;; # report: romp-ibm BSD 4.3 + *:BOSX:*:*) + echo rs6000-bull-bosx + exit ;; + DPX/2?00:B.O.S.:*:*) + echo m68k-bull-sysv3 + exit ;; + 9000/[34]??:4.3bsd:1.*:*) + echo m68k-hp-bsd + exit ;; + hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) + echo m68k-hp-bsd4.4 + exit ;; + 9000/[34678]??:HP-UX:*:*) + HPUX_REV=$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//') + case "$UNAME_MACHINE" in + 9000/31?) HP_ARCH=m68000 ;; + 9000/[34]??) HP_ARCH=m68k ;; + 9000/[678][0-9][0-9]) + if test -x /usr/bin/getconf; then + sc_cpu_version=$(/usr/bin/getconf SC_CPU_VERSION 2>/dev/null) + sc_kernel_bits=$(/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null) + case "$sc_cpu_version" in + 523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0 + 528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1 + 532) # CPU_PA_RISC2_0 + case "$sc_kernel_bits" in + 32) HP_ARCH=hppa2.0n ;; + 64) HP_ARCH=hppa2.0w ;; + '') HP_ARCH=hppa2.0 ;; # HP-UX 10.20 + esac ;; + esac + fi + if test "$HP_ARCH" = ""; then + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" + + #define _HPUX_SOURCE + #include + #include + + int main () + { + #if defined(_SC_KERNEL_BITS) + long bits = sysconf(_SC_KERNEL_BITS); + #endif + long cpu = sysconf (_SC_CPU_VERSION); + + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1"); break; + case CPU_PA_RISC2_0: + #if defined(_SC_KERNEL_BITS) + switch (bits) + { + case 64: puts ("hppa2.0w"); break; + case 32: puts ("hppa2.0n"); break; + default: puts ("hppa2.0"); break; + } break; + #else /* !defined(_SC_KERNEL_BITS) */ + puts ("hppa2.0"); break; + #endif + default: puts ("hppa1.0"); break; + } + exit (0); + } +EOF + (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=$("$dummy") + test -z "$HP_ARCH" && HP_ARCH=hppa + fi ;; + esac + if test "$HP_ARCH" = hppa2.0w + then + set_cc_for_build + + # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating + # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler + # generating 64-bit code. GNU and HP use different nomenclature: + # + # $ CC_FOR_BUILD=cc ./config.guess + # => hppa2.0w-hp-hpux11.23 + # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess + # => hppa64-hp-hpux11.23 + + if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | + grep -q __LP64__ + then + HP_ARCH=hppa2.0w + else + HP_ARCH=hppa64 + fi + fi + echo "$HP_ARCH"-hp-hpux"$HPUX_REV" + exit ;; + ia64:HP-UX:*:*) + HPUX_REV=$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//') + echo ia64-hp-hpux"$HPUX_REV" + exit ;; + 3050*:HI-UX:*:*) + set_cc_for_build + sed 's/^ //' << EOF > "$dummy.c" + #include + int + main () + { + long cpu = sysconf (_SC_CPU_VERSION); + /* The order matters, because CPU_IS_HP_MC68K erroneously returns + true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct + results, however. */ + if (CPU_IS_PA_RISC (cpu)) + { + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; + case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; + default: puts ("hppa-hitachi-hiuxwe2"); break; + } + } + else if (CPU_IS_HP_MC68K (cpu)) + puts ("m68k-hitachi-hiuxwe2"); + else puts ("unknown-hitachi-hiuxwe2"); + exit (0); + } +EOF + $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=$("$dummy") && + { echo "$SYSTEM_NAME"; exit; } + echo unknown-hitachi-hiuxwe2 + exit ;; + 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:*) + echo hppa1.1-hp-bsd + exit ;; + 9000/8??:4.3bsd:*:*) + echo hppa1.0-hp-bsd + exit ;; + *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) + echo hppa1.0-hp-mpeix + exit ;; + hp7??:OSF1:*:* | hp8?[79]:OSF1:*:*) + echo hppa1.1-hp-osf + exit ;; + hp8??:OSF1:*:*) + echo hppa1.0-hp-osf + exit ;; + i*86:OSF1:*:*) + if test -x /usr/sbin/sysversion ; then + echo "$UNAME_MACHINE"-unknown-osf1mk + else + echo "$UNAME_MACHINE"-unknown-osf1 + fi + exit ;; + parisc*:Lites*:*:*) + echo hppa1.1-hp-lites + exit ;; + C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) + echo c1-convex-bsd + exit ;; + C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit ;; + C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) + echo c34-convex-bsd + exit ;; + C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) + echo c38-convex-bsd + exit ;; + C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) + echo c4-convex-bsd + exit ;; + CRAY*Y-MP:*:*:*) + echo ymp-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*[A-Z]90:*:*:*) + echo "$UNAME_MACHINE"-cray-unicos"$UNAME_RELEASE" \ + | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ + -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ + -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*TS:*:*:*) + echo t90-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*T3E:*:*:*) + echo alphaev5-cray-unicosmk"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*SV1:*:*:*) + echo sv1-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + *:UNICOS/mp:*:*) + echo craynv-cray-unicosmp"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/' + exit ;; + F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) + FUJITSU_PROC=$(uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz) + FUJITSU_SYS=$(uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///') + FUJITSU_REL=$(echo "$UNAME_RELEASE" | sed -e 's/ /_/') + echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; + 5000:UNIX_System_V:4.*:*) + FUJITSU_SYS=$(uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///') + FUJITSU_REL=$(echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/') + echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; + i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) + echo "$UNAME_MACHINE"-pc-bsdi"$UNAME_RELEASE" + exit ;; + sparc*:BSD/OS:*:*) + echo sparc-unknown-bsdi"$UNAME_RELEASE" + exit ;; + *:BSD/OS:*:*) + echo "$UNAME_MACHINE"-unknown-bsdi"$UNAME_RELEASE" + exit ;; + arm:FreeBSD:*:*) + UNAME_PROCESSOR=$(uname -p) + set_cc_for_build + if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_PCS_VFP + then + echo "${UNAME_PROCESSOR}"-unknown-freebsd"$(echo ${UNAME_RELEASE}|sed -e 's/[-(].*//')"-gnueabi + else + echo "${UNAME_PROCESSOR}"-unknown-freebsd"$(echo ${UNAME_RELEASE}|sed -e 's/[-(].*//')"-gnueabihf + fi + exit ;; + *:FreeBSD:*:*) + UNAME_PROCESSOR=$(/usr/bin/uname -p) + case "$UNAME_PROCESSOR" in + amd64) + UNAME_PROCESSOR=x86_64 ;; + i386) + UNAME_PROCESSOR=i586 ;; + esac + echo "$UNAME_PROCESSOR"-unknown-freebsd"$(echo "$UNAME_RELEASE"|sed -e 's/[-(].*//')" + exit ;; + i*:CYGWIN*:*) + echo "$UNAME_MACHINE"-pc-cygwin + exit ;; + *:MINGW64*:*) + echo "$UNAME_MACHINE"-pc-mingw64 + exit ;; + *:MINGW*:*) + echo "$UNAME_MACHINE"-pc-mingw32 + exit ;; + *:MSYS*:*) + echo "$UNAME_MACHINE"-pc-msys + exit ;; + i*:PW*:*) + echo "$UNAME_MACHINE"-pc-pw32 + exit ;; + *:Interix*:*) + case "$UNAME_MACHINE" in + x86) + echo i586-pc-interix"$UNAME_RELEASE" + exit ;; + authenticamd | genuineintel | EM64T) + echo x86_64-unknown-interix"$UNAME_RELEASE" + exit ;; + IA64) + echo ia64-unknown-interix"$UNAME_RELEASE" + exit ;; + esac ;; + i*:UWIN*:*) + echo "$UNAME_MACHINE"-pc-uwin + exit ;; + amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) + echo x86_64-pc-cygwin + exit ;; + prep*:SunOS:5.*:*) + echo powerpcle-unknown-solaris2"$(echo "$UNAME_RELEASE"|sed -e 's/[^.]*//')" + exit ;; + *:GNU:*:*) + # the GNU system + echo "$(echo "$UNAME_MACHINE"|sed -e 's,[-/].*$,,')-unknown-$LIBC$(echo "$UNAME_RELEASE"|sed -e 's,/.*$,,')" + exit ;; + *:GNU/*:*:*) + # other systems with GNU libc and userland + echo "$UNAME_MACHINE-unknown-$(echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]")$(echo "$UNAME_RELEASE"|sed -e 's/[-(].*//')-$LIBC" + exit ;; + *:Minix:*:*) + echo "$UNAME_MACHINE"-unknown-minix + exit ;; + aarch64:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + aarch64_be:Linux:*:*) + UNAME_MACHINE=aarch64_be + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + alpha:Linux:*:*) + case $(sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' /proc/cpuinfo 2>/dev/null) in + EV5) UNAME_MACHINE=alphaev5 ;; + EV56) UNAME_MACHINE=alphaev56 ;; + PCA56) UNAME_MACHINE=alphapca56 ;; + PCA57) UNAME_MACHINE=alphapca56 ;; + EV6) UNAME_MACHINE=alphaev6 ;; + EV67) UNAME_MACHINE=alphaev67 ;; + EV68*) UNAME_MACHINE=alphaev68 ;; + esac + objdump --private-headers /bin/sh | grep -q ld.so.1 + if test "$?" = 0 ; then LIBC=gnulibc1 ; fi + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + arc:Linux:*:* | arceb:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + arm*:Linux:*:*) + set_cc_for_build + if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_EABI__ + then + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + else + if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_PCS_VFP + then + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"eabi + else + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"eabihf + fi + fi + exit ;; + avr32*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + cris:Linux:*:*) + echo "$UNAME_MACHINE"-axis-linux-"$LIBC" + exit ;; + crisv32:Linux:*:*) + echo "$UNAME_MACHINE"-axis-linux-"$LIBC" + exit ;; + e2k:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + frv:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + hexagon:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + i*86:Linux:*:*) + echo "$UNAME_MACHINE"-pc-linux-"$LIBC" + exit ;; + ia64:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + k1om:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + loongarch32:Linux:*:* | loongarch64:Linux:*:* | loongarchx32:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + m32r*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + m68*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + mips:Linux:*:* | mips64:Linux:*:*) + set_cc_for_build + IS_GLIBC=0 + test x"${LIBC}" = xgnu && IS_GLIBC=1 + sed 's/^ //' << EOF > "$dummy.c" + #undef CPU + #undef mips + #undef mipsel + #undef mips64 + #undef mips64el + #if ${IS_GLIBC} && defined(_ABI64) + LIBCABI=gnuabi64 + #else + #if ${IS_GLIBC} && defined(_ABIN32) + LIBCABI=gnuabin32 + #else + LIBCABI=${LIBC} + #endif + #endif + + #if ${IS_GLIBC} && defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 + CPU=mipsisa64r6 + #else + #if ${IS_GLIBC} && !defined(__mips64) && defined(__mips_isa_rev) && __mips_isa_rev>=6 + CPU=mipsisa32r6 + #else + #if defined(__mips64) + CPU=mips64 + #else + CPU=mips + #endif + #endif + #endif + + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) + MIPS_ENDIAN=el + #else + #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) + MIPS_ENDIAN= + #else + MIPS_ENDIAN= + #endif + #endif +EOF + eval "$($CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU\|^MIPS_ENDIAN\|^LIBCABI')" + test "x$CPU" != x && { echo "$CPU${MIPS_ENDIAN}-unknown-linux-$LIBCABI"; exit; } + ;; + mips64el:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + openrisc*:Linux:*:*) + echo or1k-unknown-linux-"$LIBC" + exit ;; + or32:Linux:*:* | or1k*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + padre:Linux:*:*) + echo sparc-unknown-linux-"$LIBC" + exit ;; + parisc64:Linux:*:* | hppa64:Linux:*:*) + echo hppa64-unknown-linux-"$LIBC" + exit ;; + parisc:Linux:*:* | hppa:Linux:*:*) + # Look for CPU level + case $(grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2) in + PA7*) echo hppa1.1-unknown-linux-"$LIBC" ;; + PA8*) echo hppa2.0-unknown-linux-"$LIBC" ;; + *) echo hppa-unknown-linux-"$LIBC" ;; + esac + exit ;; + ppc64:Linux:*:*) + echo powerpc64-unknown-linux-"$LIBC" + exit ;; + ppc:Linux:*:*) + echo powerpc-unknown-linux-"$LIBC" + exit ;; + ppc64le:Linux:*:*) + echo powerpc64le-unknown-linux-"$LIBC" + exit ;; + ppcle:Linux:*:*) + echo powerpcle-unknown-linux-"$LIBC" + exit ;; + riscv32:Linux:*:* | riscv32be:Linux:*:* | riscv64:Linux:*:* | riscv64be:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + s390:Linux:*:* | s390x:Linux:*:*) + echo "$UNAME_MACHINE"-ibm-linux-"$LIBC" + exit ;; + sh64*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + sh*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + sparc:Linux:*:* | sparc64:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + tile*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + vax:Linux:*:*) + echo "$UNAME_MACHINE"-dec-linux-"$LIBC" + exit ;; + x86_64:Linux:*:*) + set_cc_for_build + LIBCABI=$LIBC + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __ILP32__'; echo IS_X32; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_X32 >/dev/null + then + LIBCABI="$LIBC"x32 + fi + fi + echo "$UNAME_MACHINE"-pc-linux-"$LIBCABI" + exit ;; + xtensa*:Linux:*:*) + echo "$UNAME_MACHINE"-unknown-linux-"$LIBC" + exit ;; + i*86:DYNIX/ptx:4*:*) + # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. + # earlier versions are messed up and put the nodename in both + # sysname and nodename. + echo i386-sequent-sysv4 + exit ;; + i*86:UNIX_SV:4.2MP:2.*) + # Unixware is an offshoot of SVR4, but it has its own version + # number series starting with 2... + # I am not positive that other SVR4 systems won't match this, + # I just have to hope. -- rms. + # Use sysv4.2uw... so that sysv4* matches it. + echo "$UNAME_MACHINE"-pc-sysv4.2uw"$UNAME_VERSION" + exit ;; + i*86:OS/2:*:*) + # If we were able to find `uname', then EMX Unix compatibility + # is probably installed. + echo "$UNAME_MACHINE"-pc-os2-emx + exit ;; + i*86:XTS-300:*:STOP) + echo "$UNAME_MACHINE"-unknown-stop + exit ;; + i*86:atheos:*:*) + echo "$UNAME_MACHINE"-unknown-atheos + exit ;; + i*86:syllable:*:*) + echo "$UNAME_MACHINE"-pc-syllable + exit ;; + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) + echo i386-unknown-lynxos"$UNAME_RELEASE" + exit ;; + i*86:*DOS:*:*) + echo "$UNAME_MACHINE"-pc-msdosdjgpp + exit ;; + i*86:*:4.*:*) + UNAME_REL=$(echo "$UNAME_RELEASE" | sed 's/\/MP$//') + if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then + echo "$UNAME_MACHINE"-univel-sysv"$UNAME_REL" + else + echo "$UNAME_MACHINE"-pc-sysv"$UNAME_REL" + fi + exit ;; + i*86:*:5:[678]*) + # UnixWare 7.x, OpenUNIX and OpenServer 6. + case $(/bin/uname -X | grep "^Machine") in + *486*) UNAME_MACHINE=i486 ;; + *Pentium) UNAME_MACHINE=i586 ;; + *Pent*|*Celeron) UNAME_MACHINE=i686 ;; + esac + echo "$UNAME_MACHINE-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}" + exit ;; + i*86:*:3.2:*) + if test -f /usr/options/cb.name; then + UNAME_REL=$(sed -n 's/.*Version //p' /dev/null >/dev/null ; then + UNAME_REL=$( (/bin/uname -X|grep Release|sed -e 's/.*= //')) + (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 + (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ + && UNAME_MACHINE=i586 + (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ + && UNAME_MACHINE=i686 + (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ + && UNAME_MACHINE=i686 + echo "$UNAME_MACHINE"-pc-sco"$UNAME_REL" + else + echo "$UNAME_MACHINE"-pc-sysv32 + fi + exit ;; + pc:*:*:*) + # Left here for compatibility: + # uname -m prints for DJGPP always 'pc', but it prints nothing about + # the processor, so we play safe by assuming i586. + # Note: whatever this is, it MUST be the same as what config.sub + # prints for the "djgpp" host, or else GDB configure will decide that + # this is a cross-build. + echo i586-pc-msdosdjgpp + exit ;; + Intel:Mach:3*:*) + echo i386-pc-mach3 + exit ;; + paragon:*:*:*) + echo i860-intel-osf1 + exit ;; + i860:*:4.*:*) # i860-SVR4 + if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then + echo i860-stardent-sysv"$UNAME_RELEASE" # Stardent Vistra i860-SVR4 + else # Add other i860-SVR4 vendors below as they are discovered. + echo i860-unknown-sysv"$UNAME_RELEASE" # Unknown i860-SVR4 + fi + exit ;; + mini*:CTIX:SYS*5:*) + # "miniframe" + echo m68010-convergent-sysv + exit ;; + mc68k:UNIX:SYSTEM5:3.51m) + echo m68k-convergent-sysv + exit ;; + M680?0:D-NIX:5.3:*) + echo m68k-diab-dnix + exit ;; + M68*:*:R3V[5678]*:*) + test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; + 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) + OS_REL='' + test -r /etc/.relid \ + && OS_REL=.$(sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; + 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4; exit; } ;; + NCR*:*:4.2:* | MPRAS*:*:4.2:*) + OS_REL='.3' + test -r /etc/.relid \ + && OS_REL=.$(sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3"$OS_REL"; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } + /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ + && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;; + m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) + echo m68k-unknown-lynxos"$UNAME_RELEASE" + exit ;; + mc68030:UNIX_System_V:4.*:*) + echo m68k-atari-sysv4 + exit ;; + TSUNAMI:LynxOS:2.*:*) + echo sparc-unknown-lynxos"$UNAME_RELEASE" + exit ;; + rs6000:LynxOS:2.*:*) + echo rs6000-unknown-lynxos"$UNAME_RELEASE" + exit ;; + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) + echo powerpc-unknown-lynxos"$UNAME_RELEASE" + exit ;; + SM[BE]S:UNIX_SV:*:*) + echo mips-dde-sysv"$UNAME_RELEASE" + exit ;; + RM*:ReliantUNIX-*:*:*) + echo mips-sni-sysv4 + exit ;; + RM*:SINIX-*:*:*) + echo mips-sni-sysv4 + exit ;; + *:SINIX-*:*:*) + if uname -p 2>/dev/null >/dev/null ; then + UNAME_MACHINE=$( (uname -p) 2>/dev/null) + echo "$UNAME_MACHINE"-sni-sysv4 + else + echo ns32k-sni-sysv + fi + exit ;; + PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort + # says + echo i586-unisys-sysv4 + exit ;; + *:UNIX_System_V:4*:FTX*) + # From Gerald Hewes . + # How about differentiating between stratus architectures? -djm + echo hppa1.1-stratus-sysv4 + exit ;; + *:*:*:FTX*) + # From seanf@swdc.stratus.com. + echo i860-stratus-sysv4 + exit ;; + i*86:VOS:*:*) + # From Paul.Green@stratus.com. + echo "$UNAME_MACHINE"-stratus-vos + exit ;; + *:VOS:*:*) + # From Paul.Green@stratus.com. + echo hppa1.1-stratus-vos + exit ;; + mc68*:A/UX:*:*) + echo m68k-apple-aux"$UNAME_RELEASE" + exit ;; + news*:NEWS-OS:6*:*) + echo mips-sony-newsos6 + exit ;; + R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) + if test -d /usr/nec; then + echo mips-nec-sysv"$UNAME_RELEASE" + else + echo mips-unknown-sysv"$UNAME_RELEASE" + fi + exit ;; + BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. + echo powerpc-be-beos + exit ;; + BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. + echo powerpc-apple-beos + exit ;; + BePC:BeOS:*:*) # BeOS running on Intel PC compatible. + echo i586-pc-beos + exit ;; + BePC:Haiku:*:*) # Haiku running on Intel PC compatible. + echo i586-pc-haiku + exit ;; + x86_64:Haiku:*:*) + echo x86_64-unknown-haiku + exit ;; + SX-4:SUPER-UX:*:*) + echo sx4-nec-superux"$UNAME_RELEASE" + exit ;; + SX-5:SUPER-UX:*:*) + echo sx5-nec-superux"$UNAME_RELEASE" + exit ;; + SX-6:SUPER-UX:*:*) + echo sx6-nec-superux"$UNAME_RELEASE" + exit ;; + SX-7:SUPER-UX:*:*) + echo sx7-nec-superux"$UNAME_RELEASE" + exit ;; + SX-8:SUPER-UX:*:*) + echo sx8-nec-superux"$UNAME_RELEASE" + exit ;; + SX-8R:SUPER-UX:*:*) + echo sx8r-nec-superux"$UNAME_RELEASE" + exit ;; + SX-ACE:SUPER-UX:*:*) + echo sxace-nec-superux"$UNAME_RELEASE" + exit ;; + Power*:Rhapsody:*:*) + echo powerpc-apple-rhapsody"$UNAME_RELEASE" + exit ;; + *:Rhapsody:*:*) + echo "$UNAME_MACHINE"-apple-rhapsody"$UNAME_RELEASE" + exit ;; + arm64:Darwin:*:*) + echo aarch64-apple-darwin"$UNAME_RELEASE" + exit ;; + *:Darwin:*:*) + UNAME_PROCESSOR=$(uname -p) + case $UNAME_PROCESSOR in + unknown) UNAME_PROCESSOR=powerpc ;; + esac + if command -v xcode-select > /dev/null 2> /dev/null && \ + ! xcode-select --print-path > /dev/null 2> /dev/null ; then + # Avoid executing cc if there is no toolchain installed as + # cc will be a stub that puts up a graphical alert + # prompting the user to install developer tools. + CC_FOR_BUILD=no_compiler_found + else + set_cc_for_build + fi + if test "$CC_FOR_BUILD" != no_compiler_found; then + if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + case $UNAME_PROCESSOR in + i386) UNAME_PROCESSOR=x86_64 ;; + powerpc) UNAME_PROCESSOR=powerpc64 ;; + esac + fi + # On 10.4-10.6 one might compile for PowerPC via gcc -arch ppc + if (echo '#ifdef __POWERPC__'; echo IS_PPC; echo '#endif') | \ + (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_PPC >/dev/null + then + UNAME_PROCESSOR=powerpc + fi + elif test "$UNAME_PROCESSOR" = i386 ; then + # uname -m returns i386 or x86_64 + UNAME_PROCESSOR=$UNAME_MACHINE + fi + echo "$UNAME_PROCESSOR"-apple-darwin"$UNAME_RELEASE" + exit ;; + *:procnto*:*:* | *:QNX:[0123456789]*:*) + UNAME_PROCESSOR=$(uname -p) + if test "$UNAME_PROCESSOR" = x86; then + UNAME_PROCESSOR=i386 + UNAME_MACHINE=pc + fi + echo "$UNAME_PROCESSOR"-"$UNAME_MACHINE"-nto-qnx"$UNAME_RELEASE" + exit ;; + *:QNX:*:4*) + echo i386-pc-qnx + exit ;; + NEO-*:NONSTOP_KERNEL:*:*) + echo neo-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSE-*:NONSTOP_KERNEL:*:*) + echo nse-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSR-*:NONSTOP_KERNEL:*:*) + echo nsr-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSV-*:NONSTOP_KERNEL:*:*) + echo nsv-tandem-nsk"$UNAME_RELEASE" + exit ;; + NSX-*:NONSTOP_KERNEL:*:*) + echo nsx-tandem-nsk"$UNAME_RELEASE" + exit ;; + *:NonStop-UX:*:*) + echo mips-compaq-nonstopux + exit ;; + BS2000:POSIX*:*:*) + echo bs2000-siemens-sysv + exit ;; + DS/*:UNIX_System_V:*:*) + echo "$UNAME_MACHINE"-"$UNAME_SYSTEM"-"$UNAME_RELEASE" + exit ;; + *:Plan9:*:*) + # "uname -m" is not consistent, so use $cputype instead. 386 + # is converted to i386 for consistency with other x86 + # operating systems. + # shellcheck disable=SC2154 + if test "$cputype" = 386; then + UNAME_MACHINE=i386 + else + UNAME_MACHINE="$cputype" + fi + echo "$UNAME_MACHINE"-unknown-plan9 + exit ;; + *:TOPS-10:*:*) + echo pdp10-unknown-tops10 + exit ;; + *:TENEX:*:*) + echo pdp10-unknown-tenex + exit ;; + KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) + echo pdp10-dec-tops20 + exit ;; + XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) + echo pdp10-xkl-tops20 + exit ;; + *:TOPS-20:*:*) + echo pdp10-unknown-tops20 + exit ;; + *:ITS:*:*) + echo pdp10-unknown-its + exit ;; + SEI:*:*:SEIUX) + echo mips-sei-seiux"$UNAME_RELEASE" + exit ;; + *:DragonFly:*:*) + echo "$UNAME_MACHINE"-unknown-dragonfly"$(echo "$UNAME_RELEASE"|sed -e 's/[-(].*//')" + exit ;; + *:*VMS:*:*) + UNAME_MACHINE=$( (uname -p) 2>/dev/null) + case "$UNAME_MACHINE" in + A*) echo alpha-dec-vms ; exit ;; + I*) echo ia64-dec-vms ; exit ;; + V*) echo vax-dec-vms ; exit ;; + esac ;; + *:XENIX:*:SysV) + echo i386-pc-xenix + exit ;; + i*86:skyos:*:*) + echo "$UNAME_MACHINE"-pc-skyos"$(echo "$UNAME_RELEASE" | sed -e 's/ .*$//')" + exit ;; + i*86:rdos:*:*) + echo "$UNAME_MACHINE"-pc-rdos + exit ;; + *:AROS:*:*) + echo "$UNAME_MACHINE"-unknown-aros + exit ;; + x86_64:VMkernel:*:*) + echo "$UNAME_MACHINE"-unknown-esx + exit ;; + amd64:Isilon\ OneFS:*:*) + echo x86_64-unknown-onefs + exit ;; + *:Unleashed:*:*) + echo "$UNAME_MACHINE"-unknown-unleashed"$UNAME_RELEASE" + exit ;; +esac + +# No uname command or uname output not recognized. +set_cc_for_build +cat > "$dummy.c" < +#include +#endif +#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) +#if defined (vax) || defined (__vax) || defined (__vax__) || defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) +#include +#if defined(_SIZE_T_) || defined(SIGLOST) +#include +#endif +#endif +#endif +main () +{ +#if defined (sony) +#if defined (MIPSEB) + /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, + I don't know.... */ + printf ("mips-sony-bsd\n"); exit (0); +#else +#include + printf ("m68k-sony-newsos%s\n", +#ifdef NEWSOS4 + "4" +#else + "" +#endif + ); exit (0); +#endif +#endif + +#if defined (NeXT) +#if !defined (__ARCHITECTURE__) +#define __ARCHITECTURE__ "m68k" +#endif + int version; + version=$( (hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null); + if (version < 4) + printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); + else + printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); + exit (0); +#endif + +#if defined (MULTIMAX) || defined (n16) +#if defined (UMAXV) + printf ("ns32k-encore-sysv\n"); exit (0); +#else +#if defined (CMU) + printf ("ns32k-encore-mach\n"); exit (0); +#else + printf ("ns32k-encore-bsd\n"); exit (0); +#endif +#endif +#endif + +#if defined (__386BSD__) + printf ("i386-pc-bsd\n"); exit (0); +#endif + +#if defined (sequent) +#if defined (i386) + printf ("i386-sequent-dynix\n"); exit (0); +#endif +#if defined (ns32000) + printf ("ns32k-sequent-dynix\n"); exit (0); +#endif +#endif + +#if defined (_SEQUENT_) + struct utsname un; + + uname(&un); + if (strncmp(un.version, "V2", 2) == 0) { + printf ("i386-sequent-ptx2\n"); exit (0); + } + if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ + printf ("i386-sequent-ptx1\n"); exit (0); + } + printf ("i386-sequent-ptx\n"); exit (0); +#endif + +#if defined (vax) +#if !defined (ultrix) +#include +#if defined (BSD) +#if BSD == 43 + printf ("vax-dec-bsd4.3\n"); exit (0); +#else +#if BSD == 199006 + printf ("vax-dec-bsd4.3reno\n"); exit (0); +#else + printf ("vax-dec-bsd\n"); exit (0); +#endif +#endif +#else + printf ("vax-dec-bsd\n"); exit (0); +#endif +#else +#if defined(_SIZE_T_) || defined(SIGLOST) + struct utsname un; + uname (&un); + printf ("vax-dec-ultrix%s\n", un.release); exit (0); +#else + printf ("vax-dec-ultrix\n"); exit (0); +#endif +#endif +#endif +#if defined(ultrix) || defined(_ultrix) || defined(__ultrix) || defined(__ultrix__) +#if defined(mips) || defined(__mips) || defined(__mips__) || defined(MIPS) || defined(__MIPS__) +#if defined(_SIZE_T_) || defined(SIGLOST) + struct utsname *un; + uname (&un); + printf ("mips-dec-ultrix%s\n", un.release); exit (0); +#else + printf ("mips-dec-ultrix\n"); exit (0); +#endif +#endif +#endif + +#if defined (alliant) && defined (i860) + printf ("i860-alliant-bsd\n"); exit (0); +#endif + + exit (1); +} +EOF + +$CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null && SYSTEM_NAME=$($dummy) && + { echo "$SYSTEM_NAME"; exit; } + +# Apollos put the system type in the environment. +test -d /usr/apollo && { echo "$ISP-apollo-$SYSTYPE"; exit; } + +echo "$0: unable to guess system type" >&2 + +case "$UNAME_MACHINE:$UNAME_SYSTEM" in + mips:Linux | mips64:Linux) + # If we got here on MIPS GNU/Linux, output extra information. + cat >&2 <&2 <&2 </dev/null || echo unknown) +uname -r = $( (uname -r) 2>/dev/null || echo unknown) +uname -s = $( (uname -s) 2>/dev/null || echo unknown) +uname -v = $( (uname -v) 2>/dev/null || echo unknown) + +/usr/bin/uname -p = $( (/usr/bin/uname -p) 2>/dev/null) +/bin/uname -X = $( (/bin/uname -X) 2>/dev/null) + +hostinfo = $( (hostinfo) 2>/dev/null) +/bin/universe = $( (/bin/universe) 2>/dev/null) +/usr/bin/arch -k = $( (/usr/bin/arch -k) 2>/dev/null) +/bin/arch = $( (/bin/arch) 2>/dev/null) +/usr/bin/oslevel = $( (/usr/bin/oslevel) 2>/dev/null) +/usr/convex/getsysinfo = $( (/usr/convex/getsysinfo) 2>/dev/null) + +UNAME_MACHINE = "$UNAME_MACHINE" +UNAME_RELEASE = "$UNAME_RELEASE" +UNAME_SYSTEM = "$UNAME_SYSTEM" +UNAME_VERSION = "$UNAME_VERSION" +EOF +fi + +exit 1 + +# Local variables: +# eval: (add-hook 'before-save-hook 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: diff --git a/recipes/clustalw/config.sub b/recipes/clustalw/config.sub new file mode 100644 index 0000000000000..38f3d037a785f --- /dev/null +++ b/recipes/clustalw/config.sub @@ -0,0 +1,1885 @@ +#! /bin/sh +# Configuration validation subroutine script. +# Copyright 1992-2021 Free Software Foundation, Inc. + +# shellcheck disable=SC2006,SC2268 # see below for rationale + +timestamp='2021-10-27' + +# This file is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, see . +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that +# program. This Exception is an additional permission under section 7 +# of the GNU General Public License, version 3 ("GPLv3"). + + +# Please send patches to . +# +# Configuration subroutine to validate and canonicalize a configuration type. +# Supply the specified configuration type as an argument. +# If it is invalid, we print an error message on stderr and exit with code 1. +# Otherwise, we print the canonical config type on stdout and succeed. + +# You can get the latest version of this script from: +# https://git.savannah.gnu.org/cgit/config.git/plain/config.sub + +# This file is supposed to be the same for all GNU packages +# and recognize all the CPU types, system types and aliases +# that are meaningful with *any* GNU software. +# Each package is responsible for reporting which valid configurations +# it does not support. The user should be able to distinguish +# a failure to support a valid configuration from a meaningless +# configuration. + +# The goal of this file is to map all the various variations of a given +# machine specification into a single specification in the form: +# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM +# or in some cases, the newer four-part form: +# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM +# It is wrong to echo any other type of specification. + +# The "shellcheck disable" line above the timestamp inhibits complaints +# about features and limitations of the classic Bourne shell that were +# superseded or lifted in POSIX. However, this script identifies a wide +# variety of pre-POSIX systems that do not have POSIX shells at all, and +# even some reasonably current systems (Solaris 10 as case-in-point) still +# have a pre-POSIX /bin/sh. + +me=`echo "$0" | sed -e 's,.*/,,'` + +usage="\ +Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS + +Canonicalize a configuration name. + +Options: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.sub ($timestamp) + +Copyright 1992-2021 Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit ;; + --version | -v ) + echo "$version" ; exit ;; + --help | --h* | -h ) + echo "$usage"; exit ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" >&2 + exit 1 ;; + + *local*) + # First pass through any local machine types. + echo "$1" + exit ;; + + * ) + break ;; + esac +done + +case $# in + 0) echo "$me: missing argument$help" >&2 + exit 1;; + 1) ;; + *) echo "$me: too many arguments$help" >&2 + exit 1;; +esac + +# Split fields of configuration type +# shellcheck disable=SC2162 +saved_IFS=$IFS +IFS="-" read field1 field2 field3 field4 <&2 + exit 1 + ;; + *-*-*-*) + basic_machine=$field1-$field2 + basic_os=$field3-$field4 + ;; + *-*-*) + # Ambiguous whether COMPANY is present, or skipped and KERNEL-OS is two + # parts + maybe_os=$field2-$field3 + case $maybe_os in + nto-qnx* | linux-* | uclinux-uclibc* \ + | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* \ + | netbsd*-eabi* | kopensolaris*-gnu* | cloudabi*-eabi* \ + | storm-chaos* | os2-emx* | rtmk-nova*) + basic_machine=$field1 + basic_os=$maybe_os + ;; + android-linux) + basic_machine=$field1-unknown + basic_os=linux-android + ;; + *) + basic_machine=$field1-$field2 + basic_os=$field3 + ;; + esac + ;; + *-*) + # A lone config we happen to match not fitting any pattern + case $field1-$field2 in + decstation-3100) + basic_machine=mips-dec + basic_os= + ;; + *-*) + # Second component is usually, but not always the OS + case $field2 in + # Prevent following clause from handling this valid os + sun*os*) + basic_machine=$field1 + basic_os=$field2 + ;; + zephyr*) + basic_machine=$field1-unknown + basic_os=$field2 + ;; + # Manufacturers + dec* | mips* | sequent* | encore* | pc533* | sgi* | sony* \ + | att* | 7300* | 3300* | delta* | motorola* | sun[234]* \ + | unicom* | ibm* | next | hp | isi* | apollo | altos* \ + | convergent* | ncr* | news | 32* | 3600* | 3100* \ + | hitachi* | c[123]* | convex* | sun | crds | omron* | dg \ + | ultra | tti* | harris | dolphin | highlevel | gould \ + | cbm | ns | masscomp | apple | axis | knuth | cray \ + | microblaze* | sim | cisco \ + | oki | wec | wrs | winbond) + basic_machine=$field1-$field2 + basic_os= + ;; + *) + basic_machine=$field1 + basic_os=$field2 + ;; + esac + ;; + esac + ;; + *) + # Convert single-component short-hands not valid as part of + # multi-component configurations. + case $field1 in + 386bsd) + basic_machine=i386-pc + basic_os=bsd + ;; + a29khif) + basic_machine=a29k-amd + basic_os=udi + ;; + adobe68k) + basic_machine=m68010-adobe + basic_os=scout + ;; + alliant) + basic_machine=fx80-alliant + basic_os= + ;; + altos | altos3068) + basic_machine=m68k-altos + basic_os= + ;; + am29k) + basic_machine=a29k-none + basic_os=bsd + ;; + amdahl) + basic_machine=580-amdahl + basic_os=sysv + ;; + amiga) + basic_machine=m68k-unknown + basic_os= + ;; + amigaos | amigados) + basic_machine=m68k-unknown + basic_os=amigaos + ;; + amigaunix | amix) + basic_machine=m68k-unknown + basic_os=sysv4 + ;; + apollo68) + basic_machine=m68k-apollo + basic_os=sysv + ;; + apollo68bsd) + basic_machine=m68k-apollo + basic_os=bsd + ;; + aros) + basic_machine=i386-pc + basic_os=aros + ;; + aux) + basic_machine=m68k-apple + basic_os=aux + ;; + balance) + basic_machine=ns32k-sequent + basic_os=dynix + ;; + blackfin) + basic_machine=bfin-unknown + basic_os=linux + ;; + cegcc) + basic_machine=arm-unknown + basic_os=cegcc + ;; + convex-c1) + basic_machine=c1-convex + basic_os=bsd + ;; + convex-c2) + basic_machine=c2-convex + basic_os=bsd + ;; + convex-c32) + basic_machine=c32-convex + basic_os=bsd + ;; + convex-c34) + basic_machine=c34-convex + basic_os=bsd + ;; + convex-c38) + basic_machine=c38-convex + basic_os=bsd + ;; + cray) + basic_machine=j90-cray + basic_os=unicos + ;; + crds | unos) + basic_machine=m68k-crds + basic_os= + ;; + da30) + basic_machine=m68k-da30 + basic_os= + ;; + decstation | pmax | pmin | dec3100 | decstatn) + basic_machine=mips-dec + basic_os= + ;; + delta88) + basic_machine=m88k-motorola + basic_os=sysv3 + ;; + dicos) + basic_machine=i686-pc + basic_os=dicos + ;; + djgpp) + basic_machine=i586-pc + basic_os=msdosdjgpp + ;; + ebmon29k) + basic_machine=a29k-amd + basic_os=ebmon + ;; + es1800 | OSE68k | ose68k | ose | OSE) + basic_machine=m68k-ericsson + basic_os=ose + ;; + gmicro) + basic_machine=tron-gmicro + basic_os=sysv + ;; + go32) + basic_machine=i386-pc + basic_os=go32 + ;; + h8300hms) + basic_machine=h8300-hitachi + basic_os=hms + ;; + h8300xray) + basic_machine=h8300-hitachi + basic_os=xray + ;; + h8500hms) + basic_machine=h8500-hitachi + basic_os=hms + ;; + harris) + basic_machine=m88k-harris + basic_os=sysv3 + ;; + hp300 | hp300hpux) + basic_machine=m68k-hp + basic_os=hpux + ;; + hp300bsd) + basic_machine=m68k-hp + basic_os=bsd + ;; + hppaosf) + basic_machine=hppa1.1-hp + basic_os=osf + ;; + hppro) + basic_machine=hppa1.1-hp + basic_os=proelf + ;; + i386mach) + basic_machine=i386-mach + basic_os=mach + ;; + isi68 | isi) + basic_machine=m68k-isi + basic_os=sysv + ;; + m68knommu) + basic_machine=m68k-unknown + basic_os=linux + ;; + magnum | m3230) + basic_machine=mips-mips + basic_os=sysv + ;; + merlin) + basic_machine=ns32k-utek + basic_os=sysv + ;; + mingw64) + basic_machine=x86_64-pc + basic_os=mingw64 + ;; + mingw32) + basic_machine=i686-pc + basic_os=mingw32 + ;; + mingw32ce) + basic_machine=arm-unknown + basic_os=mingw32ce + ;; + monitor) + basic_machine=m68k-rom68k + basic_os=coff + ;; + morphos) + basic_machine=powerpc-unknown + basic_os=morphos + ;; + moxiebox) + basic_machine=moxie-unknown + basic_os=moxiebox + ;; + msdos) + basic_machine=i386-pc + basic_os=msdos + ;; + msys) + basic_machine=i686-pc + basic_os=msys + ;; + mvs) + basic_machine=i370-ibm + basic_os=mvs + ;; + nacl) + basic_machine=le32-unknown + basic_os=nacl + ;; + ncr3000) + basic_machine=i486-ncr + basic_os=sysv4 + ;; + netbsd386) + basic_machine=i386-pc + basic_os=netbsd + ;; + netwinder) + basic_machine=armv4l-rebel + basic_os=linux + ;; + news | news700 | news800 | news900) + basic_machine=m68k-sony + basic_os=newsos + ;; + news1000) + basic_machine=m68030-sony + basic_os=newsos + ;; + necv70) + basic_machine=v70-nec + basic_os=sysv + ;; + nh3000) + basic_machine=m68k-harris + basic_os=cxux + ;; + nh[45]000) + basic_machine=m88k-harris + basic_os=cxux + ;; + nindy960) + basic_machine=i960-intel + basic_os=nindy + ;; + mon960) + basic_machine=i960-intel + basic_os=mon960 + ;; + nonstopux) + basic_machine=mips-compaq + basic_os=nonstopux + ;; + os400) + basic_machine=powerpc-ibm + basic_os=os400 + ;; + OSE68000 | ose68000) + basic_machine=m68000-ericsson + basic_os=ose + ;; + os68k) + basic_machine=m68k-none + basic_os=os68k + ;; + paragon) + basic_machine=i860-intel + basic_os=osf + ;; + parisc) + basic_machine=hppa-unknown + basic_os=linux + ;; + psp) + basic_machine=mipsallegrexel-sony + basic_os=psp + ;; + pw32) + basic_machine=i586-unknown + basic_os=pw32 + ;; + rdos | rdos64) + basic_machine=x86_64-pc + basic_os=rdos + ;; + rdos32) + basic_machine=i386-pc + basic_os=rdos + ;; + rom68k) + basic_machine=m68k-rom68k + basic_os=coff + ;; + sa29200) + basic_machine=a29k-amd + basic_os=udi + ;; + sei) + basic_machine=mips-sei + basic_os=seiux + ;; + sequent) + basic_machine=i386-sequent + basic_os= + ;; + sps7) + basic_machine=m68k-bull + basic_os=sysv2 + ;; + st2000) + basic_machine=m68k-tandem + basic_os= + ;; + stratus) + basic_machine=i860-stratus + basic_os=sysv4 + ;; + sun2) + basic_machine=m68000-sun + basic_os= + ;; + sun2os3) + basic_machine=m68000-sun + basic_os=sunos3 + ;; + sun2os4) + basic_machine=m68000-sun + basic_os=sunos4 + ;; + sun3) + basic_machine=m68k-sun + basic_os= + ;; + sun3os3) + basic_machine=m68k-sun + basic_os=sunos3 + ;; + sun3os4) + basic_machine=m68k-sun + basic_os=sunos4 + ;; + sun4) + basic_machine=sparc-sun + basic_os= + ;; + sun4os3) + basic_machine=sparc-sun + basic_os=sunos3 + ;; + sun4os4) + basic_machine=sparc-sun + basic_os=sunos4 + ;; + sun4sol2) + basic_machine=sparc-sun + basic_os=solaris2 + ;; + sun386 | sun386i | roadrunner) + basic_machine=i386-sun + basic_os= + ;; + sv1) + basic_machine=sv1-cray + basic_os=unicos + ;; + symmetry) + basic_machine=i386-sequent + basic_os=dynix + ;; + t3e) + basic_machine=alphaev5-cray + basic_os=unicos + ;; + t90) + basic_machine=t90-cray + basic_os=unicos + ;; + toad1) + basic_machine=pdp10-xkl + basic_os=tops20 + ;; + tpf) + basic_machine=s390x-ibm + basic_os=tpf + ;; + udi29k) + basic_machine=a29k-amd + basic_os=udi + ;; + ultra3) + basic_machine=a29k-nyu + basic_os=sym1 + ;; + v810 | necv810) + basic_machine=v810-nec + basic_os=none + ;; + vaxv) + basic_machine=vax-dec + basic_os=sysv + ;; + vms) + basic_machine=vax-dec + basic_os=vms + ;; + vsta) + basic_machine=i386-pc + basic_os=vsta + ;; + vxworks960) + basic_machine=i960-wrs + basic_os=vxworks + ;; + vxworks68) + basic_machine=m68k-wrs + basic_os=vxworks + ;; + vxworks29k) + basic_machine=a29k-wrs + basic_os=vxworks + ;; + xbox) + basic_machine=i686-pc + basic_os=mingw32 + ;; + ymp) + basic_machine=ymp-cray + basic_os=unicos + ;; + *) + basic_machine=$1 + basic_os= + ;; + esac + ;; +esac + +# Decode 1-component or ad-hoc basic machines +case $basic_machine in + # Here we handle the default manufacturer of certain CPU types. It is in + # some cases the only manufacturer, in others, it is the most popular. + w89k) + cpu=hppa1.1 + vendor=winbond + ;; + op50n) + cpu=hppa1.1 + vendor=oki + ;; + op60c) + cpu=hppa1.1 + vendor=oki + ;; + ibm*) + cpu=i370 + vendor=ibm + ;; + orion105) + cpu=clipper + vendor=highlevel + ;; + mac | mpw | mac-mpw) + cpu=m68k + vendor=apple + ;; + pmac | pmac-mpw) + cpu=powerpc + vendor=apple + ;; + + # Recognize the various machine names and aliases which stand + # for a CPU type and a company and sometimes even an OS. + 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) + cpu=m68000 + vendor=att + ;; + 3b*) + cpu=we32k + vendor=att + ;; + bluegene*) + cpu=powerpc + vendor=ibm + basic_os=cnk + ;; + decsystem10* | dec10*) + cpu=pdp10 + vendor=dec + basic_os=tops10 + ;; + decsystem20* | dec20*) + cpu=pdp10 + vendor=dec + basic_os=tops20 + ;; + delta | 3300 | motorola-3300 | motorola-delta \ + | 3300-motorola | delta-motorola) + cpu=m68k + vendor=motorola + ;; + dpx2*) + cpu=m68k + vendor=bull + basic_os=sysv3 + ;; + encore | umax | mmax) + cpu=ns32k + vendor=encore + ;; + elxsi) + cpu=elxsi + vendor=elxsi + basic_os=${basic_os:-bsd} + ;; + fx2800) + cpu=i860 + vendor=alliant + ;; + genix) + cpu=ns32k + vendor=ns + ;; + h3050r* | hiux*) + cpu=hppa1.1 + vendor=hitachi + basic_os=hiuxwe2 + ;; + hp3k9[0-9][0-9] | hp9[0-9][0-9]) + cpu=hppa1.0 + vendor=hp + ;; + hp9k2[0-9][0-9] | hp9k31[0-9]) + cpu=m68000 + vendor=hp + ;; + hp9k3[2-9][0-9]) + cpu=m68k + vendor=hp + ;; + hp9k6[0-9][0-9] | hp6[0-9][0-9]) + cpu=hppa1.0 + vendor=hp + ;; + hp9k7[0-79][0-9] | hp7[0-79][0-9]) + cpu=hppa1.1 + vendor=hp + ;; + hp9k78[0-9] | hp78[0-9]) + # FIXME: really hppa2.0-hp + cpu=hppa1.1 + vendor=hp + ;; + hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) + # FIXME: really hppa2.0-hp + cpu=hppa1.1 + vendor=hp + ;; + hp9k8[0-9][13679] | hp8[0-9][13679]) + cpu=hppa1.1 + vendor=hp + ;; + hp9k8[0-9][0-9] | hp8[0-9][0-9]) + cpu=hppa1.0 + vendor=hp + ;; + i*86v32) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv32 + ;; + i*86v4*) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv4 + ;; + i*86v) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=sysv + ;; + i*86sol2) + cpu=`echo "$1" | sed -e 's/86.*/86/'` + vendor=pc + basic_os=solaris2 + ;; + j90 | j90-cray) + cpu=j90 + vendor=cray + basic_os=${basic_os:-unicos} + ;; + iris | iris4d) + cpu=mips + vendor=sgi + case $basic_os in + irix*) + ;; + *) + basic_os=irix4 + ;; + esac + ;; + miniframe) + cpu=m68000 + vendor=convergent + ;; + *mint | mint[0-9]* | *MiNT | *MiNT[0-9]*) + cpu=m68k + vendor=atari + basic_os=mint + ;; + news-3600 | risc-news) + cpu=mips + vendor=sony + basic_os=newsos + ;; + next | m*-next) + cpu=m68k + vendor=next + case $basic_os in + openstep*) + ;; + nextstep*) + ;; + ns2*) + basic_os=nextstep2 + ;; + *) + basic_os=nextstep3 + ;; + esac + ;; + np1) + cpu=np1 + vendor=gould + ;; + op50n-* | op60c-*) + cpu=hppa1.1 + vendor=oki + basic_os=proelf + ;; + pa-hitachi) + cpu=hppa1.1 + vendor=hitachi + basic_os=hiuxwe2 + ;; + pbd) + cpu=sparc + vendor=tti + ;; + pbb) + cpu=m68k + vendor=tti + ;; + pc532) + cpu=ns32k + vendor=pc532 + ;; + pn) + cpu=pn + vendor=gould + ;; + power) + cpu=power + vendor=ibm + ;; + ps2) + cpu=i386 + vendor=ibm + ;; + rm[46]00) + cpu=mips + vendor=siemens + ;; + rtpc | rtpc-*) + cpu=romp + vendor=ibm + ;; + sde) + cpu=mipsisa32 + vendor=sde + basic_os=${basic_os:-elf} + ;; + simso-wrs) + cpu=sparclite + vendor=wrs + basic_os=vxworks + ;; + tower | tower-32) + cpu=m68k + vendor=ncr + ;; + vpp*|vx|vx-*) + cpu=f301 + vendor=fujitsu + ;; + w65) + cpu=w65 + vendor=wdc + ;; + w89k-*) + cpu=hppa1.1 + vendor=winbond + basic_os=proelf + ;; + none) + cpu=none + vendor=none + ;; + leon|leon[3-9]) + cpu=sparc + vendor=$basic_machine + ;; + leon-*|leon[3-9]-*) + cpu=sparc + vendor=`echo "$basic_machine" | sed 's/-.*//'` + ;; + + *-*) + # shellcheck disable=SC2162 + saved_IFS=$IFS + IFS="-" read cpu vendor <&2 + exit 1 + ;; + esac + ;; +esac + +# Here we canonicalize certain aliases for manufacturers. +case $vendor in + digital*) + vendor=dec + ;; + commodore*) + vendor=cbm + ;; + *) + ;; +esac + +# Decode manufacturer-specific aliases for certain operating systems. + +if test x$basic_os != x +then + +# First recognize some ad-hoc cases, or perhaps split kernel-os, or else just +# set os. +case $basic_os in + gnu/linux*) + kernel=linux + os=`echo "$basic_os" | sed -e 's|gnu/linux|gnu|'` + ;; + os2-emx) + kernel=os2 + os=`echo "$basic_os" | sed -e 's|os2-emx|emx|'` + ;; + nto-qnx*) + kernel=nto + os=`echo "$basic_os" | sed -e 's|nto-qnx|qnx|'` + ;; + *-*) + # shellcheck disable=SC2162 + saved_IFS=$IFS + IFS="-" read kernel os <&2 + exit 1 + ;; +esac + +# As a final step for OS-related things, validate the OS-kernel combination +# (given a valid OS), if there is a kernel. +case $kernel-$os in + linux-gnu* | linux-dietlibc* | linux-android* | linux-newlib* \ + | linux-musl* | linux-relibc* | linux-uclibc* ) + ;; + uclinux-uclibc* ) + ;; + -dietlibc* | -newlib* | -musl* | -relibc* | -uclibc* ) + # These are just libc implementations, not actual OSes, and thus + # require a kernel. + echo "Invalid configuration \`$1': libc \`$os' needs explicit kernel." 1>&2 + exit 1 + ;; + kfreebsd*-gnu* | kopensolaris*-gnu*) + ;; + vxworks-simlinux | vxworks-simwindows | vxworks-spe) + ;; + nto-qnx*) + ;; + os2-emx) + ;; + *-eabi* | *-gnueabi*) + ;; + -*) + # Blank kernel with real OS is always fine. + ;; + *-*) + echo "Invalid configuration \`$1': Kernel \`$kernel' not known to work with OS \`$os'." 1>&2 + exit 1 + ;; +esac + +# Here we handle the case where we know the os, and the CPU type, but not the +# manufacturer. We pick the logical manufacturer. +case $vendor in + unknown) + case $cpu-$os in + *-riscix*) + vendor=acorn + ;; + *-sunos*) + vendor=sun + ;; + *-cnk* | *-aix*) + vendor=ibm + ;; + *-beos*) + vendor=be + ;; + *-hpux*) + vendor=hp + ;; + *-mpeix*) + vendor=hp + ;; + *-hiux*) + vendor=hitachi + ;; + *-unos*) + vendor=crds + ;; + *-dgux*) + vendor=dg + ;; + *-luna*) + vendor=omron + ;; + *-genix*) + vendor=ns + ;; + *-clix*) + vendor=intergraph + ;; + *-mvs* | *-opened*) + vendor=ibm + ;; + *-os400*) + vendor=ibm + ;; + s390-* | s390x-*) + vendor=ibm + ;; + *-ptx*) + vendor=sequent + ;; + *-tpf*) + vendor=ibm + ;; + *-vxsim* | *-vxworks* | *-windiss*) + vendor=wrs + ;; + *-aux*) + vendor=apple + ;; + *-hms*) + vendor=hitachi + ;; + *-mpw* | *-macos*) + vendor=apple + ;; + *-*mint | *-mint[0-9]* | *-*MiNT | *-MiNT[0-9]*) + vendor=atari + ;; + *-vos*) + vendor=stratus + ;; + esac + ;; +esac + +echo "$cpu-$vendor-${kernel:+$kernel-}$os" +exit + +# Local variables: +# eval: (add-hook 'before-save-hook 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: diff --git a/recipes/clustalw/meta.yaml b/recipes/clustalw/meta.yaml index a8ef603ac467b..0a24762959d42 100644 --- a/recipes/clustalw/meta.yaml +++ b/recipes/clustalw/meta.yaml @@ -9,7 +9,10 @@ source: - patch # [osx] build: - number: 9 + number: 10 + run_exports: + - {{ pin_subpackage('clustalw', max_pin="x.x") }} + requirements: build: @@ -27,6 +30,8 @@ about: summary: ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. extra: + additional-platforms: + - linux-aarch64 skip-lints: - should_not_be_noarch_source identifiers: From 743ae3e5abe26b6fa355b99cb934eb6d990a38ee Mon Sep 17 00:00:00 2001 From: guozhicong Date: Sat, 16 Mar 2024 15:53:56 +0800 Subject: [PATCH 0974/1813] update kallisto: enable linux-aarch64 build (#46459) --- recipes/kallisto/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/kallisto/meta.yaml b/recipes/kallisto/meta.yaml index 88a82fc9c9e7f..44bbf45c4ae97 100644 --- a/recipes/kallisto/meta.yaml +++ b/recipes/kallisto/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 030752bab3b0e33cd3f23f6d8feddd74194e5513532ffbf23519e84db2a86d34 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('kallisto', max_pin="x.x") }} @@ -51,3 +51,5 @@ extra: - mjsteinbaugh skip-lints: - missing_tests + additional-platforms: + - linux-aarch64 \ No newline at end of file From a2d6dd982650f44c12be8919243f2c3f861135a4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Mar 2024 05:51:41 -0400 Subject: [PATCH 0975/1813] Update pathogen-profiler to 4.0.0 (#46503) * Update pathogen-profiler to 4.0.0 * update dependancies --------- Co-authored-by: Jody Phelan --- recipes/pathogen-profiler/meta.yaml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/pathogen-profiler/meta.yaml b/recipes/pathogen-profiler/meta.yaml index a6d852663c109..1d2ae19016c52 100644 --- a/recipes/pathogen-profiler/meta.yaml +++ b/recipes/pathogen-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pathogen-profiler" %} -{% set version = "3.1.0" %} -{% set sha256 = "638f27205f20632624b98b4e11e176455f772f5ae35a9d7b09ab79373a324472" %} +{% set version = "4.0.0" %} +{% set sha256 = "2f32f2c74222a6dfcf4079d4a8f9a84cf7b03a2ebe1c170f887533c60e9ac4f9" %} package: name: {{name}} @@ -47,6 +47,11 @@ requirements: - rich-argparse - joblib >=1.3.0 - pysam + - pydantic >=2.6 + - tomli + - itol-config + - seqkit + - sourmash test: imports: From 33e30b3e1e428a8911cc8eb0e0a7018c26212cdf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Mar 2024 12:59:40 -0400 Subject: [PATCH 0976/1813] Update wgd to 2.0.28 (#46506) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index 039ed9ad26df7..d0b37b6c04f8f 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.27" %} +{% set version = "2.0.28" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: c596d18d59621194ba3d7db2e40c04ef302c376b2d1349e9ef2fde21938beec7 + sha256: d63d0eed83a633b0281553d0f26c4804a2538ed6bba70e7bd04918f2d30f128d build: number: 0 From a0a7d52fadb383781235475f05fb9be2bed7a65b Mon Sep 17 00:00:00 2001 From: Sam Lambert Date: Sat, 16 Mar 2024 17:18:30 +0000 Subject: [PATCH 0977/1813] Plink2 Alpha 5.10 final (5 Jan) (#46505) Update DL parameters --- recipes/plink2/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/plink2/meta.yaml b/recipes/plink2/meta.yaml index 2283e9b7d4799..c5f60a7e7a323 100644 --- a/recipes/plink2/meta.yaml +++ b/recipes/plink2/meta.yaml @@ -1,6 +1,6 @@ package: name: plink2 - version: "2.00a5" + version: "2.00a5.10" build: number: 0 @@ -8,10 +8,10 @@ build: - {{ pin_subpackage('plink2', max_pin=None) }} source: - url: https://s3.amazonaws.com/plink2-assets/alpha5/plink2_linux_x86_64_20230923.zip # [linux] - sha256: f0537f5b90315028de0f3c6be3aaa384a2aa7cd74b0d4d5b6f4d2916c262db40 # [linux] - url: https://s3.amazonaws.com/plink2-assets/alpha5/plink2_mac_20230923.zip # [osx] - sha256: 4a4264ff57abe7191a9244617d86069c370336aa726ced9a6369c0d8318e1f7c # [osx] + url: https://s3.amazonaws.com/plink2-assets/alpha5/plink2_linux_x86_64_20240105.zip # [linux] + sha256: d841fe0b3fcc42d76b2b08bcfeb95e315156b0b883b353807014a69b4867dc47 # [linux] + url: https://s3.amazonaws.com/plink2-assets/alpha5/plink2_mac_20240105.zip # [osx] + sha256: 75d78b9a94a570804a9ab130dd0dd29ff8d1c7851c386239505798cd2126c0f9 # [osx] requirements: build: @@ -19,7 +19,7 @@ requirements: test: commands: - - plink2 --help | grep "PLINK v2.00a5" + - plink2 --help | grep "PLINK v2.00a5.10" about: home: https://www.cog-genomics.org/plink2 From 57c239afe1483d7fe8af23f6cafa6fc9ba73750c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Mar 2024 22:23:47 -0400 Subject: [PATCH 0978/1813] Update salmon to 1.10.3 (#46499) * Update salmon to 1.10.3 * Update meta.yaml fix lint * Update meta.yaml run_export * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh --------- Co-authored-by: Rob Patro --- recipes/salmon/build.sh | 1 + recipes/salmon/meta.yaml | 10 ++++++++-- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/recipes/salmon/build.sh b/recipes/salmon/build.sh index 027cadd4c97e5..ec521e821cd85 100644 --- a/recipes/salmon/build.sh +++ b/recipes/salmon/build.sh @@ -8,6 +8,7 @@ mkdir -p build cd build cmake -DCMAKE_BUILD_TYPE=RELEASE \ -DCONDA_BUILD=TRUE \ + -DLIBSTADEN_LDFLAGS=-L$PREFIX/lib \ -DBoost_NO_BOOST_CMAKE=ON \ -DCMAKE_OSX_DEPLOYMENT_TARGET=10.11 \ -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX \ diff --git a/recipes/salmon/meta.yaml b/recipes/salmon/meta.yaml index f5f3ede9e394b..91a5f42d76e10 100644 --- a/recipes/salmon/meta.yaml +++ b/recipes/salmon/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.10.2" %} +{% set version="1.10.3" %} package: name: salmon @@ -6,10 +6,12 @@ package: build: number: 0 + run_exports: + - {{ pin_subpackage("salmon", max_pin="x.x") }} source: url: https://github.com/COMBINE-lab/salmon/archive/v{{ version }}.tar.gz - sha256: 976989182160fef3afb4429ee8b85d8dd39ed6ca212bb14d6a65cde0e985fb98 + sha256: a053fba63598efc4ade3684aa2c8e8e2294186927d4fcdf1041c36edc2aa0871 requirements: @@ -17,6 +19,8 @@ requirements: - autoconf - cmake - make + - bzip2 + - zlib - {{ compiler('cxx') }} - {{ compiler('c') }} host: @@ -44,6 +48,8 @@ about: summary: Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - rob-p - k3yavi From 46788dc80fc27a16f9cf2150e7ea7e559197e4f2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Mar 2024 16:35:42 -0400 Subject: [PATCH 0979/1813] Update longshot to 1.0.0 (#46501) * Update longshot to 1.0.0 * add run_exports --------- Co-authored-by: mencian --- recipes/longshot/build.sh | 20 ++++++-------------- recipes/longshot/meta.yaml | 33 +++++++++++++++++++++------------ 2 files changed, 27 insertions(+), 26 deletions(-) diff --git a/recipes/longshot/build.sh b/recipes/longshot/build.sh index 86b3387a1a49e..f7112e78ae4b7 100644 --- a/recipes/longshot/build.sh +++ b/recipes/longshot/build.sh @@ -1,19 +1,11 @@ #!/bin/bash set -ex -# this build script is taken from the rust-bio-tools recipe -# https://github.com/bioconda/bioconda-recipes/blob/master/recipes/rust-bio-tools/build.sh - -# taken from yacrd recipe, see: https://github.com/bioconda/bioconda-recipes/blob/2b02c3db6400499d910bc5f297d23cb20c9db4f8/recipes/yacrd/build.sh -#if [ "$(uname)" == "Darwin" ]; then -# # apparently the HOME variable isn't set correctly, and circle ci output indicates the following as the home directory -# #export HOME="/Users/distiller" -# export HOME="/Users/runner" -# # according to https://github.com/rust-lang/cargo/issues/2422#issuecomment-198458960 removing circle ci default configuration solves cargo trouble downloading crates -# git config --global --unset url.ssh://git@github.com.insteadOf -#fi +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" # build statically linked binary with Rust -export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" -export LD=$CC -C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib cargo install --path . --root $PREFIX +export LD="${CC}" C_INCLUDE_PATH="${PREFIX}/include" LIBRARY_PATH="${PREFIX}/lib" +RUST_BACKTRACE=1 +cargo install --path . --root "${PREFIX}" --verbose diff --git a/recipes/longshot/meta.yaml b/recipes/longshot/meta.yaml index ca77b08ec44aa..79ada8afb9463 100644 --- a/recipes/longshot/meta.yaml +++ b/recipes/longshot/meta.yaml @@ -1,26 +1,29 @@ -{% set version = "0.4.5" %} +{% set name = "longshot" %} +{% set version = "1.0.0" %} package: - name: longshot - version: {{version}} - -build: - number: 2 - skip: True # [osx] + name: {{ name }} + version: {{ version }} source: url: https://github.com/pjedge/longshot/archive/v{{ version }}.tar.gz - sha256: 7c9f570e17012b2fee386892ae64daf5f104d59adeb59dc7e710b876c1a11cad + sha256: f6981892beb966eef40986c46928301dec1fef38591cc291e00a546f9866c5e2 + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('longshot', max_pin="x") }} requirements: build: - - rust >=1.4 - - make + - {{ compiler('rust') }} - {{ compiler('c') }} - {{ compiler('cxx') }} - pkg-config # [osx] - clangdev - cmake + - make host: - zlib - xz @@ -34,6 +37,12 @@ test: about: home: https://github.com/pjedge/longshot license: MIT + license_family: MIT license_file: LICENSE - summary: | - Diploid SNV caller for error-prone reads. + summary: "Diploid SNV caller for error-prone reads." + dev_url: https://github.com/pjedge/longshot + +extra: + identifiers: + - doi:10.1038/s41467-019-12493-y + - biotools:longshot From 7b7d3e31af91e61f3a6b304c724104640b1d0522 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Mar 2024 16:35:53 -0400 Subject: [PATCH 0980/1813] Update demuxem to 0.1.7.post1 (#46498) * Update demuxem to 0.1.7.post1 * add run_exports --------- Co-authored-by: mencian --- recipes/demuxem/meta.yaml | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/recipes/demuxem/meta.yaml b/recipes/demuxem/meta.yaml index a2160ef5ce27c..59efd8c3de7d9 100644 --- a/recipes/demuxem/meta.yaml +++ b/recipes/demuxem/meta.yaml @@ -1,5 +1,5 @@ {% set name = "demuxEM" %} -{% set version = "0.1.7" %} +{% set version = "0.1.7.post1" %} package: name: "{{ name|lower }}" @@ -7,29 +7,32 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "a6d9c7f51cad81328f88c5cc298a38ce7364dc5555876a44f375113225ee1eae" + sha256: "f6e6608c37875fb2db6cbd1abe48ce1149b41c7b2b26380cd4d581dca6cac260" build: - number: 1 + number: 0 noarch: python entry_points: - demuxEM = demuxEM.__main__:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" + run_exports: + - {{ pin_subpackage('demuxem', max_pin="x.x") }} requirements: host: - - python >=3.7 + - python >=3.8 - pip - setuptools_scm run: - - python >=3.7 + - python >=3.8 + - docopt - numpy - pandas - scipy - scikit-learn - seaborn - pegasusio >=0.2.12 - - importlib_metadata >=0.7 # [py<38] + - importlib_metadata >=0.7 # [py < 38] test: imports: @@ -41,7 +44,8 @@ test: about: home: "https://github.com/lilab-bcb/demuxEM" doc_url: "https://demuxEM.readthedocs.io" - license: BSD + license: BSD-3-Clause + license_family: BSD license_file: LICENSE summary: "DemuxEM is the demultiplexing module of Pegasus, which works on cell-hashing and nucleus-hashing genomics data." From 1cf6e7f68c08ffaef16873fb96fb1f2e3ec72024 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Mar 2024 16:36:42 -0400 Subject: [PATCH 0981/1813] Update bifrost to 1.3.5 (#46491) * Update bifrost to 1.3.5 * add biotools identifier --------- Co-authored-by: mencian --- recipes/bifrost/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/bifrost/meta.yaml b/recipes/bifrost/meta.yaml index 5ca33f7b6ee0d..8ee624077f1c1 100644 --- a/recipes/bifrost/meta.yaml +++ b/recipes/bifrost/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bifrost" %} -{% set version = "1.3.1" %} +{% set version = "1.3.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/pmelsted/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: d6a9baacddba8e9508336c5adff15a8a482774c724fc0710392fed7bb9ad1e8b + sha256: e1b2491328b0cc1a32e433a8a9780f05547fa4b8d674b58abdda9ac8809f5341 build: number: 0 @@ -42,3 +42,4 @@ about: extra: identifiers: - doi:10.1101/695338 + - biotools:bifrost From 6ed5aa4bf367e60de58a8a882289768ad057fa5b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Mar 2024 16:37:17 -0400 Subject: [PATCH 0982/1813] Update pegasuspy to 1.9.1.post1 (#46504) * Update pegasuspy to 1.9.1 * Update pegasuspy to 1.9.1.post1 --- recipes/pegasuspy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pegasuspy/meta.yaml b/recipes/pegasuspy/meta.yaml index f0485e29a84ec..aa72e4d935028 100644 --- a/recipes/pegasuspy/meta.yaml +++ b/recipes/pegasuspy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pegasuspy" %} -{% set version = "1.9.0" %} +{% set version = "1.9.1.post1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ace00d403d43c91094706a8de85c6c7806e5dce8049c902f6262c808e0089c9f + sha256: 0b1cfe8c7065ad686fd167f05da5bc246ec95700b04d6f1feae3e7d8595bac89 build: From 11433d2f59f6a828928edcac3a2511a4b01c9c4c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Mar 2024 18:12:08 -0400 Subject: [PATCH 0983/1813] Update zol to 1.3.19 (#46508) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index b2c6b239d2e12..56e221e546ad4 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.18" %} +{% set version = "1.3.19" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 7c5a9693a0ca4225581b8f31da73b154d415067c5619a882a7b1d6b99efdc6f7 + sha256: 35b062a79934d83ce2d0071f91fdfb935a7f8cb32dd80f0d658e1c424c4a425b build: number: 0 From 160b864c2f25c008433b3a0ebce5dd6dd61df9c6 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 18 Mar 2024 00:37:52 +0200 Subject: [PATCH 0984/1813] bowtie: enable linux-aarch64 build (#46361) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bowtie/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/bowtie/meta.yaml b/recipes/bowtie/meta.yaml index 0ac76f61b7f94..b515beadf19d5 100644 --- a/recipes/bowtie/meta.yaml +++ b/recipes/bowtie/meta.yaml @@ -13,7 +13,9 @@ source: build: skip: True # [py<30] - number: 6 + number: 7 + run_exports: + - {{ pin_subpackage("bowtie", max_pin="x.x") }} requirements: build: @@ -50,6 +52,8 @@ about: summary: An ultrafast memory-efficient short read aligner extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:bowtie - doi:10.1186/gb-2009-10-3-r25 From 3c90fd751c8eeae954902d90c426f654bce4ebc2 Mon Sep 17 00:00:00 2001 From: tamuanand Date: Sun, 17 Mar 2024 20:08:00 -0400 Subject: [PATCH 0985/1813] Update star-fusion to 1.13.0 (#46509) * Update star-fusion to 1.13.0 Update star-fusion to 1.13.0 * add run_exports * this release has a . instead of - * fix URL --------- Co-authored-by: mencian --- recipes/star-fusion/meta.yaml | 56 +++++++++++++++++++++-------------- 1 file changed, 33 insertions(+), 23 deletions(-) diff --git a/recipes/star-fusion/meta.yaml b/recipes/star-fusion/meta.yaml index 2730d3d2414c3..1b1614c82a910 100644 --- a/recipes/star-fusion/meta.yaml +++ b/recipes/star-fusion/meta.yaml @@ -1,40 +1,42 @@ {% set name = "STAR-Fusion" %} -{% set version = "1.12.0" %} -{% set sha256 = "f99e008a69bdbd8e3cfe51a50f1a57860d4c9a30e2f4f2de80a9b32c97f50e41" %} +{% set version = "1.13.0" %} +{% set sha256 = "39087681abfea5d09e3bff54f91853588b11ec5a924481ab5dc7cfbbd0742e03" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/STAR-Fusion/STAR-Fusion/releases/download/STAR-Fusion-v{{ version }}/STAR-Fusion-v{{ version }}.FULL.tar.gz + url: https://github.com/STAR-Fusion/STAR-Fusion/releases/download/STAR-Fusion-v{{ version }}/STAR-Fusion.v0.13.0.FULL.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('star-fusion', max_pin="x") }} requirements: run: - - bbmap - - blast - - bzip2 - - gmap - - htslib - - igv-reports - - openssl - - perl - - perl-carp - - perl-carp-assert - - perl-db-file - - perl-io-gzip - - perl-json-xs - - perl-set-intervaltree - - perl-uri - - python - - samtools <1.10 - - star ==2.7.8a - - trinity <2.9 + - bbmap + - blast + - bzip2 + - gmap + - htslib + - igv-reports + - openssl + - perl + - perl-carp + - perl-carp-assert + - perl-db-file + - perl-io-gzip + - perl-json-xs + - perl-set-intervaltree + - perl-uri + - python + - samtools <1.10 + - star ==2.7.8a + - trinity <2.9 test: commands: @@ -48,3 +50,11 @@ about: license_file: LICENSE license_family: BSD summary: "STAR-Fusion fusion variant caller. All dependencies required to run FusionInspector and FusionAnnotator are included." + doc_url: https://github.com/STAR-Fusion/STAR-Fusion/wiki + dev_url: https://github.com/STAR-Fusion/STAR-Fusion + +extra: + identifiers: + - doi:10.1186/s13059-019-1842-9 + - biotools:star-fusion + - usegalaxy-eu:star_fusion From 3ae8d516b117039665ea92fb7787886b7919ccd8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 02:57:40 -0400 Subject: [PATCH 0986/1813] Update tb-profiler to 6.0.0 (#46507) * Update tb-profiler to 6.0.0 * update deps * remove indexing in build --------- Co-authored-by: Jody Phelan --- recipes/tb-profiler/build.sh | 4 ++-- recipes/tb-profiler/meta.yaml | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/tb-profiler/build.sh b/recipes/tb-profiler/build.sh index ee5d4d66e8d82..4aaad0eabd6d3 100644 --- a/recipes/tb-profiler/build.sh +++ b/recipes/tb-profiler/build.sh @@ -1,8 +1,8 @@ #!/bin/bash python -m pip install --no-deps --ignore-installed . -gatk CreateSequenceDictionary -R $PREFIX/share/tbprofiler/tbdb.fasta -samtools faidx $PREFIX/share/tbprofiler/tbdb.fasta +# gatk CreateSequenceDictionary -R $PREFIX/share/tbprofiler/tbdb.fasta +# samtools faidx $PREFIX/share/tbprofiler/tbdb.fasta bwa index $PREFIX/share/tbprofiler/tbdb.fasta # this downloads Mycobacterium_tuberculosis_h37rv DB to $PREFIX/share/snpeff-SNPEFF_VERSION/data snpEff download Mycobacterium_tuberculosis_h37rv diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml index c98196104add1..2af11a447a995 100644 --- a/recipes/tb-profiler/meta.yaml +++ b/recipes/tb-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "tb-profiler" %} -{% set version = "5.0.1" %} -{% set sha256 = "71da60ab38cd3c11f1951bac8e26e7cfe2c91700afa8132cf9001e73a2bae252" %} +{% set version = "6.0.0" %} +{% set sha256 = "a23600831f0e14d604e3a3a9330e61b852a559a539876c49b294ab31c8e8cbcf" %} package: name: {{name}} @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 0 run_exports: - {{ pin_subpackage('tb-profiler', max_pin="x") }} @@ -28,7 +28,7 @@ requirements: - python >=3.8 - git - jinja2 - - pathogen-profiler =3.1.0 + - pathogen-profiler >=4.0.0 - filelock - docxtpl - iqtree From 52c60c27049d2d7dac1d10f746ba156c4565e0d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Myl=C3=A8ne=20Mariana=20Gonzales=20Andr=C3=A9?= <103585173+mari-ga@users.noreply.github.com> Date: Mon, 18 Mar 2024 10:31:48 +0100 Subject: [PATCH 0987/1813] Add scsplit (#46438) * changes to cellhashr * yaml file for scsplit * out cellhashr folder * Lint fix * fix lint * fix lint * corrections for lint * fixes lowercase * scsplit out * scsplit back * change to link * fixes --- recipes/scsplit/meta.yaml | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 recipes/scsplit/meta.yaml diff --git a/recipes/scsplit/meta.yaml b/recipes/scsplit/meta.yaml new file mode 100644 index 0000000000000..eabd6ab147f87 --- /dev/null +++ b/recipes/scsplit/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "scSplit" %} +{% set version = "1.0.8.2" %} + +package: + name: "{{ name|lower }}" + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/scSplit-{{ version }}.tar.gz + sha256: e39e2e840ec34bec289619817d7ccee70165e79a361041b1b38e53beac1b7fa3 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('scsplit', max_pin="x.x.x") }} + +requirements: + host: + - python + - pip + run: + - python + +test: + imports: + - scSplit + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/jon-xu/scSplit + summary: Genotype-free demultiplexing of pooled single-cell RNA-Seq + license: MIT + + From ad84b16346a5f4656262b7263b2207cb628ffeda Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 18 Mar 2024 16:19:26 +0200 Subject: [PATCH 0988/1813] cutadapt: add linux-aarch64 build (#46424) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/cutadapt/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/cutadapt/meta.yaml b/recipes/cutadapt/meta.yaml index bb66d16ea076c..7931a59bdc867 100644 --- a/recipes/cutadapt/meta.yaml +++ b/recipes/cutadapt/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 8738a35b363eaf615665a4e7d1b4beb385cd93fb7ffdcf82cd4ab6457acc879b build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" skip: True # [py < 38] run_exports: @@ -43,6 +43,8 @@ about: summary: Trim adapters from high-throughput sequencing reads extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - marcelm identifiers: From b78d6d37faca0dc06e8c82497002aeec7145a81d Mon Sep 17 00:00:00 2001 From: M Bernt Date: Mon, 18 Mar 2024 15:49:47 +0100 Subject: [PATCH 0989/1813] bump revoluzer 0.1.6 (#46517) --- recipes/revoluzer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/revoluzer/meta.yaml b/recipes/revoluzer/meta.yaml index b9254298cc1b7..cd6b24a8f9070 100644 --- a/recipes/revoluzer/meta.yaml +++ b/recipes/revoluzer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "revoluzer" %} -{% set version = "0.1.5" %} +{% set version = "0.1.6" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/Bernt/{{ name }}/-/archive/{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: 80d46c701dc1614cfe63b0b7aea2973d33c2ee56ed637a1fe92df30d9305c144 + sha256: a3c73aa21c1f1d63e40939568bd963690a0df24ccfe7ba6df28ca7ef49dd3b94 build: number: 0 From 81b8ba3387eb87b307f7f5ff7e0085804a6542ac Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 12:10:13 -0400 Subject: [PATCH 0990/1813] Update pyhmmer to 0.10.10 (#46518) --- recipes/pyhmmer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 113bc216794fa..a733d33da8406 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.9" %} +{% set version = "0.10.10" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c78c6f547fb3e37f537d7f87d543e4c61584e688023d0f004107c1df157d36c5 + sha256: 2c7bda6f5c5520d708c7886a6303229a275791fe4e7074a716dbb63fec16804b build: number: 0 From 110ca33fcc2237062323d7a75b4fdffc4c096245 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 13:52:26 -0400 Subject: [PATCH 0991/1813] Update compleasm to 0.2.6 (#46532) --- recipes/compleasm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/compleasm/meta.yaml b/recipes/compleasm/meta.yaml index db6a28c2c338e..3a880d2db517b 100644 --- a/recipes/compleasm/meta.yaml +++ b/recipes/compleasm/meta.yaml @@ -1,6 +1,6 @@ {% set name = "compleasm" %} -{% set version = "0.2.5" %} -{% set hash = "d2da3f30cf6850daf8328f78986e6bfb6fac1baf2b4b207a14f2180a659a04c7" %} +{% set version = "0.2.6" %} +{% set hash = "298a50064b3ada90089912844e40c174de49c976a19ccb53d3645f312649ad25" %} package: name: "{{ name|lower }}" From a37f34e97d7712afcd6a6509ecbd0f6496d8e6ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 13:52:34 -0400 Subject: [PATCH 0992/1813] Update sevenbridges-python to 2.11.0 (#46531) --- recipes/sevenbridges-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index 346b24f70a44f..43ffddea1b422 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.10.3" %} -{% set sha256 = "eb49e2300eaba7d4f50d07cfb10e9706079741a7964e36f9158c2f4efa3ea3c4" %} +{% set version = "2.11.0" %} +{% set sha256 = "0a20b2f75cc9110adad747c0cfe7b7389b1c978008a77fae942ab66614f32534" %} package: name: sevenbridges-python From 990da1b480ac64572315ac252547adb56f032edc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 13:52:57 -0400 Subject: [PATCH 0993/1813] Update rnachipintegrator to 3.0.0 (#46520) * Update rnachipintegrator to 3.0.0 * rnachipintegrator: add missing 'run_exports' statements required by linter. --------- Co-authored-by: Peter Briggs --- recipes/rnachipintegrator/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/rnachipintegrator/meta.yaml b/recipes/rnachipintegrator/meta.yaml index b6907f8bef2de..4c0073646a6dc 100644 --- a/recipes/rnachipintegrator/meta.yaml +++ b/recipes/rnachipintegrator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "rnachipintegrator" %} -{% set version = "2.0.0" %} +{% set version = "3.0.0" %} package: name: '{{ name|lower }}' @@ -7,14 +7,16 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/RnaChipIntegrator-{{ version }}.tar.gz - sha256: 97adf6e8a71bfdef7661472540d661f0965ed6c2140f1d268f57a5e5bbd873b0 + sha256: bdb5cd278a2d93bc7c0e3a7980609db5f24ffa0199b8857818ec8481c59ea0ed build: - number: 1 + number: 0 entry_points: - RnaChipIntegrator = rnachipintegrator.cli:main script: python -m pip install --no-deps --ignore-installed . noarch: python + run_exports: + - {{ pin_subpackage('rnachipintegrator', max_pin="x") }} requirements: host: From 9625b1b7931f8e2c9f8af04bdfa12ff73e2a2075 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 13:55:00 -0400 Subject: [PATCH 0994/1813] Update ena-webin-cli to 7.1.1 (#46530) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index 728b408c42481..3201e5a7de9c9 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "7.1.0" %} -{% set sha256 = "934cd5517beaab3cd130abc31eb22c404868b7f10087067e271bca3cf9e87460" %} +{% set version = "7.1.1" %} +{% set sha256 = "88e7744f12264c0ece54a6bb73833e43b877d5af6cca5bc415d1b55bb0aba782" %} package: name: ena-webin-cli From 3c849a23a4c6603c02ecbb4ac4d8c83385cb838c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 13:55:45 -0400 Subject: [PATCH 0995/1813] Update sneep to 1.0 (#46528) --- recipes/sneep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sneep/meta.yaml b/recipes/sneep/meta.yaml index 6158e18019de4..3d68af7b52d46 100644 --- a/recipes/sneep/meta.yaml +++ b/recipes/sneep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SNEEP" %} -{% set version = "0.9" %} +{% set version = "1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/SchulzLab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3d1f0a20f4d54ae91dd555d0fb8f9d25e980be9399bf6cbec5a5ddeedf47961d + sha256: 6b6ebfa90db3ea4c5c75a0c2cb6ce4fd12ba62aa0d6a1d524f4269f2e58298d0 build: skip: True # [py2k] From f167874d79b84e60d52e16fbe33439649988e422 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 13:56:45 -0400 Subject: [PATCH 0996/1813] Update physiofit to 3.3.5 (#46526) --- recipes/physiofit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/physiofit/meta.yaml b/recipes/physiofit/meta.yaml index 090a51968a5a4..1452c97491f6f 100644 --- a/recipes/physiofit/meta.yaml +++ b/recipes/physiofit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "physiofit" %} -{% set version = "3.3.4" %} +{% set version = "3.3.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/physiofit-{{ version }}.tar.gz - sha256: 03b5e801096d9622429944ee4987ad404ffbf301db7167071f9e92d6b7c9e1f3 + sha256: 40f3484b8f70ea13ef38fe29c847aa0b76030f580091c227398e8598835ab328 build: entry_points: From 29c25bd981b3ddca8b7d97cc8a7ee22403b95267 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 13:57:03 -0400 Subject: [PATCH 0997/1813] Update pcaone to 0.4.4 (#46521) --- recipes/pcaone/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 427ea5b26e300..a2a1ec298e3f8 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.3" %} -{% set sha256 = "91467feef2fa90f168aa2b7d4f4e9b2ec21e255af21c3191bfc9c96a241126c0" %} +{% set version = "0.4.4" %} +{% set sha256 = "39e9b2fb3370ee584fbeed8522260c44bb6053489819057f1a232267a526f72a" %} package: From 20a409a7ff7e1b2954d00a89e304119a52193a9c Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 18 Mar 2024 19:58:12 +0200 Subject: [PATCH 0998/1813] fasttree: add linux-aarch64 build (#46436) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/fasttree/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/fasttree/meta.yaml b/recipes/fasttree/meta.yaml index 1051a9da464c4..a91720bc56fc7 100644 --- a/recipes/fasttree/meta.yaml +++ b/recipes/fasttree/meta.yaml @@ -10,7 +10,9 @@ source: sha256: "9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f" build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: build: @@ -33,6 +35,8 @@ about: summary: "FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences" extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:fasttree - doi:10.1093/molbev/msp077 From 03a634bf8a435f5a9b2267dfbe06c13a0257468a Mon Sep 17 00:00:00 2001 From: Matthew Berkeley <42berkeley@cua.edu> Date: Mon, 18 Mar 2024 17:59:50 +0000 Subject: [PATCH 0999/1813] fix busco patch (#46524) * fix busco patch * increment build number --- recipes/busco/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml index a6261567bb48f..f1a9e3e254dcf 100644 --- a/recipes/busco/meta.yaml +++ b/recipes/busco/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -17,6 +17,7 @@ source: sha256: {{ sha256 }} patches: - 0001-Add-default-config-path-within-prefix-updated.patch + - 0001-Set-conda-distribution.patch requirements: host: From 10ec34b667f7d11b656cc83cfef05ae6a6fdc3c2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 15:38:28 -0400 Subject: [PATCH 1000/1813] Update r-acidgenerics to 0.7.7 (#46536) --- recipes/r-acidgenerics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenerics/meta.yaml b/recipes/r-acidgenerics/meta.yaml index 98a2c9a3d8e1f..92f114f611075 100644 --- a/recipes/r-acidgenerics/meta.yaml +++ b/recipes/r-acidgenerics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.6" %} +{% set version = "0.7.7" %} {% set github = "https://github.com/acidgenomics/r-acidgenerics" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 4769b11a73bc1d159772a6caf9fb2887dc4f6a1147c7e782b68c3fbfd125136b + sha256: 67fc00a1bab3b65dcce30264439f065edb01c7a258cbb5adec8544914ff86948 build: number: 0 From c8b2ea3aa1316a97b5de5a741075f2209266a92f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 16:38:23 -0400 Subject: [PATCH 1001/1813] Update r-acidplyr to 0.5.4 (#46538) --- recipes/r-acidplyr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidplyr/meta.yaml b/recipes/r-acidplyr/meta.yaml index 39281769fbecc..e3ef97b68da93 100644 --- a/recipes/r-acidplyr/meta.yaml +++ b/recipes/r-acidplyr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.3" %} +{% set version = "0.5.4" %} {% set github = "https://github.com/acidgenomics/r-acidplyr" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: d7667aa3ec534fbe13667a30ede0fc2f7bc25f0ea63a7b4708a28e1ed999ebf5 + sha256: 6fd487f33b1ed9ccc1c2580003c8ea9907efd0fcf2b3875f27efa3ccf7d62e45 build: number: 0 From b9ce1805dbd955977df83053ec05688004a9ce5d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 18:11:56 -0400 Subject: [PATCH 1002/1813] Update checkqc to 4.0.1 (#46529) * Update checkqc to 4.0.1 * add python to run deps as package is noarch:python --------- Co-authored-by: mencian --- recipes/checkqc/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/checkqc/meta.yaml b/recipes/checkqc/meta.yaml index 4192646a5e34c..1def5f9605dfb 100644 --- a/recipes/checkqc/meta.yaml +++ b/recipes/checkqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "checkQC" %} -{% set version = "3.8.2" %} +{% set version = "4.0.1" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3aeb234d64aede3377f33b7573eb4719d7c665d68985e8713b16159a1be87988 + sha256: 03bc01d96d45c4c1a0e07d410a6f3ec74c0fab0f7125434ca3d983e70d4d568a build: - number: 1 + number: 0 noarch: python entry_points: - checkqc = checkQC.app:start @@ -24,12 +24,14 @@ requirements: - pip - python >=3.6,<3.11 run: + - python >=3.6,<3.11 - click >=8.1.1 - PyYAML >=6.0 - illumina-interop >=1.2.4 - xmltodict >=0.13.0 - tornado >=6.3.2 - sample-sheet >=0.13.0 + test: imports: - checkQC @@ -45,6 +47,8 @@ about: license_family: GPL3 license_file: LICENSE summary: "A simple program to parse Illumina NGS data and check it for quality criteria." + doc_url: "https://checkqc.readthedocs.io/en/latest/" + dev_url: "https://www.github.com/Molmed/checkQC" extra: recipe-maintainers: From 2d2ebdd114c9620804180fba1377feeea8973837 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 18:13:58 -0400 Subject: [PATCH 1003/1813] Update trust4 to 1.0.14 (#46537) --- recipes/trust4/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/trust4/meta.yaml b/recipes/trust4/meta.yaml index 5dcd3365b3e4f..247cf09d8e388 100644 --- a/recipes/trust4/meta.yaml +++ b/recipes/trust4/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.13" %} +{% set version = "1.0.14" %} package: name: trust4 @@ -11,7 +11,7 @@ build: source: url: https://github.com/liulab-dfci/TRUST4/archive/v{{ version }}.tar.gz - sha256: 64069e2cad65960471f32daaf8568c05214b1d8b6b32b7fd138e56b90d634bb8 + sha256: cea1e06976ee3887ba1bd56b6ca86864f7f136076087c7b5c52727ada66f5dfd requirements: build: From 53d9b2245b8a631c83328759df4b0e7bd1d2c37b Mon Sep 17 00:00:00 2001 From: Ralf Gabriels Date: Mon, 18 Mar 2024 23:22:31 +0100 Subject: [PATCH 1004/1813] Fix entrypoint for psm-utils (#46533) --- recipes/psm-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index f6fc17d1acfe2..b87df4c19079b 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -11,9 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 entry_points: - - psm-utils=psm-utils.__main__:main + - psm_utils=psm_utils.__main__:main script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python run_exports: From e28736e7f97340a3696460f20bd5306761079063 Mon Sep 17 00:00:00 2001 From: guozhicong Date: Tue, 19 Mar 2024 06:27:07 +0800 Subject: [PATCH 1005/1813] update python-edlib: enable python-edlib build (#46513) --- recipes/python-edlib/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/python-edlib/meta.yaml b/recipes/python-edlib/meta.yaml index 620f2a4a05d0f..902225772e83a 100644 --- a/recipes/python-edlib/meta.yaml +++ b/recipes/python-edlib/meta.yaml @@ -9,7 +9,9 @@ source: sha256: 64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766 build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("python-edlib", max_pin="x.x") }} requirements: build: @@ -29,3 +31,7 @@ about: license: MIT License summary: 'Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.' license_family: MIT + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 99d02e2b7227e64e7d80e3d9bef207bf8163d440 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 19 Mar 2024 00:27:38 +0200 Subject: [PATCH 1006/1813] muscle: add linux-aarch64 build (#46525) * muscle: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Bump muscle to 5.1.0 Signed-off-by: Martin Tzvetanov Grigorov * Add support for Linux ARM64 https://github.com/rcedgar/muscle/pull/73 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- ...-Replace-zero-macro-with-memset_zero.patch | 94 ------------------- ...start-va_end-out-of-critical-section.patch | 57 ----------- recipes/muscle/meta.yaml | 16 ++-- recipes/muscle/support-linux-aarch64.patch | 13 +++ 4 files changed, 23 insertions(+), 157 deletions(-) delete mode 100644 recipes/muscle/0001-Replace-zero-macro-with-memset_zero.patch delete mode 100644 recipes/muscle/0002-Move-va_start-va_end-out-of-critical-section.patch create mode 100644 recipes/muscle/support-linux-aarch64.patch diff --git a/recipes/muscle/0001-Replace-zero-macro-with-memset_zero.patch b/recipes/muscle/0001-Replace-zero-macro-with-memset_zero.patch deleted file mode 100644 index 95ba295a88c8d..0000000000000 --- a/recipes/muscle/0001-Replace-zero-macro-with-memset_zero.patch +++ /dev/null @@ -1,94 +0,0 @@ -From e2fc2cc23a2acbee4d9c7d0eeae289024432feec Mon Sep 17 00:00:00 2001 -From: Nicola Soranzo -Date: Thu, 10 Feb 2022 01:31:21 +0000 -Subject: [PATCH 1/2] Replace `zero` macro with `memset_zero` - -The `zero` and `memset_zero` macros defined in `myutils.h` are the same, but -`zero` interferes with LLVM's libcxx when compiling on macOS using Clang: - -In file included from addconfseq.cpp:1: -In file included from ./muscle.h:23: -In file included from ./multisequence.h:4: -In file included from ./sequence.h:6: -In file included from /usr/local/miniconda/envs/bioconda/conda-bld/muscle_1644453677064/_build_env/bin/../include/c++/v1/fstream:184: -In file included from /usr/local/miniconda/envs/bioconda/conda-bld/muscle_1644453677064/_build_env/bin/../include/c++/v1/ostream:137: -In file included from /usr/local/miniconda/envs/bioconda/conda-bld/muscle_1644453677064/_build_env/bin/../include/c++/v1/ios:215: -In file included from /usr/local/miniconda/envs/bioconda/conda-bld/muscle_1644453677064/_build_env/bin/../include/c++/v1/__locale:18: -In file included from /usr/local/miniconda/envs/bioconda/conda-bld/muscle_1644453677064/_build_env/bin/../include/c++/v1/mutex:190: -/usr/local/miniconda/envs/bioconda/conda-bld/muscle_1644453677064/_build_env/bin/../include/c++/v1/__mutex_base:447:25: error: too few arguments provided to function-like macro invocation - if (__d <= __d.zero()) - ^ -./myutils.h:361:9: note: macro 'zero' defined here -> #define zero(a, n) memset((a), 0, (n)*sizeof(a[0])) - ^ -1 error generated. -make: *** [Makefile:53: Darwin/addconfseq.o] Error 1 - -This is the call to `zero` in libcxx: - -https://github.com/llvm/llvm-project/blob/b35be6fe98e30b2373e8fdf024ef8c13a32121d7/libcxx/include/__mutex_base#L444 - -which is supposed to call: - -https://en.cppreference.com/w/cpp/chrono/duration/zero ---- - src/countsort.h | 2 +- - src/ensemble.cpp | 2 +- - src/myutils.cpp | 2 +- - src/myutils.h | 1 - - 4 files changed, 3 insertions(+), 4 deletions(-) - -diff --git a/src/countsort.h b/src/countsort.h -index 3f8d3f7..61b76e6 100644 ---- a/src/countsort.h -+++ b/src/countsort.h -@@ -20,7 +20,7 @@ public: - CountSortMem() - { - m_MaxValueCount = 0; -- zero(m_Vecs, NVEC); -+ memset_zero(m_Vecs, NVEC); - } - - void Free() -diff --git a/src/ensemble.cpp b/src/ensemble.cpp -index 7382db2..331f5f7 100644 ---- a/src/ensemble.cpp -+++ b/src/ensemble.cpp -@@ -41,7 +41,7 @@ void Ensemble::SortMSA(MSA &M) - M.GetLabelToSeqIndex(Labels2, LabelToSeqIndex2); - - char **szSeqsSorted = myalloc(char *, SeqCount); -- zero(szSeqsSorted, SeqCount); -+ memset_zero(szSeqsSorted, SeqCount); - for (uint SeqIndex = 0; SeqIndex < SeqCount; ++SeqIndex) - { - const string &Label = Labels2[SeqIndex]; -diff --git a/src/myutils.cpp b/src/myutils.cpp -index 8eca591..9d7d53c 100644 ---- a/src/myutils.cpp -+++ b/src/myutils.cpp -@@ -807,7 +807,7 @@ static char *GetThreadStr() - { - unsigned NewThreadStrCount = ThreadIndex + 4; - char **NewThreadStrs = myalloc(char *, NewThreadStrCount); -- zero(NewThreadStrs, NewThreadStrCount); -+ memset_zero(NewThreadStrs, NewThreadStrCount); - if (g_ThreadStrCount > 0) - memcpy(NewThreadStrs, g_ThreadStrs, g_ThreadStrCount*sizeof(char *)); - g_ThreadStrs = NewThreadStrs; -diff --git a/src/myutils.h b/src/myutils.h -index d242607..49d28ef 100644 ---- a/src/myutils.h -+++ b/src/myutils.h -@@ -358,7 +358,6 @@ inline bool feq(double x, double y) - #define asserteq(x, y) assert(feq(x, y)) - #define assertaeq(x, y) asserta(feq(x, y)) - --#define zero(a, n) memset((a), 0, (n)*sizeof(a[0])) - #define memset_zero(a, n) memset((a), 0, (n)*sizeof(a[0])) - - void ResetRand(unsigned Seed); --- -2.25.1 - diff --git a/recipes/muscle/0002-Move-va_start-va_end-out-of-critical-section.patch b/recipes/muscle/0002-Move-va_start-va_end-out-of-critical-section.patch deleted file mode 100644 index 5f9236c4b0234..0000000000000 --- a/recipes/muscle/0002-Move-va_start-va_end-out-of-critical-section.patch +++ /dev/null @@ -1,57 +0,0 @@ -From 02f38400c37f54d31b9be31aaa25ee11110cb5f6 Mon Sep 17 00:00:00 2001 -From: Nicola Soranzo -Date: Thu, 10 Feb 2022 03:31:26 +0000 -Subject: [PATCH 2/2] Move va_start/va_end out of critical section - -Fix the following error when compiling with Clang++: - -``` -myutils.cpp:912:2: error: 'va_start' cannot be used in a captured statement - va_start(ArgList, Format); - ^ -1 error generated. -make: *** [Makefile:53: Darwin/myutils.o] Error 1 -``` - -Solution inspired by: - -https://github.com/Ultimaker/CuraEngine/pull/1124 ---- - src/myutils.cpp | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/src/myutils.cpp b/src/myutils.cpp -index 9d7d53c..ccc4fa3 100644 ---- a/src/myutils.cpp -+++ b/src/myutils.cpp -@@ -898,6 +898,8 @@ void Log(const char *Format, ...) - - void Die_(const char *Format, ...) - { -+ va_list ArgList; -+ va_start(ArgList, Format); - #pragma omp critical - { - static bool InDie = false; -@@ -908,10 +910,7 @@ void Die_(const char *Format, ...) - - if (g_fLog != 0) - setbuf(g_fLog, 0); -- va_list ArgList; -- va_start(ArgList, Format); - myvstrprintf(Msg, Format, ArgList); -- va_end(ArgList); - - fprintf(stderr, "\n\n"); - Log("\n"); -@@ -944,6 +943,7 @@ void Die_(const char *Format, ...) - - exit(1); - } -+ va_end(ArgList); - } - - void Warning_(const char *Format, ...) --- -2.25.1 - diff --git a/recipes/muscle/meta.yaml b/recipes/muscle/meta.yaml index 6d0cee1af6e6d..16e21de4c8ff2 100644 --- a/recipes/muscle/meta.yaml +++ b/recipes/muscle/meta.yaml @@ -1,19 +1,21 @@ {% set name = "muscle" %} -{% set version = "5.1" %} +{% set version = "5.1.0" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/rcedgar/muscle/archive/refs/tags/v{{ version }}.tar.gz - sha256: 091d9f8733b92ff106c2a8eb274d1e5a57960d397a2068d8638d6002e8880dab + url: https://github.com/rcedgar/muscle/archive/refs/tags/{{ version }}.tar.gz + sha256: 2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d patches: - - 0001-Replace-zero-macro-with-memset_zero.patch - - 0002-Move-va_start-va_end-out-of-critical-section.patch + - support-linux-aarch64.patch build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + requirements: build: @@ -31,5 +33,7 @@ about: summary: "MUSCLE: multiple sequence alignment with high accuracy and high throughput" extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:muscle diff --git a/recipes/muscle/support-linux-aarch64.patch b/recipes/muscle/support-linux-aarch64.patch new file mode 100644 index 0000000000000..9308bf3333e2b --- /dev/null +++ b/recipes/muscle/support-linux-aarch64.patch @@ -0,0 +1,13 @@ +diff --git i/src/myutils.h w/src/myutils.h +index 49d28ef..8e8167e 100644 +--- i/src/myutils.h ++++ w/src/myutils.h +@@ -11,7 +11,7 @@ + #define TRACK_ALLOC 0 + #define ALLOC_TOTALS 0 + +-#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__) ++#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__) || defined(__aarch64__) + #define BITS 64 + #else + #define BITS 32 From 12c9fc45a3d2e64c5170916a6264ccde3ff8f4f0 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 19 Mar 2024 00:32:56 +0200 Subject: [PATCH 1007/1813] hmmcopy: enable linux-aarch64 build (#46359) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/hmmcopy/build.sh | 2 +- recipes/hmmcopy/meta.yaml | 8 +++++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/hmmcopy/build.sh b/recipes/hmmcopy/build.sh index 221ea7f18365c..2e2b0710805e5 100644 --- a/recipes/hmmcopy/build.sh +++ b/recipes/hmmcopy/build.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # Source archive contains some macOS junk files, # which prevent hoisting the HMMcopy on Linux only. diff --git a/recipes/hmmcopy/meta.yaml b/recipes/hmmcopy/meta.yaml index 950876a55c956..bf1639367da71 100644 --- a/recipes/hmmcopy/meta.yaml +++ b/recipes/hmmcopy/meta.yaml @@ -7,7 +7,9 @@ source: md5: 205a719e7ac9b9f9ba811cdd7cbdae0a build: - number: 9 + number: 10 + run_exports: + - {{ pin_subpackage("hmmcopy", max_pin="x.x") }} requirements: build: @@ -31,3 +33,7 @@ about: home: http://compbio.bccrc.ca/software/hmmcopy/ license: GPL-3 summary: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From ca3606dcb10ebd5caecba80a994aacddccd5e155 Mon Sep 17 00:00:00 2001 From: sunqian2002 <50086972+huazhong28@users.noreply.github.com> Date: Tue, 19 Mar 2024 06:37:30 +0800 Subject: [PATCH 1008/1813] linux-aarch64 build for alcor (#46388) * linux-aarch64 build for alcor * linux-aarch64 build for alcor * linux-aarch64 build for alcor * linux-aarch64 build for alcor --- recipes/alcor/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/alcor/meta.yaml b/recipes/alcor/meta.yaml index 538f6076de517..29a3cfed328af 100644 --- a/recipes/alcor/meta.yaml +++ b/recipes/alcor/meta.yaml @@ -10,7 +10,9 @@ package: build: # Passes some invalid flags for clang skip: True # [osx] - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage("alcor", max_pin="x.x") }} source: url: https://github.com/cobilab/alcor/archive/v{{ version }}.tar.gz @@ -37,3 +39,7 @@ about: license_file: LICENSE license_family: GPL summary: Software for alignment-free simulation, mapping, and visualization of low-complexity regions in FASTA data. + +extra: + additional-platforms: + - linux-aarch64 From 89847807731f5409ce8d3197158c69b66c740a42 Mon Sep 17 00:00:00 2001 From: sunqian2002 <50086972+huazhong28@users.noreply.github.com> Date: Tue, 19 Mar 2024 06:37:46 +0800 Subject: [PATCH 1009/1813] linux-aarch64 build for ac (#46362) * linux-aarch64 build for ac * linux-aarch64 build for ac --- recipes/ac/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/ac/meta.yaml b/recipes/ac/meta.yaml index 3b66857bde87b..17b4fbc7a327c 100644 --- a/recipes/ac/meta.yaml +++ b/recipes/ac/meta.yaml @@ -7,7 +7,9 @@ package: build: # Passes some invalid flags for clang skip: True # [osx] - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("ac", max_pin="x.x") }} source: url: https://github.com/cobilab/ac/archive/v{{ version }}.tar.gz @@ -30,3 +32,7 @@ about: license_file: LICENSE license_family: GPL summary: A lossless compression tool for Amino Acid sequences + +extra: + additional-platforms: + - linux-aarch64 From 0f89ad17a21013e9b271389832bbfbb933c2dd95 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 18:39:25 -0400 Subject: [PATCH 1010/1813] Update treeswift to 1.1.40 (#46541) --- recipes/treeswift/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/treeswift/meta.yaml b/recipes/treeswift/meta.yaml index 54fd1362581cd..96939ec1e97d6 100644 --- a/recipes/treeswift/meta.yaml +++ b/recipes/treeswift/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.39" %} +{% set version = "1.1.40" %} package: name: "treeswift" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/t/treeswift/treeswift-{{ version }}.tar.gz - sha256: bdb432acea1fd7c13111e101062f75cf0a7ee721a90d7bc86057ee3cea4edfaa + sha256: 51c1bf1f0455866f10980d042831d4c1c244d4861808eb53d7730db99279ec14 build: noarch: python From f30cd2c88ff080bee24032f6439cfebde8786a1c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 18:48:03 -0400 Subject: [PATCH 1011/1813] Update phykit to 1.19.0 (#46542) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index c762c75156615..ae6066f0ad672 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.17.0" %} +{% set version = "1.19.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: eb4087ff616aeb8935016f2f5b929fe49731190e99d6c4df89da2f49252bdd2a + sha256: da276adaf07f65a1d693db5f3f3c790ddc77610436a1178f49f6d3ab57b4c44b build: noarch: python From d62d95f2d0b1dd6f14f51f579f051c9a84b41db9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 18:54:02 -0400 Subject: [PATCH 1012/1813] Update r-azimuth to 0.5.0 (#46495) * Update r-azimuth to 0.5.0 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/r-azimuth/meta.yaml | 26 ++++++++++++++++++++------ 1 file changed, 20 insertions(+), 6 deletions(-) diff --git a/recipes/r-azimuth/meta.yaml b/recipes/r-azimuth/meta.yaml index ee0ab9c9b5eb4..ece8b017733ac 100644 --- a/recipes/r-azimuth/meta.yaml +++ b/recipes/r-azimuth/meta.yaml @@ -1,10 +1,13 @@ -{% set version = '0.4.6' %} +{% set version = '0.5.0' %} + package: name: r-azimuth version: {{ version|replace("-", "_") }} + source: url: https://github.com/satijalab/azimuth/archive/refs/tags/v{{ version }}.tar.gz - sha256: 14f2c307590dec6184702be4042f62def674b91f75af5153a6ae0d89277f5fd2 + sha256: 0001e425d48a6f4ed71b99239d414285a09d06a138c393ad2227e186ef34c38f + build: script: $R CMD INSTALL --build . run_exports: @@ -12,6 +15,7 @@ build: number: 0 rpaths: - lib/R/lib/ + requirements: build: - {{ compiler('c') }} @@ -20,12 +24,13 @@ requirements: - r-base - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - 'r-dt >=0.15' + - 'bioconductor-ensdb.hsapiens.v86' - 'r-matrix >=1.2.18' - 'r-rcpp >=1.0.7' - - 'r-seurat >=4.0.0' + - 'r-seurat >=5.0.0' - 'r-seurat-data ==0.2.1' - 'r-seurat-disk ==0.0.0.9021' - - 'r-seuratobject' + - 'r-seuratobject >=5.0.0' - 'r-future >=1.19.1' - 'r-ggplot2 >=3.3.2' - 'bioconductor-glmgampoi >=1.0.0' @@ -33,6 +38,7 @@ requirements: - 'r-hdf5r >=1.3.2' - 'r-htmltools >=0.5.0' - 'r-httr >=1.4.2' + - 'bioconductor-jaspar2020' - 'r-jsonlite >=1.7.0' - 'r-patchwork >=1.0.1' - 'r-plotly' @@ -43,17 +49,20 @@ requirements: - 'r-shinybs >=0.61' - 'r-shinydashboard >=0.7.1' - 'r-shinyjs >=2.0.0' + - 'r-signac >=1.12.0' - 'r-stringr >=1.4.0' + - 'bioconductor-tfbstools' - 'r-withr >=2.3.0' run: - r-base - 'r-dt >=0.15' + - 'bioconductor-ensdb.hsapiens.v86' - 'r-matrix >=1.2.18' - 'r-rcpp >=1.0.7' - - 'r-seurat >=4.0.0' + - 'r-seurat >=5.0.0' - 'r-seurat-data ==0.2.1' - 'r-seurat-disk ==0.0.0.9021' - - 'r-seuratobject' + - 'r-seuratobject >=5.0.0' - 'r-future >=1.19.1' - 'r-ggplot2 >=3.3.2' - 'bioconductor-glmgampoi >=1.0.0' @@ -61,6 +70,7 @@ requirements: - 'r-hdf5r >=1.3.2' - 'r-htmltools >=0.5.0' - 'r-httr >=1.4.2' + - 'bioconductor-jaspar2020' - 'r-jsonlite >=1.7.0' - 'r-patchwork >=1.0.1' - 'r-plotly' @@ -71,11 +81,15 @@ requirements: - 'r-shinybs >=0.61' - 'r-shinydashboard >=0.7.1' - 'r-shinyjs >=2.0.0' + - 'r-signac >=1.12.0' - 'r-stringr >=1.4.0' + - 'bioconductor-tfbstools' - 'r-withr >=2.3.0' + test: commands: - '$R -e "library(''Azimuth'')"' + about: home: https://github.com/satijalab/azimuth license: GPL-3.0-only From b6dcdc5e3268b833e31bffeadc79c571ed165d2e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 18:57:42 -0400 Subject: [PATCH 1013/1813] Update augur to 24.3.0 (#46534) --- recipes/augur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index afe0aac0b2035..9e8fbdf584bdd 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.2.3" %} +{% set version = "24.3.0" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: 67f21f0de7d5cbf8e7f95d01f27d6a42d0e8e0c63e373969609d879c5f4785d0 + sha256: 39c648ec2c226e90f3f3b242ee0deda3760760efb567687b5430f76d0b2b5180 build: number: 0 From 922346e4fad9635a3bef4bd2209761d287574fc2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 19:13:27 -0400 Subject: [PATCH 1014/1813] Update psm-utils to 0.7.4 (#46535) * Update psm-utils to 0.7.4 * reset build number --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian --- recipes/psm-utils/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index b87df4c19079b..ed079a377b69a 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.7.3" %} -{% set sha256 = "d97b197276c7ebfa14aa74119e0f576466f1c87949ad00ce60ce1bba2fdc43b2" %} +{% set version = "0.7.4" %} +{% set sha256 = "bf36ad6246568841a5c4b658fdbbb0bf3a70f6f3b24b31b141f6018de24d4ad8" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 entry_points: - psm_utils=psm_utils.__main__:main script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" From 3b29d02a88dcfec0c7bb658df6be7b91e8fbdfcd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Mar 2024 19:48:51 -0400 Subject: [PATCH 1015/1813] Update freyja to 1.5.0 (#46544) --- recipes/freyja/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/freyja/meta.yaml b/recipes/freyja/meta.yaml index 6c3686a0eef7c..361f0291e6932 100644 --- a/recipes/freyja/meta.yaml +++ b/recipes/freyja/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.9" %} +{% set version = "1.5.0" %} {% set name = "Freyja" %} package: @@ -16,7 +16,7 @@ build: source: url: https://github.com/andersen-lab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: aeaa1697d7e12386e50c96880ab976e2cc68989bd7fdf4bfe802cb02bb3982ba + sha256: b7d95ec0a632ffda019ab01d1170bd4550f8ef41039e1987a5bc93bdc5fa0edb requirements: host: From 3002b9cf10f07f97a74ac2f6b32b100a2b88ba83 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 18 Mar 2024 20:12:15 -0500 Subject: [PATCH 1016/1813] Update mgatk recipe (#46545) --- recipes/mgatk/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/mgatk/meta.yaml b/recipes/mgatk/meta.yaml index dcc431be31cd5..3a641253df822 100644 --- a/recipes/mgatk/meta.yaml +++ b/recipes/mgatk/meta.yaml @@ -10,13 +10,13 @@ source: sha256: f42f5eb8fcfd38dd6ef3db853764071311cb70d841a73ff2f40f0a0c9e9d7de9 build: - number: 0 + number: 1 noarch: python entry_points: - mgatk = mgatk.cli:main - mgatk-del-find = mgatk.deletioncalling.clifind:main - mgatk-del = mgatk.deletioncalling.clidel:main - script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir run_exports: - {{ pin_subpackage('mgatk', max_pin="x.x") }} @@ -29,7 +29,8 @@ requirements: - click - pysam - pytest - - snakemake-minimal + - snakemake-minimal <8 + - pulp <2.8 - biopython - numpy - pandas From ebadf6f2f76ce64e3a5434bdb92821f0cc508751 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 18 Mar 2024 20:15:24 -0500 Subject: [PATCH 1017/1813] Update maegatk recipe (#46546) --- recipes/maegatk/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/maegatk/meta.yaml b/recipes/maegatk/meta.yaml index 6e622c1497f78..a7a26ecda678c 100644 --- a/recipes/maegatk/meta.yaml +++ b/recipes/maegatk/meta.yaml @@ -10,11 +10,11 @@ source: sha256: fce1ec287914e03ce2b317a4f6a338f1806cd82e5c77f4e4cb1efbd48c87bdda build: - number: 0 + number: 1 noarch: python entry_points: - maegatk = maegatk.cli:main - script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir run_exports: - {{ pin_subpackage('maegatk', max_pin="x.x") }} @@ -27,7 +27,8 @@ requirements: - click - pysam - pytest - - snakemake-minimal + - snakemake-minimal <8 + - pulp <2.8 - biopython - optparse-pretty - regex From ac58d6cbb1ce2cb242fd9809e9ec2eceaaf40393 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Mar 2024 00:03:54 -0400 Subject: [PATCH 1018/1813] Update yacht to 1.2.2 (#46547) --- recipes/yacht/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/yacht/meta.yaml b/recipes/yacht/meta.yaml index c8f57cc59af75..660b5f47c822d 100644 --- a/recipes/yacht/meta.yaml +++ b/recipes/yacht/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: yacht @@ -6,7 +6,7 @@ package: source: url: https://github.com/KoslickiLab/YACHT/releases/download/v{{ version }}/yacht-{{ version }}.tar.gz - sha256: 248c85c52e88c576d7afd9842b06fec2a6f89fbb9b1150885486e6adf72ac3ca + sha256: a5c97eecac7aee24e5850f29537cfe5f0b3647ac2766b7876321d369e8bdf514 build: number: 0 From 62ab5cada03808809a546cf6ac9963aaa7eaf7e6 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 19 Mar 2024 06:11:15 +0200 Subject: [PATCH 1019/1813] bowtie2: add linux-aarch64 build (#46423) * bowtie2: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * bowtie2: [linux-aarch64] Git clone the third party dependencies Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bowtie2/build.sh | 5 +++++ recipes/bowtie2/meta.yaml | 5 ++++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/recipes/bowtie2/build.sh b/recipes/bowtie2/build.sh index 90c802dd1d54d..0add48e56f0b0 100644 --- a/recipes/bowtie2/build.sh +++ b/recipes/bowtie2/build.sh @@ -1,5 +1,10 @@ #!/bin/bash +# Fetch third party dependencies +# (Git submodules - https://github.com/BenLangmead/bowtie2/blob/a43fa6f43f54989468a294967898f85b9fe4cefa/.gitmodules) +git clone --branch master https://github.com/simd-everywhere/simde-no-tests.git third_party/simde +git clone https://github.com/ch4rr0/libsais third_party/libsais + LDFLAGS="" make CXX=$CXX CPP=$CXX CC=$CC LDLIBS="-L$PREFIX/lib -lz -lzstd -ltbb -ltbbmalloc -lpthread" WITH_ZSTD=1 diff --git a/recipes/bowtie2/meta.yaml b/recipes/bowtie2/meta.yaml index ece3f06a3d3f0..aca45e7cc57e5 100644 --- a/recipes/bowtie2/meta.yaml +++ b/recipes/bowtie2/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 4ac3ece3db011322caab14678b9d80cfc7f75208cdaf0c58b24a6ea0f1a0a60e build: - number: 0 + number: 1 skip: True # [py2k] run_exports: - {{ pin_subpackage('bowtie2', max_pin="x") }} @@ -18,6 +18,7 @@ requirements: build: - {{ compiler('cxx') }} - make + - git host: - python - zlib @@ -54,6 +55,8 @@ about: summary: Fast and sensitive gapped read alignment extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:bowtie2 - doi:10.1038/nmeth.1923 From 027fbbc06e59737773dd7ede06c3000145b21a42 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Mar 2024 00:16:23 -0500 Subject: [PATCH 1020/1813] pyspoa: enable linux-aarch64 build (#46549) --- recipes/pyspoa/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pyspoa/meta.yaml b/recipes/pyspoa/meta.yaml index 94deab4fe5d7f..4e1d12c9e6cac 100644 --- a/recipes/pyspoa/meta.yaml +++ b/recipes/pyspoa/meta.yaml @@ -11,11 +11,11 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py < 38] script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation run_exports: - - {{ pin_subpackage('pyspoa', max_pin="x") }} + - {{ pin_subpackage('pyspoa', max_pin="x.x") }} requirements: build: @@ -25,8 +25,6 @@ requirements: host: - python - pip - - setuptools - - wheel - pybind11 - scikit-build - zlib @@ -50,3 +48,5 @@ extra: recipe-maintainers: - cjw85 - iiSeymour + additional-platforms: + - linux-aarch64 From 6466b72a1f47d6cdb1649c3731706293714679ba Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Mar 2024 01:42:13 -0500 Subject: [PATCH 1021/1813] pyrodigal: enable linux-aarch64 build (#46553) * pyrodigal: enable linux-aarch64 build * bump build number --- recipes/pyrodigal/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml index 944dd7eb5dd58..437c6da734fc4 100644 --- a/recipes/pyrodigal/meta.yaml +++ b/recipes/pyrodigal/meta.yaml @@ -10,13 +10,13 @@ source: sha256: 68f92cd83f9cd2883b99433847a827dd84ccb27edc51cb3f415664f0f08b0325 build: - number: 0 + number: 1 skip: True # [py < 36] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --use-pep517 -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" entry_points: - pyrodigal = pyrodigal.cli:main run_exports: - - {{ pin_subpackage("pyrodigal", max_pin="x.x") }} + - {{ pin_subpackage("pyrodigal", max_pin="x") }} requirements: build: @@ -25,7 +25,6 @@ requirements: - python - pip - cython - - setuptools run: - python - archspec >=0.2.0 @@ -39,14 +38,17 @@ test: about: home: https://github.com/althonos/pyrodigal - license: GPL-3 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: COPYING summary: Python bindings to Prodigal, an ORF finder for microbial sequences. doc_url: https://pyrodigal.readthedocs.org/ + dev_url: https://github.com/althonos/pyrodigal extra: recipe-maintainers: - althonos identifiers: - doi:10.21105/joss.04296 # JOSS paper + additional-platforms: + - linux-aarch64 From 5b9a5c0b5e692ef51f1c994a21341c4fd7acd3a0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Mar 2024 07:15:27 -0400 Subject: [PATCH 1022/1813] Update phold to 0.1.3 (#46557) --- recipes/phold/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phold/meta.yaml b/recipes/phold/meta.yaml index 3324ee9259f6f..44650fb63f6e9 100644 --- a/recipes/phold/meta.yaml +++ b/recipes/phold/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phold" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4afe2f591f904ea3dd361ad0565e3d837b2d7a0e8eaa717a7208681dfc6f1c35 + sha256: a89c24d063784fa3a318ccc795fff3c5d2d8c00b4ed22bb8ee188052871778e7 build: number: 0 From c47bb585be9496842599e2e512a35dd120239528 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Mar 2024 07:15:52 -0400 Subject: [PATCH 1023/1813] Update snakemake to 8.9.0 (#46565) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 62c423e0f7660..c103bc15844b0 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.8.0" %} +{% set version = "8.9.0" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: d676ea965a2bef00f7b3b5e1707482f2728e52abc5c85c2600e614e3a405bb1a + sha256: 1c36d231da92a1e37ab9f96d35346f5268949fbd1cebf4c9d429816a05538066 build: number: 0 From c6d4da02d2d43368ceaf5a01ee5fb45e6fc83a57 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Mar 2024 09:17:32 -0500 Subject: [PATCH 1024/1813] pyhmmer: enable linux-aarch64 build (#46551) --- recipes/pyhmmer/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index a733d33da8406..035907bda7054 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -10,9 +10,9 @@ source: sha256: 2c7bda6f5c5520d708c7886a6303229a275791fe4e7074a716dbb63fec16804b build: - number: 0 - skip: True #[py2k or win] - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" + number: 1 + skip: True # [py2k or win] + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" run_exports: - {{ pin_subpackage('pyhmmer', max_pin="x.x") }} @@ -23,7 +23,6 @@ requirements: - python - pip - cython - - setuptools >=46.4 - psutil >=5.8 run: - python @@ -44,9 +43,12 @@ about: license_file: COPYING summary: Cython bindings and Python interface to HMMER3. doc_url: https://pyhmmer.readthedocs.io + dev_url: https://github.com/althonos/pyhmmer extra: recipe-maintainers: - althonos identifiers: - DOI:10.1093/bioinformatics/btad214 + additional-platforms: + - linux-aarch64 From eecb5257affece5d5c2d7bbdd361260863ca781d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Mar 2024 14:34:31 -0400 Subject: [PATCH 1025/1813] Update bioconda-utils to 2.12.0 (#46577) --- recipes/bioconda-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 223a443b5d610..e6f5a9ee840bb 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.11.1" %} -{% set sha256 = "7ed52d449b19beecf9461a998aeb8194b5930538ec6468996448bf28f1bab2f5" %} +{% set version = "2.12.0" %} +{% set sha256 = "b481f5232f55e53decc732856604d4e949a85522804efe1ec8f9edb45f065ca5" %} package: name: bioconda-utils From cf271e89e8a6742aea0af5dc20099808f7c3a32d Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Tue, 19 Mar 2024 19:36:20 +0100 Subject: [PATCH 1026/1813] update fastp adding new platform (#46576) --- recipes/fastp/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/fastp/meta.yaml b/recipes/fastp/meta.yaml index 69d01a796d934..5ab71115f3ff3 100644 --- a/recipes/fastp/meta.yaml +++ b/recipes/fastp/meta.yaml @@ -9,7 +9,9 @@ source: sha256: 4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5 build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage("fastp", max_pin="x.x") }} requirements: build: @@ -27,6 +29,10 @@ test: commands: - fastp --help +extra: + additional-platforms: + - linux-aarch64 + about: home: https://github.com/OpenGene/fastp license: MIT From d0778e0460aa035ffa3368f7c66033ea80468e8d Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Tue, 19 Mar 2024 19:39:04 +0100 Subject: [PATCH 1027/1813] update stringtie adding new platform (#46569) * update stringtie adding new platform * add run_exports * add zlib --- recipes/stringtie/build.sh | 2 ++ recipes/stringtie/meta.yaml | 7 ++++++- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/recipes/stringtie/build.sh b/recipes/stringtie/build.sh index 5e2d7207edd0d..cb22d7d109407 100644 --- a/recipes/stringtie/build.sh +++ b/recipes/stringtie/build.sh @@ -1,5 +1,7 @@ #!/bin/sh +ln -s $PREFIX/lib/libz.so.1 $PREFIX/lib/libz.so + export C_INCLUDE_PATH=$PREFIX/include export CPLUS_INCLUDE_PATH=$PREFIX/include export LINKER="$CXX" diff --git a/recipes/stringtie/meta.yaml b/recipes/stringtie/meta.yaml index a005ac59713ab..bb60dcb570181 100644 --- a/recipes/stringtie/meta.yaml +++ b/recipes/stringtie/meta.yaml @@ -13,7 +13,9 @@ source: - patch build: - number: 5 + number: 6 + run_exports: + - {{ pin_subpackage("stringtie", max_pin="x.x") }} # TODO currently fails to build on osx. # Feel free to re-enable and debug. skip: true # [osx] @@ -21,6 +23,7 @@ build: requirements: build: - make + - zlib - {{ compiler('c') }} - {{ compiler('cxx') }} host: @@ -44,6 +47,8 @@ about: dev_url: https://github.com/gpertea/stringtie extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:StringTie - usegalaxy-eu:stringtie From 6aa50fa201d0bb759a46e3995ab98d62b23965cd Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 20 Mar 2024 02:43:04 +0800 Subject: [PATCH 1028/1813] make linux-aarch64 build for age_metasv (#46563) * linux-aarch64 build for age-metasv * linux-aarch64 build for age-metasv --------- Co-authored-by: HWsunqian0027 --- recipes/age-metasv/meta.yaml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/recipes/age-metasv/meta.yaml b/recipes/age-metasv/meta.yaml index 2eefecbaee314..212bb76c1a0d5 100644 --- a/recipes/age-metasv/meta.yaml +++ b/recipes/age-metasv/meta.yaml @@ -10,7 +10,9 @@ source: build: skip: True # [osx] - number: 7 + number: 8 + run_exports: + - {{ pin_subpackage("age-metasv", max_pin="x.x.x") }} requirements: build: @@ -18,6 +20,7 @@ requirements: - {{ compiler('cxx') }} - llvm-openmp # [osx] - libgomp # [linux] + - libstdcxx-ng >=12 host: run: @@ -29,3 +32,7 @@ about: home: https://github.com/marghoob/AGE/tree/simple-parseable-output license: CCPL (Creative Commons Public License) summary: optimal alignment of sequences with structural variants (SVs), modifiied for MetaSV integration + +extra: + additional-platforms: + - linux-aarch64 From aa8619c180ea06cd674806a6af2bd236de23c135 Mon Sep 17 00:00:00 2001 From: Enrico <75318813+GitEnricoNeko@users.noreply.github.com> Date: Tue, 19 Mar 2024 19:45:39 +0100 Subject: [PATCH 1029/1813] Add srahunter/meta.yaml (#46243) * Changes to be committed: new file: srahunter/meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/srahunter/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/srahunter/meta.yaml diff --git a/recipes/srahunter/meta.yaml b/recipes/srahunter/meta.yaml new file mode 100644 index 0000000000000..2efaca256b3a9 --- /dev/null +++ b/recipes/srahunter/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "srahunter" %} +{% set version = "0.0.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/GitEnricoNeko/srahunter/archive/refs/tags/{{version}}.tar.gz + sha256: 635dbea61296fc84857b8290fb8858b5dbc26301031d8fce3a5de2e340c78740 +build: + entry_points: + - srahunter=scripts.cli:main + noarch: python + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps -vvv + number: 0 + run_exports: + - {{ pin_subpackage('srahunter', max_pin="x") }} + +requirements: + host: + - python >=3.6 + - pip + run: + - datavzrd + - entrez-direct + - python >=3.6 + - pandas >=2.0.2 + - psutil >=5.7 + - pyfiglet + - requests >=2.31.0 + - tqdm >=4.66.1 + - sra-tools + +test: + commands: + - pip check + - srahunter --help + requires: + - pip + +about: + home: https://github.com/GitEnricoNeko/srahunter + license: MIT + license_file: LICENSE + summary: "srahunter is a tool for processing SRA accession numbers." From 88bbff37fdde4690fbdb8756154068aa4ae940c4 Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Tue, 19 Mar 2024 19:52:01 +0100 Subject: [PATCH 1030/1813] update star adding new platform (#46555) * update star adding new platform * fix make flags --- recipes/star/build.sh | 2 +- recipes/star/meta.yaml | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/star/build.sh b/recipes/star/build.sh index fd1118c08c27b..c10bb36255423 100644 --- a/recipes/star/build.sh +++ b/recipes/star/build.sh @@ -23,7 +23,7 @@ else cp ../simd-dispatch.sh $PREFIX/bin/STAR cp ../simd-dispatch.sh $PREFIX/bin/STARlong else - make pj "$(nproc)" STAR STARlong + make -pj "$(nproc)" STAR STARlong cp STAR $PREFIX/bin/STAR cp STARlong $PREFIX/bin/STARlong fi diff --git a/recipes/star/meta.yaml b/recipes/star/meta.yaml index fd2d21ffee404..d0504bcb00d36 100644 --- a/recipes/star/meta.yaml +++ b/recipes/star/meta.yaml @@ -15,7 +15,7 @@ source: - patches/0003-create-simd-dispatch.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('star', max_pin="x") }} @@ -44,6 +44,8 @@ about: summary: An RNA-seq read aligner. extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:star - usegalaxy-eu:rna_starsolo From 80948c301f89fb8626b41aa89ec1304accea1dad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Mar 2024 15:30:34 -0400 Subject: [PATCH 1031/1813] Update assemblycomparator2 to 2.6.1 (#46566) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index 1558758fef16b..a42dba3fb3e72 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.18" %} +{% set version = "2.6.1" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 74d1f4959405c8ad01dd2cb2ad842c8ac71211b9ae8a125f4e58e44016cfd4a6 + sha256: 247d04a61c59b7849d79479f921f5d1ed4c112d5fa17e244add14321173aa74a build: From d388d388a953153945fad30ca7718defcfc16a6f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Mar 2024 15:31:05 -0400 Subject: [PATCH 1032/1813] Update boms to 1.1.0 (#46571) --- recipes/boms/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/boms/meta.yaml b/recipes/boms/meta.yaml index 7097126eefac7..4368691e40f3d 100644 --- a/recipes/boms/meta.yaml +++ b/recipes/boms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "boms" %} -{% set version = "1.0.5" %} +{% set version = "1.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 75187e1e78ac9eacda923dee3943936625676f2382859636448f14a64e57ea54 + sha256: c64a867233148dab9d32257e86b127793022f893321a43210ceaafa02870cd7c build: run_exports: From 2027bf945524169266dd62110bbcc2bceafee125 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Mar 2024 18:22:10 -0400 Subject: [PATCH 1033/1813] Update perl-minion to 10.29 (#46579) --- recipes/perl-minion/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-minion/meta.yaml b/recipes/perl-minion/meta.yaml index 87a845511735d..450b3bb30e26a 100644 --- a/recipes/perl-minion/meta.yaml +++ b/recipes/perl-minion/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-minion" %} -{% set version = "10.28" %} -{% set sha256 = "0bd774d2f42b36a5e1293cd3d5241ed35f45eb041599498e28d6f00f6ae910d5" %} +{% set version = "10.29" %} +{% set sha256 = "a8cbe9eedc9481e50a82652f8c070ca2a0e366077139c9fa809aa3be6c36bf88" %} package: name: {{ name }} From a736eeea48b87adc12cfb3bad61e22539ff86454 Mon Sep 17 00:00:00 2001 From: RolandFaure <64131971+RolandFaure@users.noreply.github.com> Date: Tue, 19 Mar 2024 23:22:58 +0100 Subject: [PATCH 1034/1813] Add recipe hairsplitter (#46564) * added hairsplitter * correct linting * corrected hairsplitter recipe --- recipes/hairsplitter/build.sh | 29 ++++++++++++ recipes/hairsplitter/conda_build_config.yaml | 7 +++ recipes/hairsplitter/meta.yaml | 49 ++++++++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 recipes/hairsplitter/build.sh create mode 100644 recipes/hairsplitter/conda_build_config.yaml create mode 100644 recipes/hairsplitter/meta.yaml diff --git a/recipes/hairsplitter/build.sh b/recipes/hairsplitter/build.sh new file mode 100644 index 0000000000000..978ddf0265bd8 --- /dev/null +++ b/recipes/hairsplitter/build.sh @@ -0,0 +1,29 @@ +mkdir -p $PREFIX/bin + +mkdir src/build +cd src/build/ +cmake .. +make + +cp ../../hairsplitter.py $PREFIX/bin +chmod +x $PREFIX/bin/hairsplitter.py +cp -r ./HS_call_variants $PREFIX/bin +cp -r ./HS_create_new_contigs $PREFIX/bin +cp -r ./HS_fa2gfa $PREFIX/bin +cp -r ./HS_gfa2fa $PREFIX/bin +cp -r ./HS_separate_reads $PREFIX/bin +cp -r ./HS_GenomeTailor/HS_GenomeTailor $PREFIX/bin +cp -r ../cut_gfa.py $PREFIX/bin +chmod +x $PREFIX/bin/cut_gfa.py + +cp -r ../GraphUnzip/graphunzip.py $PREFIX/bin +chmod +x $PREFIX/bin/graphunzip.py +cp -r ../GraphUnzip/segment.py $PREFIX/bin +cp -r ../GraphUnzip/finish_untangling.py $PREFIX/bin +cp -r ../GraphUnzip/simple_unzip.py $PREFIX/bin +cp -r ../GraphUnzip/repolish.py $PREFIX/bin +cp -r ../GraphUnzip/transform_gfa.py $PREFIX/bin +cp -r ../GraphUnzip/input_output.py $PREFIX/bin +cp -r ../GraphUnzip/determine_multiplicity.py $PREFIX/bin +chmod +x $PREFIX/bin/determine_multiplicity.py + diff --git a/recipes/hairsplitter/conda_build_config.yaml b/recipes/hairsplitter/conda_build_config.yaml new file mode 100644 index 0000000000000..f08c687e0ef69 --- /dev/null +++ b/recipes/hairsplitter/conda_build_config.yaml @@ -0,0 +1,7 @@ +c_compiler_version: + - 11.2.0 # [linux] + - 11.1.0 # [osx] + +cxx_compiler_version: + - 11.2.0 # [linux] + - 11.1.0 # [osx] diff --git a/recipes/hairsplitter/meta.yaml b/recipes/hairsplitter/meta.yaml new file mode 100644 index 0000000000000..9b7b60fea5adc --- /dev/null +++ b/recipes/hairsplitter/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "HairSplitter" %} +{% set version = "1.7.13" %} +{% set sha256 = "4387ae2076fd4b8b5e5610ad3a8e678979522403a4735fa4a0522db2feb653f7" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/RolandFaure/HairSplitter/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number : 0 + run_exports: + - {{ pin_subpackage("hairsplitter", max_pin="x.x") }} + +requirements: + build: + - cmake + - make + - openmp + - {{ compiler('cxx') }} + run: + - python + - scipy + - numpy + - minimap2 + - minigraph >=0.20 + - racon + - samtools >=1.16 + - openmp + - raven-assembler + +test: + commands: + - hairsplitter.py --help + +extra: + recipe-maintainers: + - rolandfaure + +about: + home: https://github.com/RolandFaure/HairSplitter + license: GPL-3.0-or-later + license_file: LICENSE + summary: "Recovers collapsed haplotypes from a draft assembly and long reads" + maintainer : RolandFaure # Optional + From 88e2bd21fe0fb14d160cfe5a9ebe0e1d83c3b9c0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Mar 2024 19:50:43 -0400 Subject: [PATCH 1035/1813] Update diffacto to 1.0.7 (#46561) * Update diffacto to 1.0.7 * add run_exports --------- Co-authored-by: mencian --- recipes/diffacto/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/diffacto/meta.yaml b/recipes/diffacto/meta.yaml index ad0a23a0bd854..30a547e5fe097 100644 --- a/recipes/diffacto/meta.yaml +++ b/recipes/diffacto/meta.yaml @@ -1,5 +1,5 @@ {% set name = "diffacto" %} -{% set version = "1.0.6" %} +{% set version = "1.0.7" %} package: name: "{{ name|lower }}" @@ -7,14 +7,16 @@ package: source: url: https://github.com/statisticalbiotechnology/diffacto/archive/refs/tags/v{{ version }}.tar.gz - sha256: fde7d7f350abc28de0cce23e68d375028a1d3d0969c988a7d07268fe56085f85 + sha256: 372d46e43509b2d0cbc5499a651ef51f175f24e211219598127f5f3ba13755fe build: noarch: python number: 0 entry_points: - diffacto = diffacto.diffacto:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('diffacto', max_pin="x") }} requirements: host: @@ -37,7 +39,8 @@ test: about: home: "https://github.com/statisticalbiotechnology/diffacto" - license: "Apache Software" + license: "Apache-2.0" license_family: "APACHE" license_file: "LICENSE.txt" summary: "A protein summarization method for shotgun proteomics experiments" + dev_url: "https://github.com/statisticalbiotechnology/diffacto" From 4a2dcf332f16b60f3b3dfd064b9856ed0a48207a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Mar 2024 19:58:28 -0400 Subject: [PATCH 1036/1813] Update tracegroomer to 0.1.3 (#46583) --- recipes/tracegroomer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tracegroomer/meta.yaml b/recipes/tracegroomer/meta.yaml index 5b435366e63af..b85ee45217450 100644 --- a/recipes/tracegroomer/meta.yaml +++ b/recipes/tracegroomer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tracegroomer" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/tracegroomer-{{ version }}.tar.gz - sha256: a1b951583f6016d96799a270def0472b6b7a93c5fe94e685fb30916f73d32662 + sha256: d81c872e9ca5f52d10413c4b9c0aff3aa54cc977125b531229dd8a1e4e6a5cdf build: entry_points: From 9142b851ff7296629cbc03aca288027dc2caf6a8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Mar 2024 21:17:50 -0400 Subject: [PATCH 1037/1813] Update genomad to 1.7.6 (#46589) * Update genomad to 1.7.6 * edit run_exports --------- Co-authored-by: mencian --- recipes/genomad/meta.yaml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/recipes/genomad/meta.yaml b/recipes/genomad/meta.yaml index 21506ba0e10de..4ac261bc491b2 100644 --- a/recipes/genomad/meta.yaml +++ b/recipes/genomad/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genomad" %} -{% set version = "1.7.5" %} +{% set version = "1.7.6" %} package: name: "{{ name|lower }}" @@ -7,16 +7,16 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 9f981c56d2c59774fb17fae144800a09db809a957b547073b54f6bbf72cec2ae + sha256: a42891daab9cf604c6ed89b3af6fc78b0e20f224844b7ae66f820a1ea155ceca build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: - genomad=genomad.cli:cli run_exports: - - {{ pin_subpackage("genomad", max_pin="x.x") }} + - {{ pin_subpackage("genomad", max_pin="x") }} requirements: host: @@ -48,3 +48,8 @@ about: license_file: LICENSE summary: "Identification of mobile genetic elements" dev_url: https://github.com/apcamargo/genomad/ + doc_url: https://portal.nersc.gov/genomad/ + +extra: + identifiers: + - biotools:genomad From e4b24063d397cb1156473aa7d1e6071b40521a54 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Mar 2024 20:18:07 -0500 Subject: [PATCH 1038/1813] pybigwig: enable linux-aarch64 build (#46588) --- recipes/pybigwig/build.sh | 2 +- recipes/pybigwig/meta.yaml | 14 +++++++++++--- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/recipes/pybigwig/build.sh b/recipes/pybigwig/build.sh index 24412f55aa1c3..241c28a9c0951 100644 --- a/recipes/pybigwig/build.sh +++ b/recipes/pybigwig/build.sh @@ -1,4 +1,4 @@ #!/bin/bash export C_INCLUDE_PATH=$PREFIX/include -$PYTHON setup.py install --single-version-externally-managed --record=record.txt +$PYTHON -m pip install --no-deps --no-build-isolation . -vvv diff --git a/recipes/pybigwig/meta.yaml b/recipes/pybigwig/meta.yaml index 426ae16d1509d..be5c68cf5d54e 100644 --- a/recipes/pybigwig/meta.yaml +++ b/recipes/pybigwig/meta.yaml @@ -9,15 +9,17 @@ source: sha256: 5d4426f754bd7b7f6dc21d6c3f93b58a96a65b6eb2e578ae03b31a71272d2243 build: - skip: true # [py2k] - number: 1 + skip: True # [py < 37] + number: 2 + run_exports: + - {{ pin_subpackage('pybigwig', max_pin="x.x") }} requirements: build: - {{ compiler('c') }} host: - python - - setuptools + - pip - curl - libcurl - zlib @@ -37,5 +39,11 @@ test: about: home: https://github.com/dpryan79/pyBigWig license: MIT + license_family: MIT license_file: LICENSE.txt summary: A python extension written in C for quick access to bigWig files. + dev_url: https://github.com/dpryan79/pyBigWig + +extra: + additional-platforms: + - linux-aarch64 From f3c52f0d33681bad86b6964801083990c74f5bec Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Mar 2024 20:18:23 -0500 Subject: [PATCH 1039/1813] pyfamsa: enable linux-aarch64 build (#46582) --- recipes/pyfamsa/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/pyfamsa/meta.yaml b/recipes/pyfamsa/meta.yaml index 587c9a9ee11d7..86a093edaab7e 100644 --- a/recipes/pyfamsa/meta.yaml +++ b/recipes/pyfamsa/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c926d6fe00029d712dd277a1544e632c2b20546da322e13bd92780ea3f756dae build: - number: 0 + number: 1 skip: True # [py2k] script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" run_exports: @@ -46,3 +46,5 @@ about: extra: recipe-maintainers: - althonos + additional-platforms: + - linux-aarch64 From d0f9bd2358f0515dd8ad93f6e7801c654dd27697 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Mar 2024 20:19:03 -0500 Subject: [PATCH 1040/1813] bx-python: enable linux-aarch64 build (#46584) --- recipes/bx-python/meta.yaml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/recipes/bx-python/meta.yaml b/recipes/bx-python/meta.yaml index 4190c732ecd3c..61d42af5848fa 100644 --- a/recipes/bx-python/meta.yaml +++ b/recipes/bx-python/meta.yaml @@ -11,11 +11,11 @@ source: sha256: {{ sha256 }} build: - number: 0 - skip: True # [py < 37] - script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv + number: 1 + skip: True # [py < 38] + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv run_exports: - - {{ pin_subpackage(name|lower, max_pin='x') }} + - {{ pin_subpackage(name|lower, max_pin='x.x') }} requirements: build: @@ -24,9 +24,6 @@ requirements: - python - cython - pip - - setuptools - - wheel - - python-lzo - numpy - zlib run: @@ -62,8 +59,10 @@ about: license_family: MIT license_file: LICENSE doc_url: 'https://buildmedia.readthedocs.org/media/pdf/bx-python/latest/bx-python.pdf' - dev_url: 'https://pypi.org/project/bx-python/' + dev_url: 'https://github.com/bxlab/bx-python' extra: identifiers: - biotools:bx-python + additional-platforms: + - linux-aarch64 From edaf68c7742f4bc06f162abb8b870ffea92485b8 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Mar 2024 20:19:25 -0500 Subject: [PATCH 1041/1813] parasail-python: enable linux-aarch64 build (#46585) --- recipes/parasail-python/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/parasail-python/meta.yaml b/recipes/parasail-python/meta.yaml index 9806e254863e3..1694669f24f95 100644 --- a/recipes/parasail-python/meta.yaml +++ b/recipes/parasail-python/meta.yaml @@ -13,9 +13,11 @@ source: - darwin-libtool-name.patch build: - number: 0 + number: 1 skip: True # [py < 37] - script: {{ PYTHON }} -m pip install . --use-pep517 -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv + run_exports: + - {{ pin_subpackage('parasail-python', max_pin="x") }} requirements: build: @@ -29,7 +31,6 @@ requirements: host: - python - pip - - wheel - zlib run: - python @@ -45,8 +46,10 @@ about: license: BSD-3-Clause license_family: BSD license_file: COPYING - dev_url: https://pypi.org/project/parasail/ + dev_url: https://github.com/jeffdaily/parasail-python extra: identifiers: - doi:10.1186/s12859-016-0930-z + additional-platforms: + - linux-aarch64 From f9c22b00f00d7968d7c82cc83a2e73d8e4361da3 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Mar 2024 21:13:21 -0500 Subject: [PATCH 1042/1813] pyabpoa: enable linux-aarch64 build (#46586) --- recipes/pyabpoa/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/pyabpoa/meta.yaml b/recipes/pyabpoa/meta.yaml index f25d359f54d23..b99ebbd5a2c25 100644 --- a/recipes/pyabpoa/meta.yaml +++ b/recipes/pyabpoa/meta.yaml @@ -10,10 +10,11 @@ source: sha256: f0e1b41b1c9e18ecd2096df9b60ad053260ec773d70eecb307b02cca0efab89d build: - number: 0 - script: {{ PYTHON }} -m pip install . -vvv + number: 1 + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv run_exports: - - {{ pin_subpackage(name, max_pin="x.x") }} + - {{ pin_subpackage(name, max_pin="x") }} + requirements: build: - {{ compiler('c') }} @@ -35,6 +36,7 @@ about: license: MIT license_family: MIT license_file: LICENSE + dev_url: https://github.com/yangao07/abPOA extra: recipe-maintainers: @@ -42,3 +44,5 @@ extra: identifiers: - doi:10.1093/bioinformatics/btaa963 - biotools:abpoa + additional-platforms: + - linux-aarch64 From e4699ba453572c32c55a10bffd7d49553947b765 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 19 Mar 2024 22:45:37 -0500 Subject: [PATCH 1043/1813] cyvcf2: enable linux-aarch64 build (#46591) --- recipes/cyvcf2/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/cyvcf2/meta.yaml b/recipes/cyvcf2/meta.yaml index 2ebb65713d6f9..71d64a2a0c42c 100644 --- a/recipes/cyvcf2/meta.yaml +++ b/recipes/cyvcf2/meta.yaml @@ -14,9 +14,9 @@ source: - patches/setup.py.patch build: - number: 0 + number: 1 skip: True # [py < 37] - script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv entry_points: - cyvcf2 = cyvcf2.__main__:cli run_exports: @@ -32,8 +32,6 @@ requirements: - python - cython - pip - - setuptools - - wheel - curl - zlib - htslib >=1.10 @@ -64,3 +62,5 @@ extra: identifiers: - doi:10.1093/bioinformatics/btx057 - biotools:cyvcf2 + additional-platforms: + - linux-aarch64 From 0e113061c6ae08061ad9135e06ed8c43432db4e6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Mar 2024 00:03:36 -0400 Subject: [PATCH 1044/1813] Update fibertools-rs to 0.4.1 (#46593) --- recipes/fibertools-rs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fibertools-rs/meta.yaml b/recipes/fibertools-rs/meta.yaml index 7186c17f62c4d..8fd559bc4711c 100644 --- a/recipes/fibertools-rs/meta.yaml +++ b/recipes/fibertools-rs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.9" %} +{% set version = "0.4.1" %} {% set name = "fibertools-rs" %} {% set build_number = "0" %} @@ -9,7 +9,7 @@ package: source: url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz - sha256: 9ba952338f60108d957caa0b89fbe38263e1d3df08351cbf09f4c1acb1acc73b + sha256: d3fedfcac7f3429854b3d80856f0bb03ba7b94cb940bc73b3cf745f5c0e98dd5 build: From e96995fd93fcb587eb7dcc4e88bb8cc9ed891e32 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Salom=C3=A9=20Brunon?= <91611978+Salome-Brunon@users.noreply.github.com> Date: Wed, 20 Mar 2024 14:38:41 +0100 Subject: [PATCH 1045/1813] Updated ToulligQC to v2.5.3 (#46574) * Updated ToulligQC to v2.5.3 and dependencies * Update matplotlib to matplotlib-base * Changed python 3.11.0 to 3.10.0 * Remove pip * Incorrect sha256 --- recipes/toulligqc/meta.yaml | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/recipes/toulligqc/meta.yaml b/recipes/toulligqc/meta.yaml index ac481b2417169..485f2b7a4b0f2 100644 --- a/recipes/toulligqc/meta.yaml +++ b/recipes/toulligqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "toulligqc" %} -{% set version = "2.5.2" %} +{% set version = "2.5.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: df12bbd9383857c33a997e44913625a430579e116763c069f38af9de4701d945 + sha256: 254f1f21227a15e51612523cc642fe58660e519661d61cb09d88270be9259965 build: number: 0 @@ -20,20 +20,18 @@ build: requirements: host: - - pip - - python >=3.8 + - python >=3.10.0 run: - - h5py >=2.10 - - matplotlib-base >=3.1.2 - - numpy >=1.17.4 - - scipy >=1.3.3 - - pandas >=0.25.3 - - plotly >=4.5.0 - - pysam - - python >=3.8 - - seaborn >=0.10 - - scikit-learn >=0.22 - - tqdm + - h5py >=3.7.0 + - matplotlib-base >=3.6.3 + - numpy >=1.24.2 + - scipy >=1.10.1 + - pandas >=1.5.3 + - plotly >=5.15.0 + - pysam >=0.21.0 + - python >=3.10.0 + - scikit-learn >=1.2.1 + - tqdm >=4.64.1 test: imports: From 3db13de51d35bec028d6a83b11e20b0c86e9fa40 Mon Sep 17 00:00:00 2001 From: Johan Dahlberg Date: Wed, 20 Mar 2024 14:39:44 +0100 Subject: [PATCH 1046/1813] Update pixelator to 0.16.2 (#46606) --- recipes/pixelator/LICENSE.txt | 21 +++++++++++++ recipes/pixelator/meta.yaml | 58 +++++++++++++++++++---------------- 2 files changed, 52 insertions(+), 27 deletions(-) create mode 100644 recipes/pixelator/LICENSE.txt diff --git a/recipes/pixelator/LICENSE.txt b/recipes/pixelator/LICENSE.txt new file mode 100644 index 0000000000000..b8a6b593ecff8 --- /dev/null +++ b/recipes/pixelator/LICENSE.txt @@ -0,0 +1,21 @@ +MIT License + +Copyright © 2023 Pixelgen Technologies AB + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. \ No newline at end of file diff --git a/recipes/pixelator/meta.yaml b/recipes/pixelator/meta.yaml index d92a24e509c76..cb7d3376e7db6 100644 --- a/recipes/pixelator/meta.yaml +++ b/recipes/pixelator/meta.yaml @@ -1,37 +1,35 @@ {% set name = "pixelator" %} -{% set version = "0.15.2" %} +{% set pypi_name = "pixelgen-pixelator" %} +{% set version = "0.16.2" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/pixelgentechnologies/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 2b41e14fba232691513e4f16eb215deca8e21694ebb9ad676968d320645212d4 + url: https://pypi.io/packages/source/{{ pypi_name[0] }}/{{ pypi_name }}/pixelgen_pixelator-{{ version }}.tar.gz + sha256: 0fcf1c3e88b2b43fe4a330c99aaa73bd68c809641951a2dafc33f7bb8cac8a3e build: + entry_points: + - pixelator = pixelator.cli:main_cli noarch: python - script_env: - - POETRY_DYNAMIC_VERSIONING_BYPASS={{ version }} - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 run_exports: - {{ pin_subpackage('pixelator', max_pin="x.x") }} requirements: host: - - python + - python >=3.10,<3.12 - poetry-core >=1.0.0 - - poetry-dynamic-versioning >=1.1.0 + - poetry-dynamic-versioning >=1.0.1 - pip run: - - python >=3.8,<3.12 - - igraph >=0.10.2,<=0.11.0 - - louvain >=0.8.0,<=0.9.0 + - python >=3.10,<3.12 - click - yapf - cutadapt >=4.2 - - fastp - umi_tools <=1.1.4 - pyfastx - yappi @@ -39,40 +37,46 @@ requirements: - numpy <1.24.0 - python-annoy <=1.17.0 - esda - - libpysal - - xopen + - libpysal >=4.9.2 + # I had to lock xopen < 1.9.0 because zlib-ng which is required by xopen + # does not install as expected + - xopen <1.9.0 - anndata >=0.8.0 - numba >=0.56.4 - scanpy - - leidenalg - lxml - cssselect - typing_extensions - scipy - - pyarrow >=13.0.0 + - pyarrow >=13,<15 - semver >=3.0.0,<4.0.0 - ruamel.yaml >=0.17.21,<0.18.0 - pydantic >=1.10.7,<2.0.0 - - polars >=0.17.12,<0.18.0 + - polars >=0.19.0,<0.20.0 - importlib-resources >=5.12.0,<6.0.0 - - fsspec =>2023.9.0 - - fastparquet =>2023.8.0 + - fsspec >=2023.9.0,<2024.0.0 + - fastparquet >=2023.8.0,<2024.0.0 + - graspologic >=3.3.0,<4.0.0 + - fastp test: imports: - pixelator commands: + - pip check - pixelator --help - - pixelator --version | grep -E "^pixelator, version {{ version }}$" + requires: + - pip about: home: https://github.com/PixelgenTechnologies/pixelator - summary: | - A commandline tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays. - license: GPL-2.0 - license_file: LICENSE - license_family: GPL + summary: A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays. + license: MIT + license_family: MIT + license_file: LICENSE.txt extra: - maintainers: - - fbdtemme \ No newline at end of file + recipe-maintainers: + - johandahlberg + - ambarrio + - fbdtemme From 6ac2f221331b0d26b8b3773f12c2821c6f56d08e Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Wed, 20 Mar 2024 14:41:06 +0100 Subject: [PATCH 1047/1813] update preseq adding new platform (#46596) * update preseq adding new platform * skip for osx-arm64 * Revert "skip for osx-arm64" This reverts commit 506b52a65353b1b8aeb267e7b7a408983e80b36d. --- recipes/preseq/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/preseq/meta.yaml b/recipes/preseq/meta.yaml index b6726b24549a3..462b966c1500e 100644 --- a/recipes/preseq/meta.yaml +++ b/recipes/preseq/meta.yaml @@ -5,7 +5,9 @@ package: version: {{ version }} build: - number: 5 + number: 6 + run_exports: + - {{ pin_subpackage("preseq", max_pin="x.x") }} source: url: https://github.com/smithlabcode/preseq/releases/download/v{{ version }}/preseq-{{ version }}.tar.gz @@ -38,5 +40,7 @@ test: - to-mr extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - andrewdavidsmith From ce6257c37d1f5605043db3f1e853bcc7975a1d6f Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 20 Mar 2024 22:06:43 +0800 Subject: [PATCH 1048/1813] linux-aarch64 build for bioawk (#46604) Co-authored-by: HWsunqian0027 --- recipes/bioawk/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/bioawk/meta.yaml b/recipes/bioawk/meta.yaml index 12bf54695780a..c5dd0a636caf2 100644 --- a/recipes/bioawk/meta.yaml +++ b/recipes/bioawk/meta.yaml @@ -7,7 +7,9 @@ source: sha256: 5cbef3f39b085daba45510ff450afcf943cfdfdd483a546c8a509d3075ff51b5 build: - number: 9 + number: 10 + run_exports: + - {{ pin_subpackage("bioawk", max_pin="x.x.x") }} requirements: build: @@ -28,3 +30,7 @@ about: home: https://github.com/lh3/bioawk license: Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1) summary: BWK awk modified for biological data + +extra: + additional-platforms: + - linux-aarch64 From 3ecc4eac69a0279783bb10b53b64d853ea80fa2e Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 20 Mar 2024 22:07:33 +0800 Subject: [PATCH 1049/1813] linux-aarch64 build for bedops (#46603) Co-authored-by: HWsunqian0027 --- recipes/bedops/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/bedops/meta.yaml b/recipes/bedops/meta.yaml index d6e6046f96376..8224cdd389f9a 100644 --- a/recipes/bedops/meta.yaml +++ b/recipes/bedops/meta.yaml @@ -5,7 +5,9 @@ package: version: {{ version }} build: - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage("bedops", max_pin="x.x.x") }} source: url: https://github.com/bedops/bedops/archive/v{{ version }}.tar.gz @@ -33,3 +35,5 @@ extra: identifiers: - biotools:Bedops - doi:10.1093/bioinformatics/bts277 + additional-platforms: + - linux-aarch64 From 59e65cc1e77cb936a94d3659d5cdc5a2ed0d05a4 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 20 Mar 2024 22:09:24 +0800 Subject: [PATCH 1050/1813] linux-aarch64 build for bedtk (#46602) Co-authored-by: HWsunqian0027 --- recipes/bedtk/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/bedtk/meta.yaml b/recipes/bedtk/meta.yaml index cb51dc445d8c3..13e1ffd1868b4 100644 --- a/recipes/bedtk/meta.yaml +++ b/recipes/bedtk/meta.yaml @@ -14,7 +14,9 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("bedtk", max_pin="x.x.x") }} requirements: build: @@ -48,3 +50,5 @@ about: extra: identifiers: - biotools:bedtk + additional-platforms: + - linux-aarch64 From 74b021ad91a2028e5ec363f41e75e618e0824594 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 20 Mar 2024 22:11:09 +0800 Subject: [PATCH 1051/1813] linux-aarch64 build for bfc (#46601) Co-authored-by: HWsunqian0027 --- recipes/bfc/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/bfc/meta.yaml b/recipes/bfc/meta.yaml index 36d92acead4e4..48efced8289a0 100644 --- a/recipes/bfc/meta.yaml +++ b/recipes/bfc/meta.yaml @@ -3,7 +3,9 @@ package: version: "r181" build: - number: 9 + number: 10 + run_exports: + - {{ pin_subpackage("bfc", max_pin="x.x.x") }} source: url: https://github.com/lh3/bfc/archive/a73dad248dc56d9d4d22eacbbbc51ac276045168.tar.gz @@ -29,3 +31,7 @@ about: license: MIT license_file: LICENSE.txt summary: BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. + +extra: + additional-platforms: + - linux-aarch64 From 2ed191370045962bd68e1e59a0727f56a3b63922 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 20 Mar 2024 22:12:05 +0800 Subject: [PATCH 1052/1813] linux-aarch64 build for bcalm (#46600) Co-authored-by: HWsunqian0027 --- recipes/bcalm/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/bcalm/meta.yaml b/recipes/bcalm/meta.yaml index 7dcb72552226d..225521b463c93 100644 --- a/recipes/bcalm/meta.yaml +++ b/recipes/bcalm/meta.yaml @@ -11,7 +11,9 @@ source: sha256: '{{sha256}}' build: - number: 5 + number: 6 + run_exports: + - {{ pin_subpackage("bcalm", max_pin="x.x.x") }} requirements: build: @@ -33,3 +35,7 @@ about: home: https://github.com/GATB/bcalm license: MIT License summary: BCALM 2 is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data. + +extra: + additional-platforms: + - linux-aarch64 From 41e33b30d6bcb7dcdfe99ab9700a8eae007493ed Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Wed, 20 Mar 2024 15:13:03 +0100 Subject: [PATCH 1053/1813] update fq adding new platform (#46599) --- recipes/fq/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/fq/meta.yaml b/recipes/fq/meta.yaml index a4e3c0e00dae3..473e91edef61f 100644 --- a/recipes/fq/meta.yaml +++ b/recipes/fq/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('fq', max_pin="x") }} @@ -33,6 +33,8 @@ about: validating FASTQ files. extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - claymcleod - Midnighter From 1ac722944d19e2ed2ea8a7a07ff363b435a8e54a Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Wed, 20 Mar 2024 15:15:14 +0100 Subject: [PATCH 1054/1813] update gffread adding new platform (#46595) --- recipes/gffread/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/gffread/meta.yaml b/recipes/gffread/meta.yaml index cf0bd29fad6db..5ae18c806919d 100644 --- a/recipes/gffread/meta.yaml +++ b/recipes/gffread/meta.yaml @@ -12,7 +12,9 @@ source: - Makefile.patch build: - number: 3 + number: 4 + run_exports: + - {{ pin_subpackage("gffread", max_pin="x.x") }} requirements: build: @@ -34,6 +36,8 @@ about: dev_url: "https://github.com/gpertea/gffread" extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:gffread skip-lints: From da014a34274ab3ad8fde0971f6e9dab36329dffc Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 20 Mar 2024 22:17:29 +0800 Subject: [PATCH 1055/1813] linux-aarch64 build for aragorn (#46592) Co-authored-by: HWsunqian0027 --- recipes/aragorn/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/aragorn/meta.yaml b/recipes/aragorn/meta.yaml index b2936b72349f6..8292bad9d714a 100644 --- a/recipes/aragorn/meta.yaml +++ b/recipes/aragorn/meta.yaml @@ -7,7 +7,9 @@ source: url: http://www.ansikte.se/ARAGORN/Downloads/aragorn1.2.41.c build: - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage("aragorn", max_pin="x.x.x") }} requirements: build: @@ -21,3 +23,7 @@ about: home: http://www.ansikte.se/ARAGORN/ license: GPLv3 summary: 'ARAGORN, tRNA (and tmRNA) detection' + +extra: + additional-platforms: + - linux-aarch64 From f2a808bc3542e1bed4450ef1692a2376db2a2129 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Mar 2024 11:03:29 -0400 Subject: [PATCH 1056/1813] Update pathogen-profiler to 4.1.0 (#46612) * Update pathogen-profiler to 4.1.0 * update deps and shasum --------- Co-authored-by: Jody Phelan --- recipes/pathogen-profiler/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/pathogen-profiler/meta.yaml b/recipes/pathogen-profiler/meta.yaml index 1d2ae19016c52..7f7282124371c 100644 --- a/recipes/pathogen-profiler/meta.yaml +++ b/recipes/pathogen-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pathogen-profiler" %} -{% set version = "4.0.0" %} -{% set sha256 = "2f32f2c74222a6dfcf4079d4a8f9a84cf7b03a2ebe1c170f887533c60e9ac4f9" %} +{% set version = "4.1.0" %} +{% set sha256 = "ddf7570f46f11ea7dae48dbd2d66811f4ed9c8d1b80a3e62049369ed01f22024" %} package: name: {{name}} @@ -22,7 +22,7 @@ requirements: - python - pip run: - - python >=3.7 + - python >=3.10 - git - trimmomatic - bwa @@ -34,7 +34,7 @@ requirements: - delly >=0.8.7 - gatk4 - bedtools - - freebayes >=1.3.5,<1.3.7 + - freebayes =1.3.6 - samclip - snpeff >=5.1 - requests @@ -43,7 +43,6 @@ requirements: - openjdk >=11.0.8 - kmc >=3.2.1 - dsk >=2.2 - - cryptography >=39.0.1 - rich-argparse - joblib >=1.3.0 - pysam From e5a861881695da29ef8cbdb5610616981cbd434e Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Wed, 20 Mar 2024 17:02:46 +0100 Subject: [PATCH 1057/1813] update bedgraphtobigwig with additional platform (#46516) * add additional platform * increase build number * add patch * fix typo --------- Co-authored-by: Pablo --- recipes/ucsc-bedgraphtobigwig/meta.yaml | 7 ++++++- recipes/ucsc-bedgraphtobigwig/patch1.patch | 19 +++++++++++++++++++ 2 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 recipes/ucsc-bedgraphtobigwig/patch1.patch diff --git a/recipes/ucsc-bedgraphtobigwig/meta.yaml b/recipes/ucsc-bedgraphtobigwig/meta.yaml index 14a8480f5135d..9aec6cf66f7a4 100644 --- a/recipes/ucsc-bedgraphtobigwig/meta.yaml +++ b/recipes/ucsc-bedgraphtobigwig/meta.yaml @@ -12,9 +12,10 @@ source: sha256: "{{ sha256 }}" patches: - "include.patch" + - "patch1.patch" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -40,6 +41,10 @@ test: # just check for existence, because the individual packages have no unified behavior - which {{ program }} +extra: + additional-platforms: + - linux-aarch64 + about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" diff --git a/recipes/ucsc-bedgraphtobigwig/patch1.patch b/recipes/ucsc-bedgraphtobigwig/patch1.patch new file mode 100644 index 0000000000000..483b0342a43da --- /dev/null +++ b/recipes/ucsc-bedgraphtobigwig/patch1.patch @@ -0,0 +1,19 @@ +--- userApps/kent/src/lib/htmshell.c.old 2022-10-28 08:32:08.344445121 +0000 ++++ userApps/kent/src/lib/htmshell.c 2022-10-28 08:32:31.708262420 +0000 +@@ -711,11 +711,11 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) +- { +- vfprintf(stdout, format, args); +- fprintf(stdout, "\n"); +- } ++if (format != NULL) ++ { ++ vfprintf(stdout, format, args); ++ fprintf(stdout, "\n"); ++ } + exit(-1); + } + From 96bdacaed2ae27915f66aa3dd382fde6e618a110 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Mar 2024 12:54:08 -0400 Subject: [PATCH 1058/1813] Update pymlst to 2.1.6 (#46615) --- recipes/pymlst/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pymlst/meta.yaml b/recipes/pymlst/meta.yaml index e4ecec72d61bb..8f481b91a588a 100644 --- a/recipes/pymlst/meta.yaml +++ b/recipes/pymlst/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pymlst" %} -{% set version = "2.1.5" %} +{% set version = "2.1.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/bvalot/pyMLST/archive/refs/tags/{{ version }}.tar.gz" - sha256: 505a0a0e79645f385e13e33e8ecd054fa436cb60e6bbec6f25a513e21903faf6 + sha256: 4387893638d2bcee02d91ca82fee3875f81247a4db6b8bdf86b98f445b8a4d61 build: noarch: python From 404f490f6957465486344629d5a303fd48fcc572 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Mar 2024 12:54:13 -0400 Subject: [PATCH 1059/1813] Update hmftools-orange to 3.3.1 (#46614) --- recipes/hmftools-orange/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-orange/meta.yaml b/recipes/hmftools-orange/meta.yaml index 78bc9d85b10cc..12b5ae774a8cb 100644 --- a/recipes/hmftools-orange/meta.yaml +++ b/recipes/hmftools-orange/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.3.0" %} -{% set sha256 = "6de088a73e354927fa782453d7fb7fc52a925a0fb9e8b14d54f83c238435cdb1" %} +{% set version = "3.3.1" %} +{% set sha256 = "31f0845ab593b7939e02d17605704ba371162f3874ed958b451f9f247ac64847" %} package: name: hmftools-orange From 29a0497b3c6032d8658cd32558b9a36f8fd89577 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Mar 2024 12:54:22 -0400 Subject: [PATCH 1060/1813] Update skyline2isocor to 1.0.0 (#46608) --- recipes/skyline2isocor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skyline2isocor/meta.yaml b/recipes/skyline2isocor/meta.yaml index 738ece2929b3a..be8a9b9d96ae9 100644 --- a/recipes/skyline2isocor/meta.yaml +++ b/recipes/skyline2isocor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skyline2isocor" %} -{% set version = "0.3.0" %} +{% set version = "1.0.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/skyline2isocor-{{ version }}.tar.gz - sha256: 220ed8f18f94c53f9349ceb62379633e373775aed7c39be6dfe5bbe19a7babdd + sha256: b202927c63bd10693c5b423cc6a4bd93efcbac0fb0ab86d5a68fae69b026a6d2 build: entry_points: From b887d097eefbb1605739320c68f425a6cbed7031 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Mar 2024 16:39:33 -0400 Subject: [PATCH 1061/1813] Update pybiolib to 1.1.1881 (#46616) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 0b30582e2b188..30221cbc876d2 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1879" %} +{% set version = "1.1.1881" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 09c1c44e4128bdf41798d6327c6cf58192df0a489cfbe5976dc24c4570824f47 + sha256: beceb650d8708f7c2c2d537ac6f04acf3ed55818ed0df4a6512d6fdc4e119a94 build: noarch: python From f33f400a2ef07fbc39d129633357aa097e15de3e Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Thu, 21 Mar 2024 05:37:42 +0800 Subject: [PATCH 1062/1813] linux-aarch64 build for addrg (#46609) * linux-aarch64 build for addrg * Set max_pin to x.x * Add zlib developer dependency --------- Co-authored-by: HWsunqian0027 --- recipes/addrg/meta.yaml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/recipes/addrg/meta.yaml b/recipes/addrg/meta.yaml index 9a92b45beccbd..6b55770d98737 100644 --- a/recipes/addrg/meta.yaml +++ b/recipes/addrg/meta.yaml @@ -6,7 +6,9 @@ package: version: {{ version }} build: - number: 11 + number: 12 + run_exports: + - {{ pin_subpackage("addrg", max_pin="x.x") }} source: url: https://github.com/holtgrewe/addrg/archive/v{{ version }}.tar.gz @@ -17,6 +19,7 @@ requirements: - {{ compiler('c') }} host: - htslib + - zlib run: - htslib @@ -28,3 +31,7 @@ about: home: https://github.com/holtgrewe/addrg license: MIT summary: Add read group to BAM files + +extra: + additional-platforms: + - linux-aarch64 From 7b4c4119cccee8d10baea7fbea7d843991fdff0e Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 20 Mar 2024 22:53:03 +0100 Subject: [PATCH 1063/1813] Add linux-aarch64 build for seqkit (#46620) --- recipes/seqkit/meta.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index 7d426309ab185..9c3439e60dc09 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -11,8 +11,11 @@ source: url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux] md5: d53457672a8f7873bc17698bad9e8514 # [linux] + url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_arm64.tar.gz # [aarch64] + md5: d055c755dcf44cf9f4f59be69a3c884f # [aarch64] + build: - number: 0 + number: 1 skip: False run_exports: - {{ pin_subpackage("seqkit", max_pin="x.x") }} @@ -26,6 +29,8 @@ about: license: MIT extra: + additional-platforms: + - linux-aarch64 skip-lints: - should_be_noarch_generic - should_not_be_noarch_source From d53be1a9cba4a5eff6e1629e6ff8bf6fe655d313 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pawe=C5=82?= <38688203+pawelqs@users.noreply.github.com> Date: Thu, 21 Mar 2024 03:29:25 +0100 Subject: [PATCH 1064/1813] Add SigProfilerPlotting recipe (#46607) * Add SigProfilerPlotting recipe * update test command * Update meta.yaml --------- Co-authored-by: Robert A. Petit III --- recipes/sigprofilerplotting/meta.yaml | 45 +++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 recipes/sigprofilerplotting/meta.yaml diff --git a/recipes/sigprofilerplotting/meta.yaml b/recipes/sigprofilerplotting/meta.yaml new file mode 100644 index 0000000000000..22cc7d698df97 --- /dev/null +++ b/recipes/sigprofilerplotting/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "SigProfilerPlotting" %} +{% set version = "1.3.21" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sigProfilerPlotting-{{ version }}.tar.gz + sha256: 2b7805adc9d00c275bc7cb9af16a732ea3d7cccea68dc8ea3f96b4cd2a405550 + +build: + entry_points: + - SigProfilerPlotting=sigProfilerPlotting.sigProfilerPlotting_CLI:main_function + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + +requirements: + host: + - python + - pip + run: + - python + - matplotlib-base >=3.4.3 + - pandas >=1.2.4,<2.0.0 + - scikit-learn >=1.1.3 + - pillow >=10.0.0 + +test: + imports: + - sigProfilerPlotting + commands: + - pip check + - SigProfilerPlotting plotSBS --help + requires: + - pip + +about: + home: https://github.com/alexandrovlab/SigProfilerPlotting + summary: SigProfiler plotting tool + license: BSD-2-Clause + license_file: LICENSE From e55af718aeb48716c708e4ed91900eafb9839cbc Mon Sep 17 00:00:00 2001 From: Ammar Aziz Date: Thu, 21 Mar 2024 13:54:25 +1100 Subject: [PATCH 1065/1813] Update: Musgy - Fix issue with sed on macos m1 (#46625) * Update meta.yaml attempt to fix sed issue on macos m1 * Update meta.yaml added run_exports for linting check --- recipes/mugsy/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/mugsy/meta.yaml b/recipes/mugsy/meta.yaml index d2923a91a8e4f..697b022bb83fd 100644 --- a/recipes/mugsy/meta.yaml +++ b/recipes/mugsy/meta.yaml @@ -10,11 +10,14 @@ source: build: noarch: generic - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage('mugsy', max_pin="x") }} requirements: run: - perl + - sed about: home: http://mugsy.sourceforge.net From ae3ab29f15f21280955efca7dc0e77daed1cea25 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 04:17:04 -0400 Subject: [PATCH 1066/1813] Update tb-profiler to 6.1.0 (#46622) --- recipes/tb-profiler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml index 2af11a447a995..da2b87dc25d14 100644 --- a/recipes/tb-profiler/meta.yaml +++ b/recipes/tb-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "tb-profiler" %} -{% set version = "6.0.0" %} -{% set sha256 = "a23600831f0e14d604e3a3a9330e61b852a559a539876c49b294ab31c8e8cbcf" %} +{% set version = "6.1.0" %} +{% set sha256 = "9ef62a6da769bdf745e70e35e02bf61fba5e1eb4d52bf228e01c4daf6ad4c910" %} package: name: {{name}} From 4e79d301aedb003f7661946c54e3bcc24990fe45 Mon Sep 17 00:00:00 2001 From: tamuanand Date: Thu, 21 Mar 2024 05:00:58 -0400 Subject: [PATCH 1067/1813] Update mosdepth to 0.3.7 (#46627) Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> --- recipes/mosdepth/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mosdepth/meta.yaml b/recipes/mosdepth/meta.yaml index a4a4b1000eeec..14d5aaa549798 100755 --- a/recipes/mosdepth/meta.yaml +++ b/recipes/mosdepth/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.6" %} +{% set version = "0.3.7" %} package: name: mosdepth @@ -15,7 +15,7 @@ requirements: - curl - nim <=1.6.2 host: - - htslib >=1.10 + - htslib >=1.19.1 run: test: From 8a258f378ea3497d55bf7bc79c554cf328b5d668 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 07:05:33 -0400 Subject: [PATCH 1068/1813] Update mitos to 2.1.8 (#46639) --- recipes/mitos/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index 04f527f772168..23b7f8a7d3a1f 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "2.1.7" %} +{% set version = "2.1.8" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b6c6e5173f37a6ff9e5c2b7ac3f45645f0db3093371a7804e3e336e203c5abe4 + sha256: b97a1bb0270676816dcca73487d92e9794676327862dc059f797ac1df81bf3c1 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " noarch: python run_exports: From a7454c03673849057c0c50a692a55d74806a6c3d Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Thu, 21 Mar 2024 09:38:08 -0400 Subject: [PATCH 1069/1813] bump baredsc to test build (#46613) * bump baredsc to test build * unbump baredsc * add space to rebuild --- recipes/baredsc/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/baredsc/meta.yaml b/recipes/baredsc/meta.yaml index 3816c34d391ee..48c80ba130384 100644 --- a/recipes/baredsc/meta.yaml +++ b/recipes/baredsc/meta.yaml @@ -49,3 +49,5 @@ about: extra: recipe-maintainers: - lldelisle + + \ No newline at end of file From da7b26a596f61f8c2ae145634c4f537a2daf680d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pawe=C5=82?= <38688203+pawelqs@users.noreply.github.com> Date: Thu, 21 Mar 2024 15:17:34 +0100 Subject: [PATCH 1070/1813] Add SigProfilerMatrixGenerator recipe (#46605) * recipe added * run_exports added * Recipe update * test commands update --- recipes/sigprofilermatrixgenerator/meta.yaml | 47 ++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/sigprofilermatrixgenerator/meta.yaml diff --git a/recipes/sigprofilermatrixgenerator/meta.yaml b/recipes/sigprofilermatrixgenerator/meta.yaml new file mode 100644 index 0000000000000..731b6038b1fc1 --- /dev/null +++ b/recipes/sigprofilermatrixgenerator/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "SigProfilerMatrixGenerator" %} +{% set version = "1.2.25" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/SigProfilerMatrixGenerator-{{ version }}.tar.gz + sha256: 6de36147ddd19befe1066d5e482bc9a94a9006a95e757c8e47d52fb5cd2862eb + +build: + entry_points: + - SigProfilerMatrixGenerator=SigProfilerMatrixGenerator.scripts.SigProfilerMatrixGenerator_CLI:main_function + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - matplotlib-base >=2.2.2 + - sigprofilerplotting >=1.3.16 + - statsmodels >=0.9.0 + - scipy >=1.1.0 + - numpy >=1.18.5 + - pandas >=0.23.4,<2.0.0 + +test: + imports: + - SigProfilerMatrixGenerator + commands: + - pip check + - SigProfilerMatrixGenerator install --help + requires: + - pip + +about: + home: https://github.com/AlexandrovLab/SigProfilerMatrixGenerator.git + summary: SigProfiler matrix generator tool + license: BSD-2-Clause + license_file: LICENSE From 6da2e71cc1a35759dd648f8bc95db3badbbf6fac Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 10:19:28 -0400 Subject: [PATCH 1071/1813] Update prokbert to 0.0.44 (#45794) * Update prokbert to 0.0.41 * Update prokbert to 0.0.43 * Update prokbert to 0.0.44 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/prokbert/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/prokbert/meta.yaml b/recipes/prokbert/meta.yaml index aad92e9121840..6fd3153cb17c7 100644 --- a/recipes/prokbert/meta.yaml +++ b/recipes/prokbert/meta.yaml @@ -1,5 +1,5 @@ {% set name = "prokbert" %} -{% set version = "0.0.40" %} +{% set version = "0.0.44" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/prokbert-{{ version }}.tar.gz - sha256: 8705d47d1d22ecd1e9c1b67345661b298f116b7c2ec65b167a01c25645ec4a03 + sha256: 19a6c9890c7689d795a8898061d48e7023b64226388c1c67f2f68a91c42a5012 build: number: 0 From e4e72ab6dd9c361f6b08b2bf7cc473193bc5b823 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 10:19:59 -0400 Subject: [PATCH 1072/1813] Update ampcombi to 0.2.2 (#46641) --- recipes/ampcombi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ampcombi/meta.yaml b/recipes/ampcombi/meta.yaml index 58b3df97bdaef..1bb7752d2c957 100644 --- a/recipes/ampcombi/meta.yaml +++ b/recipes/ampcombi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "AMPcombi" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: da699d66190e654b6c9ca333228678fd759f4ce8e84b8022c24417cf5a300c86 + sha256: da9a179851a8f2041d05ccd10dd45b58099e84059e2e66a9ee405d1913471b58 build: noarch: python From 2f020bdc664e6fbb99bcce11fd780420777eb62c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 10:20:37 -0400 Subject: [PATCH 1073/1813] Update hmftools-mark-dups to 1.1.3 (#46628) --- recipes/hmftools-mark-dups/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-mark-dups/meta.yaml b/recipes/hmftools-mark-dups/meta.yaml index 535227f7b06c6..7ea235b90e2b7 100644 --- a/recipes/hmftools-mark-dups/meta.yaml +++ b/recipes/hmftools-mark-dups/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.2" %} -{% set sha256 = "e1a8e5ea860627a9cb04eb7fd1ad501b22d4676092dfbb6f42077c34d6bf98fd" %} +{% set version = "1.1.3" %} +{% set sha256 = "46ee9419c5e0809feb54a1a7a0a4646aedd7c9fcada7dd346844d7c2b7c86561" %} package: name: hmftools-mark-dups From 9a1348585150940bb35b3ffa7824bd19a2a7f2fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 10:32:31 -0400 Subject: [PATCH 1074/1813] Update treetime to 0.11.3 (#46647) --- recipes/treetime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/treetime/meta.yaml b/recipes/treetime/meta.yaml index 06d0ced896a94..55bc9b5fb05f4 100644 --- a/recipes/treetime/meta.yaml +++ b/recipes/treetime/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.11.2" %} -{% set sha256 = "c6fe577580a1ed83dcfc7530f85b678bd9d890366ba83d50444cd8e7371a71af" %} +{% set version = "0.11.3" %} +{% set sha256 = "c19b336691fcf3fddbb2b0e55000ff6d4aafca1f2bdf75b4ab39631a57a73e2b" %} package: name: treetime From 958808d15200259009fdb465062cbc487473f5c1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 11:41:03 -0400 Subject: [PATCH 1075/1813] Update ppanggolin to 2.0.5 (#46648) --- recipes/ppanggolin/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ppanggolin/meta.yaml b/recipes/ppanggolin/meta.yaml index b1b30becbd7d7..8d196cd333118 100644 --- a/recipes/ppanggolin/meta.yaml +++ b/recipes/ppanggolin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.4" %} +{% set version = "2.0.5" %} package: name: ppanggolin @@ -6,7 +6,7 @@ package: source: url: https://github.com/labgem/PPanGGOLiN/archive/{{ version }}.tar.gz - sha256: 7ad714d4ab7a81e3a51119aa9ba04d86455eabad175c1da751b0a27501ac76a9 + sha256: a0eecbb3f66df8d2df5c2b37c25696c264cd3812386e942314748a8800ecc52f build: number: 0 From ddbd16bbcef22b8ec8e667e6f154f8bbcc953fc5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 12:15:18 -0400 Subject: [PATCH 1076/1813] Update ebi-eva-common-pyutils to 0.6.4 (#46645) --- recipes/ebi-eva-common-pyutils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ebi-eva-common-pyutils/meta.yaml b/recipes/ebi-eva-common-pyutils/meta.yaml index 2cb79f2171346..8769334eca87a 100644 --- a/recipes/ebi-eva-common-pyutils/meta.yaml +++ b/recipes/ebi-eva-common-pyutils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ebi-eva-common-pyutils" %} -{% set version = "0.6.3" %} +{% set version = "0.6.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ebi_eva_common_pyutils-{{ version }}.tar.gz - sha256: 6e5480b12b11fad97412c95a2d6687c0022f4f3f753fd0cb0c6d6c928a064728 + sha256: 71dc20212bc7899c65cdabda042cd3aca78b51e7acc0d60b506a478454e9852e build: script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation From efceb3437a469962978633d7466f6661a81c24b4 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 22 Mar 2024 05:36:16 +1300 Subject: [PATCH 1077/1813] ltr_harvest_parallel: Removed ver for genometools-genometools (#46623) * Removed ver for genometools-genometools * Incremented build number --- recipes/ltr_harvest_parallel/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ltr_harvest_parallel/meta.yaml b/recipes/ltr_harvest_parallel/meta.yaml index 0c0366ea3aca4..31bb99212a8ba 100644 --- a/recipes/ltr_harvest_parallel/meta.yaml +++ b/recipes/ltr_harvest_parallel/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('ltr_harvest_parallel', max_pin='x') }} @@ -20,7 +20,7 @@ build: requirements: run: - perl - - genometools-genometools ==1.6.5 + - genometools-genometools test: commands: From 83bad6ac20a19fbd3765a5f88b9c5dd5d0f8fab1 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 22 Mar 2024 05:36:30 +1300 Subject: [PATCH 1078/1813] Removed ver constraint for ltr_finder (#46624) --- recipes/ltr_finder_parallel/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ltr_finder_parallel/meta.yaml b/recipes/ltr_finder_parallel/meta.yaml index 70c9f77428cf8..90c1ab418a74c 100644 --- a/recipes/ltr_finder_parallel/meta.yaml +++ b/recipes/ltr_finder_parallel/meta.yaml @@ -11,14 +11,14 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('ltr_finder_parallel', max_pin='x') }} requirements: run: - - ltr_finder ==1.07 + - ltr_finder test: commands: From 0015b301d836861cec20569ae18694a40ca20ff4 Mon Sep 17 00:00:00 2001 From: Delaney Sullivan Date: Thu, 21 Mar 2024 10:48:31 -0700 Subject: [PATCH 1079/1813] Add splitcode recipe (#46543) * Add splitcode recipe * Add splitcode recipe: set build number 0 * Update recipes/splitcode/meta.yaml Co-authored-by: Ryan Dale --------- Co-authored-by: Ryan Dale --- recipes/splitcode/build.sh | 8 +++++++ recipes/splitcode/meta.yaml | 45 +++++++++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 recipes/splitcode/build.sh create mode 100644 recipes/splitcode/meta.yaml diff --git a/recipes/splitcode/build.sh b/recipes/splitcode/build.sh new file mode 100644 index 0000000000000..ef216459a9484 --- /dev/null +++ b/recipes/splitcode/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +mkdir -p "${PREFIX}/bin" +mkdir -p build +cd build || exit 1 +cmake -DCMAKE_INSTALL_PREFIX:PATH="$PREFIX" .. +make +make install diff --git a/recipes/splitcode/meta.yaml b/recipes/splitcode/meta.yaml new file mode 100644 index 0000000000000..7b1bc1431eb64 --- /dev/null +++ b/recipes/splitcode/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.29.4" %} + +package: + name: splitcode + version: {{ version }} + +source: + url: https://github.com/pachterlab/splitcode/archive/v0.29.4.tar.gz + sha256: 1e815543ba62628f5e65fc68fa324f8c871fa3f3b182385b0e381b89948b38d8 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('splitcode', max_pin="x.x") }} + +requirements: + build: + - make + - cmake + - {{ compiler('cxx') }} + host: + - zlib + run: + - zlib + +test: + commands: + - splitcode --version + +about: + home: "https://github.com/pachterlab/splitcode" + license: BSD-2-Clause + license_family: BSD + summary: Flexible parsing, interpretation, and editing of technical sequences + dev_url: https://github.com/pachterlab/splitcode + doc_url: "https://splitcode.readthedocs.io" + +extra: + identifiers: + - biotools:splitcode + - doi:10.1101/2023.03.20.533521 + recipe-maintainers: + - Yenaled + additional-platforms: + - linux-aarch64 From a977f9469c324a6b9e8434fbd062f760569ca648 Mon Sep 17 00:00:00 2001 From: Agnieszka Danek Date: Thu, 21 Mar 2024 18:52:00 +0100 Subject: [PATCH 1080/1813] Update agc to 3.1 (#46540) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update recipes/agc/meta.yaml Co-authored-by: Ryan Dale --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Ryan Dale --- recipes/agc/meta.yaml | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/recipes/agc/meta.yaml b/recipes/agc/meta.yaml index ad87d0fd1beb9..ea93af4029d36 100644 --- a/recipes/agc/meta.yaml +++ b/recipes/agc/meta.yaml @@ -1,20 +1,26 @@ -{% set version = "3.0" %} -{% set system = "linux"%} # [linux] -{% set system = "mac"%} # [osx] -{% set sha256 = "3ee3245e556221d246f9afe5d9ad86888f4eb5aea6b10f621241c3170ef8835e" %} # [linux] -{% set sha256 = "3d68b6b76948b6d9a36c4e848e37969eda6ae0ec1abace4ca61a7cc585dcdabf" %} # [osx] +{% set version = "3.1" %} + package: name: agc version: {{ version }} + build: number: 0 script: "mkdir -p ${PREFIX}/bin; cp agc ${PREFIX}/bin" + run_exports: + - {{ pin_subpackage('agc', max_pin="x") }} source: - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64-{{ system }}.tar.gz - sha256: {{ sha256 }} + - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_arm_linux.tar.gz # [aarch64] + sha256: 5fee3ccbb2691d82a877987e204c5946dbdbe40b9603af5d2421cb8506577534 # [aarch64] + - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64_linux.tar.gz # [linux64] + sha256: 4868dd45c1ed31a7f36bcbc536174249de27b87ec83858d22b128cbec8deef53 # [linux64] + - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64_mac.tar.gz # [osx and x86_64] + sha256: 0ef911e6bb8df791593ee6e89b5bddbf82b5823684955d249d6a67a39e6d0d4e # [osx and x86_64] + - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_m1_mac.tar.gz # [osx and arm64] + sha256: ff8cc5dd4c5825a41e042567a93e9e01ef43fc91624c983640a29fd3c7ac03e4 # [osx and arm64] requirements: build: - run: + run: about: home: https://github.com/refresh-bio/agc summary: "Assembled Genomes Compressor (AGC) is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans)." @@ -23,6 +29,8 @@ test: commands: - agc extra: + additional-platforms: + - linux-aarch64 skip-lints: - should_be_noarch_generic - should_not_be_noarch_source From 78d67b612a3842768431f4c5aadadeb1e8440730 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 14:05:31 -0400 Subject: [PATCH 1081/1813] Update agat to 1.3.2 (#46652) --- recipes/agat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/agat/meta.yaml b/recipes/agat/meta.yaml index 15d356d0d9d71..87f39ec90c60c 100755 --- a/recipes/agat/meta.yaml +++ b/recipes/agat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "AGAT" %} -{% set version = "1.3.1" %} -{% set sha256 = "0361f5f5708b0010045a410e3656d6b16571d5ebaf72898f6df846c49f282a3c" %} +{% set version = "1.3.2" %} +{% set sha256 = "f5ceadceca0ad8b423e51c199a6ae66921b88021ebf969c971da59df53b72fc5" %} package: name: "{{ name|lower }}" From 318e43b3aed89782efe28382d423af67fb6574a8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 14:29:32 -0400 Subject: [PATCH 1082/1813] Update anchorwave to 1.2.3 (#46631) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/anchorwave/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/anchorwave/meta.yaml b/recipes/anchorwave/meta.yaml index 2480797be239b..d4e34368db76c 100644 --- a/recipes/anchorwave/meta.yaml +++ b/recipes/anchorwave/meta.yaml @@ -1,7 +1,7 @@ {% set name = "anchorwave" %} -{% set version = "1.2.2" %} -{% set tag = "v1.2.2" %} -{% set sha256 = "db951e2fc8e493ce29e8c6e4f0226a68dc2fdc62631c1fe65077988647e98d01" %} +{% set version = "1.2.3" %} +{% set tag = "v1.2.3" %} +{% set sha256 = "1f689c06f9bbc8e1ed64c0addf4aaf5d172a2fea1e55660b8d3f6dfdffe3f157" %} package: name: {{ name }} From 6ff2f47e8c343b3a7e10d63e324384ffa4cdfbf6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 14:41:55 -0400 Subject: [PATCH 1083/1813] Update itsxpress to 2.0.2 (#46654) --- recipes/itsxpress/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/itsxpress/meta.yaml b/recipes/itsxpress/meta.yaml index 5339657193c68..728781e65e5e5 100644 --- a/recipes/itsxpress/meta.yaml +++ b/recipes/itsxpress/meta.yaml @@ -1,8 +1,8 @@ {% set name = "itsxpress" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "b5797107ee3f21cbaba0b9625aa931741babdee3eeb5a3218a8b8bc9783e2e72" %} +{% set hash_value = "f89b17cb74b5194fd57e310af53c6973832b91c2183da8fa5b6ed80530a2f1f1" %} package: name: '{{ name|lower }}' From a42a98e3c411ec569ccf21f97b395e427e67381e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 15:28:22 -0400 Subject: [PATCH 1084/1813] Update snakemake-interface-executor-plugins to 9.0.1 (#46651) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index aeea231e43ace..cde4219db9d39 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "9.0.0" %} +{% set version = "9.0.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: 22b7337d9ea4f9e32679b96fa873337608d73f2d41443cc6bde18de4549acdb7 + sha256: 9a206832d2d8e64de57606cec3e0b60a035451c9fc71e8bcdbe7b678555301b3 build: noarch: python From f047d600d0fcb6df77f95c1304018ecd795ee71c Mon Sep 17 00:00:00 2001 From: M Bernt Date: Thu, 21 Mar 2024 22:08:31 +0100 Subject: [PATCH 1085/1813] bimp mitos (#46638) --- recipes/mitos/mitos1/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mitos/mitos1/meta.yaml b/recipes/mitos/mitos1/meta.yaml index 0e010a1780797..90b791e4f9731 100644 --- a/recipes/mitos/mitos1/meta.yaml +++ b/recipes/mitos/mitos1/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "1.1.5" %} +{% set version = "1.1.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 1727e5037c679648b4633b4bd811d9f818a2b41d2c8d322bd51ec5b6a94faa02 + sha256: c86c6e01d409de41619a3b7dce32908b4f568fbbeb67b336a7b99a93a642440c build: number: 0 From 6387fa56ccb391d265c3f906ec919f02294e466b Mon Sep 17 00:00:00 2001 From: Mike Tisza Date: Thu, 21 Mar 2024 16:09:31 -0500 Subject: [PATCH 1086/1813] Update meta.yaml (#46619) --- recipes/cenote-taker3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cenote-taker3/meta.yaml b/recipes/cenote-taker3/meta.yaml index 8a3b8e9aadc5e..fd08cffc8d837 100644 --- a/recipes/cenote-taker3/meta.yaml +++ b/recipes/cenote-taker3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cenote-taker3" %} -{% set version = "3.2.1" %} +{% set version = "3.3.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/mtisza1/{{ name }}/archive/v{{ version }}.tar.gz" - sha256: ffda0fcc8bee4c9200e46833008664bbe9155b6aae2b62d741943f27f6532a16 + sha256: 43bd01d7cc236d738d98a093fbf688f72a91659718b5380c63eb70856dde420b build: number: 0 From 7789eaa821eccfed8c1b7fd2cbb275257bc7d46c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 17:13:45 -0400 Subject: [PATCH 1087/1813] Update ms2deepscore to 2.0.0 (#46637) * Update ms2deepscore to 2.0.0 * update dependencies --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian --- recipes/ms2deepscore/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/ms2deepscore/meta.yaml b/recipes/ms2deepscore/meta.yaml index c631294d07e8b..6389bdadf0716 100644 --- a/recipes/ms2deepscore/meta.yaml +++ b/recipes/ms2deepscore/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ms2deepscore" %} -{% set version = "1.0.0" %} -{% set sha256 = "76f88b8e4b0d296df77262c1d8078f7f902852608ca50f259f12d407047d52db" %} +{% set version = "2.0.0" %} +{% set sha256 = "50b700319a07461a0ac2be0a6f67c1cf1b23a681cb76b8c4488d948f8976f5b2" %} package: name: {{ name|lower }} @@ -19,16 +19,18 @@ build: requirements: host: - - python >=3.8 + - python >=3.9 - pip run: - - python >=3.8 - - matchms >=0.14.0 + - python >=3.9 + - matchms >=0.18.0 + - matplotlib-base ==3.7.2 - numba - numpy >=1.20.3 - pandas + - pytorch + - scikit-learn - tqdm - - tensorflow <2.14 test: imports: From 3decafbb0d8782b0e0edfc3b498300aa1253ce06 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 17:14:26 -0400 Subject: [PATCH 1088/1813] Update callingcardstools to 1.5.2 (#46657) --- recipes/callingcardstools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/callingcardstools/meta.yaml b/recipes/callingcardstools/meta.yaml index 08159508bcc91..71fe9244deaa1 100644 --- a/recipes/callingcardstools/meta.yaml +++ b/recipes/callingcardstools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "callingcardstools" %} -{% set version = "1.5.1" %} +{% set version = "1.5.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 05d19fa9a41c086413fd4067c69170bd9f7cdfb786cf40d5217b48926854d3ec + sha256: 7ee834c5e7855d1613f6eb9759f7ea0496e70ffbf0b132ab9b76f03685cf652e build: noarch: python From 79554d2823dc90743f2ec5fc31260a5ebe566339 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 18:04:34 -0400 Subject: [PATCH 1089/1813] Update fibertools-rs to 0.4.2 (#46660) --- recipes/fibertools-rs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fibertools-rs/meta.yaml b/recipes/fibertools-rs/meta.yaml index 8fd559bc4711c..589520189e587 100644 --- a/recipes/fibertools-rs/meta.yaml +++ b/recipes/fibertools-rs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} {% set name = "fibertools-rs" %} {% set build_number = "0" %} @@ -9,7 +9,7 @@ package: source: url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz - sha256: d3fedfcac7f3429854b3d80856f0bb03ba7b94cb940bc73b3cf745f5c0e98dd5 + sha256: 8d73b8160d93731435afbccad3f8f8ea33c291383783303e2f88a98815cc3425 build: From f76973d854edc94ae6b1c052c28f617463388a0d Mon Sep 17 00:00:00 2001 From: Jody Phelan Date: Thu, 21 Mar 2024 22:13:19 +0000 Subject: [PATCH 1090/1813] update tb-profiler dependencies (#46649) * update dependencies * update build number --- recipes/tb-profiler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml index da2b87dc25d14..9fc9e95ddbdeb 100644 --- a/recipes/tb-profiler/meta.yaml +++ b/recipes/tb-profiler/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 run_exports: - {{ pin_subpackage('tb-profiler', max_pin="x") }} @@ -28,7 +28,7 @@ requirements: - python >=3.8 - git - jinja2 - - pathogen-profiler >=4.0.0 + - pathogen-profiler =4.1.0 - filelock - docxtpl - iqtree From 947552dbb8aeccd48606f237ad8e351acacd1bfc Mon Sep 17 00:00:00 2001 From: Bob <55469084+yhhan19@users.noreply.github.com> Date: Thu, 21 Mar 2024 19:04:27 -0400 Subject: [PATCH 1091/1813] Update TREE-QMC to 3.0.0 (#46656) * tqmc * build.sh fixed * "folder_and_package_name_must_match" fixed * missing_run_exports fixed * g++ not found fix * build error fixed * build error fix * build.sh fix * osx compilation fix * made the name and version number consistent * minor * tree-qmc 3.0.0 updates * tree-qmc 3.0.0 updates * build.sh fixed * build.sh fixed * build.sh fixed * build.sh * build.sh * debug * build --- recipes/tree-qmc/build.sh | 16 ++++++++++------ recipes/tree-qmc/meta.yaml | 7 ++++--- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/recipes/tree-qmc/build.sh b/recipes/tree-qmc/build.sh index afeec38073355..1577713af44f0 100644 --- a/recipes/tree-qmc/build.sh +++ b/recipes/tree-qmc/build.sh @@ -1,9 +1,13 @@ -cd MQLib -make \ - GXX="${CXX}" \ - AR="${AR}" -cd .. -$CXX -std=c++11 -O2 -I MQLib/include -o TREE-QMC src/*.cpp MQLib/bin/MQLib.a +cd external/MQLib +sed -i.bak "s#g++#${CXX}#" Makefile +make +cd ../.. +$CXX -std=c++11 -O2 \ + -I external/MQLib/include -I external/toms743 \ + -o TREE-QMC \ + src/*.cpp external/toms743/toms743.cpp \ + external/MQLib/bin/MQLib.a -lm \ + -DVERSION=\"$(cat version.txt)\" mkdir -p $PREFIX/bin cp TREE-QMC $PREFIX/bin/ chmod a+x $PREFIX/bin/TREE-QMC diff --git a/recipes/tree-qmc/meta.yaml b/recipes/tree-qmc/meta.yaml index 66298530a9cb3..a4d3178e290d8 100644 --- a/recipes/tree-qmc/meta.yaml +++ b/recipes/tree-qmc/meta.yaml @@ -1,13 +1,14 @@ {% set name = "TREE-QMC" %} -{% set version = "2.0.0" %} +{% set version = "3.0.0" %} + package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/molloy-lab/{{ name|upper }}/releases/download/{{ version }}/{{ name|upper }}-{{ version }}.zip - sha256: f8530dd6d106c63ffde0d728eeef835b8bded16e69620e78bd45f562129f86a9 + url: https://github.com/molloy-lab/{{ name|upper }}/archive/refs/tags/v3-f40cc44.zip + sha256: cdabdc24b2f2f203fe0c075227d61d66e78155fca91e7fe3a32d162abb6216f0 build: number: 0 From 5da2179c5668ccd4929025ff31c15e8ea5b87397 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 19:19:09 -0400 Subject: [PATCH 1092/1813] Update sourmash to 4.8.7 (#46655) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/sourmash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sourmash/meta.yaml b/recipes/sourmash/meta.yaml index 262fde0161307..45294de4a0f6a 100644 --- a/recipes/sourmash/meta.yaml +++ b/recipes/sourmash/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.8.6" %} +{% set version = "4.8.7" %} package: name: sourmash @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/sourmash/sourmash-{{ version }}.tar.gz - sha256: 5a09c5d12cb07f8d73eb60db8dbd30e4e74aabf53a718610ddb5e6c91b341dca + sha256: 0cd18ea49d94ce92f5c85b2337cf7b7328ef3013c33311414db71b29962a93fd build: number: 0 From f811faacf22b96203ab76c28d6e804bca5853380 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 22 Mar 2024 08:09:02 +0800 Subject: [PATCH 1093/1813] linux-aarch64 build for 3seq (#46610) * linux-aarch64 build for 3seq * updated pin_subpackage --------- Co-authored-by: HWsunqian0027 Co-authored-by: Thanh Lee --- recipes/3seq/meta.yaml | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/3seq/meta.yaml b/recipes/3seq/meta.yaml index fc3d68b5e7018..00113808e3473 100644 --- a/recipes/3seq/meta.yaml +++ b/recipes/3seq/meta.yaml @@ -7,7 +7,9 @@ package: version: {{ version }} build: - number: 3 + number: 4 + run_exports: + - {{ pin_subpackage("3seq", max_pin="x") }} source: url: https://gitlab.com/lamhm/{{ name|lower }}/-/archive/v{{ version }}/3seq-v{{ version }}.tar.gz @@ -28,6 +30,10 @@ test: about: home: https://mol.ax/software/3seq/ - license: CC BY-NC-SA 4.0 + license: CC-BY-NC-SA-4.0 license_file: LICENSE.md summary: '3SEQ tests all sequence triplets in an alignment for a mosaic recombination signal.' + +extra: + additional-platforms: + - linux-aarch64 From b0ad8e8ee28d3277cbb8155a037970a84e210f48 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 22 Mar 2024 08:15:25 +0800 Subject: [PATCH 1094/1813] linux-aarch64 build for abundancebin (#46633) Co-authored-by: HWsunqian0027 --- recipes/abundancebin/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/abundancebin/meta.yaml b/recipes/abundancebin/meta.yaml index d01609dd35e02..1fc298ebc42e5 100644 --- a/recipes/abundancebin/meta.yaml +++ b/recipes/abundancebin/meta.yaml @@ -14,7 +14,9 @@ source: - 0001-Use-CXX-and-flags.patch build: - number: 6 + number: 7 + run_exports: + - {{ pin_subpackage("abundancebin", max_pin="x.x.x") }} skip: True # [osx] requirements: @@ -45,3 +47,5 @@ extra: - keuv-grvl identifiers: - doi:10.1007/978-3-642-12683-3_35 + additional-platforms: + - linux-aarch64 From 99858195f4517e4fce717650eaffcbfe31802c89 Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Fri, 22 Mar 2024 02:03:14 +0100 Subject: [PATCH 1095/1813] update ucsc-bedclip adding new platform (#46626) * update ucsc-bedclip adding new platform * add patch * fix compilation for arm * remove from blacklist * try another way to specify compiler version * edit pin_subpackage --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- build-fail-blacklist | 1 - recipes/ucsc-bedclip/build.sh | 13 +++++++++++-- recipes/ucsc-bedclip/conda_build_config.yaml | 2 ++ recipes/ucsc-bedclip/meta.yaml | 9 ++++++++- recipes/ucsc-bedclip/patch1.patch | 19 +++++++++++++++++++ 5 files changed, 40 insertions(+), 4 deletions(-) create mode 100644 recipes/ucsc-bedclip/conda_build_config.yaml create mode 100644 recipes/ucsc-bedclip/patch1.patch diff --git a/build-fail-blacklist b/build-fail-blacklist index f3f7e72ee6305..8f4d12ec4436f 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -802,7 +802,6 @@ recipes/ucsc-axtsort recipes/ucsc-axtswap recipes/ucsc-axttomaf recipes/ucsc-bamtopsl -recipes/ucsc-bedclip recipes/ucsc-bedcommonregions recipes/ucsc-bedcoverage recipes/ucsc-bedextendranges diff --git a/recipes/ucsc-bedclip/build.sh b/recipes/ucsc-bedclip/build.sh index af41c472a9323..d77ce6d815f3a 100644 --- a/recipes/ucsc-bedclip/build.sh +++ b/recipes/ucsc-bedclip/build.sh @@ -1,8 +1,17 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +if [ $(arch) = "aarch64" ] +then + export CFLAGS+=" -O3 -mcpu=neoverse-n1 " + export CPPFLAGS+=" -O3 -mcpu=neoverse-n1 " +else + export MACHTYPE=x86_64 +fi + export BINDIR=$(pwd)/bin export L="${LDFLAGS}" + +mkdir -p "$PREFIX/bin" mkdir -p "$BINDIR" (cd kent/src/lib && make) (cd kent/src/htslib && make) diff --git a/recipes/ucsc-bedclip/conda_build_config.yaml b/recipes/ucsc-bedclip/conda_build_config.yaml new file mode 100644 index 0000000000000..d8d0c3f0dc913 --- /dev/null +++ b/recipes/ucsc-bedclip/conda_build_config.yaml @@ -0,0 +1,2 @@ +c_compiler_version: + - 8 diff --git a/recipes/ucsc-bedclip/meta.yaml b/recipes/ucsc-bedclip/meta.yaml index 68be7e4c5b546..6501ba30fd427 100644 --- a/recipes/ucsc-bedclip/meta.yaml +++ b/recipes/ucsc-bedclip/meta.yaml @@ -12,10 +12,13 @@ source: sha256: "{{ sha256 }}" patches: - "include.patch" + - "patch1.patch" build: skip: True # [osx] - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage("ucsc-bedclip", max_pin=None) }} requirements: build: @@ -40,6 +43,10 @@ test: # just check for existence, because the individual packages have no unified behavior - which {{ program }} +extra: + additional-platforms: + - linux-aarch64 + about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" diff --git a/recipes/ucsc-bedclip/patch1.patch b/recipes/ucsc-bedclip/patch1.patch new file mode 100644 index 0000000000000..483b0342a43da --- /dev/null +++ b/recipes/ucsc-bedclip/patch1.patch @@ -0,0 +1,19 @@ +--- userApps/kent/src/lib/htmshell.c.old 2022-10-28 08:32:08.344445121 +0000 ++++ userApps/kent/src/lib/htmshell.c 2022-10-28 08:32:31.708262420 +0000 +@@ -711,11 +711,11 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) +- { +- vfprintf(stdout, format, args); +- fprintf(stdout, "\n"); +- } ++if (format != NULL) ++ { ++ vfprintf(stdout, format, args); ++ fprintf(stdout, "\n"); ++ } + exit(-1); + } + From c1209b0d846c93883995c9a3e53be81856214dfb Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Thu, 21 Mar 2024 18:07:30 -0700 Subject: [PATCH 1096/1813] Update ntsynt build (#46659) --- recipes/ntsynt/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ntsynt/meta.yaml b/recipes/ntsynt/meta.yaml index 0fa8488dc1a91..2ae5caf0befcf 100644 --- a/recipes/ntsynt/meta.yaml +++ b/recipes/ntsynt/meta.yaml @@ -10,7 +10,7 @@ source: sha256: db3fe491233d93967120d091a19abbef1fa5dfa637814bb617814a1b3e3f1331 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("ntsynt", max_pin="x") }} @@ -24,10 +24,10 @@ requirements: - ninja - llvm-openmp # [osx] - libgomp # [linux] - - btllib + - btllib <1.7.0 run: - python - - btllib + - btllib <1.7.0 - intervaltree - pybedtools - ncls From 51c290ad347474b9a140e41fc853ab898eab9cb7 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Thu, 21 Mar 2024 18:09:40 -0700 Subject: [PATCH 1097/1813] Update ntlink build (#46663) * Pinning btllib version for now due to possible bug in the most recent release --- recipes/ntlink/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ntlink/meta.yaml b/recipes/ntlink/meta.yaml index f67d1d7829657..5a3753c1f1796 100644 --- a/recipes/ntlink/meta.yaml +++ b/recipes/ntlink/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 3a6fe7ca9c7a0226cf51b7e55804e235ac2b959e82a30f9bce55b9caea5bb03b build: - number: 3 + number: 4 noarch: generic run_exports: - {{ pin_subpackage('ntlink', max_pin="x") }} @@ -20,7 +20,7 @@ requirements: - python - pip - zlib - - btllib + - btllib <1.7.0 run: - python - zlib @@ -28,7 +28,7 @@ requirements: - numpy - python-igraph - abyss >=2.3.0 - - btllib + - btllib <1.7.0 test: From 3cdf5822826610f7b81269168b44ad20aedc9749 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Mar 2024 21:14:43 -0400 Subject: [PATCH 1098/1813] Update r-liger to 2.0.0 (#46621) * Update r-liger to 2.0.0 * add missing deps * oops, bioconductor- not r- --------- Co-authored-by: mencian --- recipes/r-liger/meta.yaml | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/recipes/r-liger/meta.yaml b/recipes/r-liger/meta.yaml index 47619e1464082..b2dc397fdbd31 100644 --- a/recipes/r-liger/meta.yaml +++ b/recipes/r-liger/meta.yaml @@ -1,14 +1,15 @@ -{% set version = '1.0.1' %} +{% set name = "liger" %} +{% set version = '2.0.0' %} package: - name: r-liger + name: r-{{ name }} version: {{ version|replace("-", "_") }} source: url: - {{ cran_mirror }}/src/contrib/rliger_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/rliger/rliger_{{ version }}.tar.gz - sha256: 5a48c8c18c66c3b692d99ff7eb1595acd4659595cc633c09c55e3f4f44094b74 + sha256: a189285513e5a11d658056de55670fe877bcf2f52ce65837f9b8a4b3ff7bab2f build: number: 0 @@ -17,7 +18,7 @@ build: - lib/R/lib/ - lib/ run_exports: - - {{ pin_subpackage("r-liger", max_pin="x.x") }} + - {{ pin_subpackage("r-liger", max_pin="x") }} requirements: build: @@ -51,6 +52,10 @@ requirements: - r-rcppeigen - r-rann - r-scattermore >=0.7 + - r-circlize + - bioconductor-complexheatmap + - r-leidenalg >=1.1.1 + - bioconductor-s4vectors run: - r-base - r-fnn @@ -82,6 +87,10 @@ requirements: - r-scattermore >=0.7 - openjdk >=6 - umap-learn + - r-circlize + - bioconductor-complexheatmap + - r-leidenalg >=1.1.1 + - bioconductor-s4vectors test: commands: @@ -89,7 +98,7 @@ test: about: home: https://github.com/MacoskoLab/liger - license: GPL-3 + license: GPL-3.0-or-later summary: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) , and Liu J, Gao C, Sodicoff J, et al (2020) for more @@ -97,7 +106,11 @@ about: license_family: GPL3 license_file: - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + doc_url: https://welch-lab.github.io/liger/index.html + dev_url: https://github.com/MacoskoLab/liger extra: recipe-maintainers: - raivivek + identifiers: + - doi:10.1016/j.cell.2019.05.006 From 90835a4b2c366e65973db9c2c6867a2b165f3e67 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Mar 2024 00:46:48 -0400 Subject: [PATCH 1099/1813] Update oakvar to 2.9.92 (#46668) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 15fd58b64bed5..80a6adf5390e4 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.91" %} -{% set sha256 = "74a98819e230dc2120752b5f81e194e38d7de46c48e2cd051a4feb62b5fa51da" %} +{% set version = "2.9.92" %} +{% set sha256 = "f12cd22f67d3f84abfa8b8037983f16094d6971f1fa1ed8165e30812cf7d5af9" %} package: name: {{ name|lower }} From c0a74cb79226a7737dc37857a2ed63bce18f9d41 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Fri, 22 Mar 2024 13:22:54 +0100 Subject: [PATCH 1100/1813] Update comet-ms from v2023.01.0 to v2023.01.2 (#46567) * Update meta.yaml * Update build number and run_exports * add -lrt to makefile due to chrono error * add escapes in build.sh * Update build.sh * Update build.sh * Update recipes/comet-ms/build.sh Co-authored-by: Julianus Pfeuffer * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Create conda_build_config.yaml to control glibc version during test * Update meta.yaml * Update meta.yaml * Update meta.yaml * Delete recipes/comet-ms/conda_build_config.yaml * Update meta.yaml * ad gcc to build (which implicitely adds libgcc during host and runtime) * static with glibc 2.17 --------- Co-authored-by: Julianus Pfeuffer --- recipes/comet-ms/build.sh | 3 +++ recipes/comet-ms/meta.yaml | 14 +++++++++----- 2 files changed, 12 insertions(+), 5 deletions(-) diff --git a/recipes/comet-ms/build.sh b/recipes/comet-ms/build.sh index 4201a024dcc62..6ed5c0ccc5bb9 100644 --- a/recipes/comet-ms/build.sh +++ b/recipes/comet-ms/build.sh @@ -5,6 +5,9 @@ set -x export INCLUDE_PATH="${PREFIX}/MSToolkit/include" export CPPFLAGS="-I${PREFIX}/MSToolkit/include" +# To switch from static to dynamic linking on linux. The Makefile does not have this flag for macOS +# Dynamic linking does not work with mulled container tests +#sed -i.bak 's#-static##' Makefile sed -i.bak "s#gcc#${CC}#;s#g++#${CXX}#" MSToolkit/Makefile sed -i.bak "s#gcc#${CC}#;s#g++#${CXX}#" CometSearch/Makefile diff --git a/recipes/comet-ms/meta.yaml b/recipes/comet-ms/meta.yaml index ca7c83e01a164..e7c9fb4700b11 100644 --- a/recipes/comet-ms/meta.yaml +++ b/recipes/comet-ms/meta.yaml @@ -1,25 +1,29 @@ {% set name = "comet-ms" %} -{% set version = "2023010" %} -{% set md5 = "f1899e07eeeefddedf22b93133f9aea8" %} +{% set version = "2023012" %} +{% set md5 = "d60433652e5a5e682288ddbdfb014eb4" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/UWPR/Comet/archive/refs/tags/v2023.01.0.zip + url: https://github.com/UWPR/Comet/archive/refs/tags/v2023.01.2.zip md5: {{ md5 }} build: + run_exports: + - {{ pin_subpackage('comet-ms', max_pin=None) }} skip: True # [osx] - number: 2 + number: 0 requirements: build: - make + - unzip - {{ compiler('c') }} - {{ compiler('cxx') }} - - unzip + # To have clock_gettime in glibc. Linking to librt did not work due to inflexible Makefiles + - sysroot_linux-64 2.17 # [linux64] test: commands: From 64c912644aefbe5d8645ed4d9a68941fe8fbaba6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Mar 2024 09:50:13 -0400 Subject: [PATCH 1101/1813] Update snakemake-interface-executor-plugins to 9.0.2 (#46684) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index cde4219db9d39..27912ce5814d8 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "9.0.1" %} +{% set version = "9.0.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: 9a206832d2d8e64de57606cec3e0b60a035451c9fc71e8bcdbe7b678555301b3 + sha256: aea5544fda5affc899ec3c6f580cd3f839aa88f10123af341c40019f2c04ef10 build: noarch: python From 1aa11ee117c8f63f2dd832c51c26299440a0f1d4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Mar 2024 11:04:14 -0400 Subject: [PATCH 1102/1813] Update sequali to 0.5.1 (#46694) --- recipes/sequali/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index 57275892e7239..c59a316126691 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b21cc15395091da6f094b102e0285c595e7727f1db5ff59b8bcb08cc0b236d29 + sha256: ac8cf49fa3c2dcfd3eb976c60a4c5e482db82d902c016570c6aebc6869d2f9ea build: number: 0 From 8e32fb537aaa56cb9ceb90682a92d22234128c89 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Mar 2024 11:05:03 -0400 Subject: [PATCH 1103/1813] Update ntm-profiler to 0.4.0 (#46667) * Update ntm-profiler to 0.4.0 * Update pathogen profiler pinning * update deps --------- Co-authored-by: Robert A. Petit III Co-authored-by: Jody Phelan --- recipes/ntm-profiler/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ntm-profiler/meta.yaml b/recipes/ntm-profiler/meta.yaml index 55ce1e0cf751b..d920b448d61cc 100644 --- a/recipes/ntm-profiler/meta.yaml +++ b/recipes/ntm-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ntm-profiler" %} -{% set version = "0.3.0" %} -{% set sha256 = "1617d07625cce501980ed93146e520d5eea41c6beae5093da69accac48479f07" %} +{% set version = "0.4.0" %} +{% set sha256 = "6d9625d3b0ad2ee8a757cf6ab69381fd8d63c7d9adde76e56076b616f3039deb" %} package: name: {{name}} @@ -28,7 +28,7 @@ requirements: run: - python >=3.7 - mash =2.3 - - pathogen-profiler =3.1.0 + - pathogen-profiler =4.1.0 - jinja2 - sourmash >=4.8.3 From 12e6cbff25ac06e101e9633514337d70eef28b55 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Salom=C3=A9=20Brunon?= <91611978+Salome-Brunon@users.noreply.github.com> Date: Fri, 22 Mar 2024 18:11:44 +0100 Subject: [PATCH 1104/1813] Updated ToulligQc to v2.5.4 (#46689) --- recipes/toulligqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/toulligqc/meta.yaml b/recipes/toulligqc/meta.yaml index 485f2b7a4b0f2..c47895becce79 100644 --- a/recipes/toulligqc/meta.yaml +++ b/recipes/toulligqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "toulligqc" %} -{% set version = "2.5.3" %} +{% set version = "2.5.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 254f1f21227a15e51612523cc642fe58660e519661d61cb09d88270be9259965 + sha256: 27524706a9483b9fd38b1122b8622214126b02fa13cb2c198c6686346bd7c880 build: number: 0 From 6573a34b0fd35e3d28ef34c75de48d5988c3b6b9 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Sat, 23 Mar 2024 01:23:00 +0800 Subject: [PATCH 1105/1813] linux-aarch64 build for mappy (#46674) Co-authored-by: yejianbang --- recipes/mappy/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/mappy/meta.yaml b/recipes/mappy/meta.yaml index fd0f7edcf8930..e26e609345c22 100644 --- a/recipes/mappy/meta.yaml +++ b/recipes/mappy/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 47df11e7cecee9138680d6d2312e44397d0484a02ecf1f5908dea50d94a0efe4 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('mappy', max_pin="x") }} @@ -36,3 +36,7 @@ about: license_family: MIT license_file: LICENSE.txt summary: 'Minimap2 Python binding' + +extra: + additional-platforms: + - linux-aarch64 From aa368475f09a51936965b9789f8aa43b0f4865cf Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Sat, 23 Mar 2024 01:32:36 +0800 Subject: [PATCH 1106/1813] inux-aarch64 build for altair-mf (#46673) * linux-aarch64 build for altair-mf * Update meta.yaml --------- Co-authored-by: yejianbang Co-authored-by: yejianbang <145335562+yejianbang@users.noreply.github.com> --- recipes/altair-mf/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/altair-mf/meta.yaml b/recipes/altair-mf/meta.yaml index 353e78b5929a8..0deed9c024b96 100644 --- a/recipes/altair-mf/meta.yaml +++ b/recipes/altair-mf/meta.yaml @@ -10,7 +10,9 @@ package: build: # Passes some invalid flags for clang skip: True # [osx] - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage("altair-mf", max_pin="x.x.x") }} source: url: https://github.com/cobilab/altair/archive/v{{ version }}.tar.gz @@ -37,3 +39,7 @@ about: license_file: LICENSE license_family: GPL summary: Software for alignment-free and spatial-temporal analysis of multi-FASTA data + +extra: + additional-platforms: + - linux-aarch64 From e364c87ca7ad76feddb71606af451c4d8f6bdc29 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Mar 2024 15:04:24 -0400 Subject: [PATCH 1107/1813] Update pbstarphase to 0.8.2 (#46699) --- recipes/pbstarphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml index 1416f4902aaa7..9df0b989ccb6b 100644 --- a/recipes/pbstarphase/meta.yaml +++ b/recipes/pbstarphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbstarphase" %} -{% set version = "0.8.1" %} -{% set sha256 = "cea59d70ebefe3660e90b566944e5c2928ce5a1107916199f5700b1117cc85ee" %} +{% set version = "0.8.2" %} +{% set sha256 = "a5db035cc26dc097f20ef1943caf99ae9387475e9ac23d50441aab2b81765992" %} package: name: {{ name }} From 419b80da560c635b6c8e6e81f2cfca36b1e7385f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Mar 2024 16:28:38 -0400 Subject: [PATCH 1108/1813] Update snakemake-executor-plugin-lsf to 0.2.3 (#46693) --- recipes/snakemake-executor-plugin-lsf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-lsf/meta.yaml b/recipes/snakemake-executor-plugin-lsf/meta.yaml index c98403fa5b16f..1c8ea46a2f0c2 100644 --- a/recipes/snakemake-executor-plugin-lsf/meta.yaml +++ b/recipes/snakemake-executor-plugin-lsf/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-lsf" %} -{% set version = "0.2.2" %} +{% set version = "0.2.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_lsf-{{ version }}.tar.gz - sha256: 4d0cf9954ca95df71d9dce92416daf730539b11a0f2ea86319baaf41e58c60ff + sha256: da628c4388d7d37c45190184e02c972acfa398bcd18d571d1ad3ca41ca8bb834 build: noarch: python From 9ffff7ea374384b3dc9c7d93ee2155d56f6cba6c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Mar 2024 17:46:19 -0400 Subject: [PATCH 1109/1813] Update bactopia-py to 1.0.9 (#46704) --- recipes/bactopia-py/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bactopia-py/meta.yaml b/recipes/bactopia-py/meta.yaml index 15bfa479cdcff..751efeead926f 100644 --- a/recipes/bactopia-py/meta.yaml +++ b/recipes/bactopia-py/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bactopia-py" %} -{% set version = "1.0.8" %} +{% set version = "1.0.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/bactopia/bactopia-{{ version }}.tar.gz - sha256: ce7277f229045af00b687f7121535f9423b4c346b9f27eb7eef6d83b8e6947c1 + sha256: 7f3ff7f1123ad22605098f81686650e3a0631ddcaeaede78dee9e93099d9fdac build: noarch: python From 8f76ee18a54257c1157c8d4e9ace2fc0d412e3fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Mar 2024 20:35:54 -0400 Subject: [PATCH 1110/1813] Update phables to 1.3.2 (#46676) --- recipes/phables/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phables/meta.yaml b/recipes/phables/meta.yaml index eb65405a8a2a0..06e9839de03da 100644 --- a/recipes/phables/meta.yaml +++ b/recipes/phables/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phables" %} -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/Vini2/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 75509327984bdf0b8d28ea84c188800ec8054ef6af08ae4b47b142b40065fbc0 + sha256: 79dad165c2ba314c77d0e4b4aca9b5876b6347c362c7f7c6bd2d9c979d3a7f7d build: number: 0 From d313409d5cc03d2e2d3dc9f97859b3522985bd49 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Mar 2024 16:56:10 -0400 Subject: [PATCH 1111/1813] Update zol to 1.3.20 (#46709) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index 56e221e546ad4..ec2a9f1b68aa6 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.19" %} +{% set version = "1.3.20" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 35b062a79934d83ce2d0071f91fdfb935a7f8cb32dd80f0d658e1c424c4a425b + sha256: 0f2ac63b09bfad5f0cf701911e32284d3e031983100fb391b3311f67bb3c883d build: number: 0 From 7299ffac41b5cb732e7c7544bf763987403afb4b Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Sat, 23 Mar 2024 17:50:11 -0400 Subject: [PATCH 1112/1813] moved arborator v1.0.0 (#46650) arborator v1.0.0 moved arborator to the right folder --- recipes/arborator/meta.yaml | 50 +++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 recipes/arborator/meta.yaml diff --git a/recipes/arborator/meta.yaml b/recipes/arborator/meta.yaml new file mode 100644 index 0000000000000..59b2d10137088 --- /dev/null +++ b/recipes/arborator/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "arborator" %} +{% set version = "1.0.0" %} +{% set sha256 = "682f022481203da36368e46942213767068ecdb4fae4d0ab7580d8556d961d0e" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/arborator-{{ version }}.tar.gz + sha256: {{ sha256 }} + + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv + entry_points: + - arborator=arborator.main:main + +requirements: + host: + - python >=3.8,<3.10 + - pip + run: + - python >=3.8,<3.10 + - {{ pin_compatible('numpy', max_pin="x") }} + - pyarrow ==12.0.0 + - pandas ==2.0.2 + - numba ==0.57.1 + - pytables + - psutil + - six + - profile_dists + - genomic_address_service + + +test: + commands: + - arborator -h + +about: + home: 'https://pypi.org/project/arborator/' + summary: 'Arborator: Simplifying operationalized pathogen surveillance and outbreak detection' + license: Apache-2.0 + license_file: LICENSE + dev_url: 'https://github.com/phac-nml/arborator' + From 059998729428d9c7f3d5d9788f94bc722730a1df Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Mar 2024 18:15:15 -0400 Subject: [PATCH 1113/1813] Update wfmash to 0.13.0 (#46710) --- recipes/wfmash/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/wfmash/meta.yaml b/recipes/wfmash/meta.yaml index c01b522985de1..29722f9ff046e 100644 --- a/recipes/wfmash/meta.yaml +++ b/recipes/wfmash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "wfmash" %} -{% set version = "0.12.6" %} +{% set version = "0.13.0" %} package: name: "{{ name }}" @@ -7,13 +7,13 @@ package: source: url: https://github.com/waveygang/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 1be1a103bf2a346b8b31aaf2a945e2477a43bb03ff4484090deedb5bb0b4e78d + sha256: d358dfadef8efa32c923de9a7c35891f7178efc70c0de08234db58bc3ab8c82c build: skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} - number: 1 + number: 0 requirements: build: From 3bb3e2aa8d5fb53f7311bc13cb3311c0521d0dd4 Mon Sep 17 00:00:00 2001 From: Michael Knudsen Date: Sat, 23 Mar 2024 23:44:02 +0100 Subject: [PATCH 1114/1813] Add recipe for REViewer (#46514) --- recipes/reviewer/LICENSE.txt | 674 +++++++++++++++++++++++++++ recipes/reviewer/build.sh | 8 + recipes/reviewer/cpp-fixes.patch | 25 + recipes/reviewer/external-libs.patch | 115 +++++ recipes/reviewer/meta.yaml | 51 ++ 5 files changed, 873 insertions(+) create mode 100644 recipes/reviewer/LICENSE.txt create mode 100644 recipes/reviewer/build.sh create mode 100644 recipes/reviewer/cpp-fixes.patch create mode 100644 recipes/reviewer/external-libs.patch create mode 100644 recipes/reviewer/meta.yaml diff --git a/recipes/reviewer/LICENSE.txt b/recipes/reviewer/LICENSE.txt new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/reviewer/LICENSE.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/reviewer/build.sh b/recipes/reviewer/build.sh new file mode 100644 index 0000000000000..bddd1b6140eae --- /dev/null +++ b/recipes/reviewer/build.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +mkdir build +cd build +cmake -DCMAKE_INSTALL_PREFIX="$PREFIX" -DCMAKE_BUILD_TYPE=Release .. +cmake --build . +mkdir -p $PREFIX/bin +install -m 755 install/bin/REViewer $PREFIX/bin diff --git a/recipes/reviewer/cpp-fixes.patch b/recipes/reviewer/cpp-fixes.patch new file mode 100644 index 0000000000000..db3341103708e --- /dev/null +++ b/recipes/reviewer/cpp-fixes.patch @@ -0,0 +1,25 @@ +diff --git a/reviewer/app/Workflow.cpp b/reviewer/app/Workflow.cpp +index 3954aca71..badd1b2e8 100644 +--- a/reviewer/app/Workflow.cpp ++++ b/reviewer/app/Workflow.cpp +@@ -21,6 +21,7 @@ + #include "Workflow.hh" + + #include ++#include + + #include + +diff --git a/reviewer/thirdparty/graph-tools/src/graphcore/GraphCoordinates.cpp b/reviewer/thirdparty/graph-tools/src/graphcore/GraphCoordinates.cpp +index 2550eda8b..622243c4e 100644 +--- a/reviewer/thirdparty/graph-tools/src/graphcore/GraphCoordinates.cpp ++++ b/reviewer/thirdparty/graph-tools/src/graphcore/GraphCoordinates.cpp +@@ -22,6 +22,8 @@ + #include "graphutils/PairHashing.hh" + + #include ++#include ++#include + + namespace graphtools + { diff --git a/recipes/reviewer/external-libs.patch b/recipes/reviewer/external-libs.patch new file mode 100644 index 0000000000000..bfd12a58d692a --- /dev/null +++ b/recipes/reviewer/external-libs.patch @@ -0,0 +1,115 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 022aa4d90..a2da3de32 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -5,67 +5,12 @@ set(CMAKE_CXX_STANDARD 11) + set(CMAKE_CXX_STANDARD_REQUIRED ON) + + # Check for required packages: +-find_package(ZLIB REQUIRED) +-find_package(BZip2 REQUIRED) +-find_package(LibLZMA REQUIRED) + + include(ExternalProject) + + set(installDir ${CMAKE_CURRENT_BINARY_DIR}/install) + + +-ExternalProject_Add(htslib +- BUILD_IN_SOURCE YES +- URL https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz2 +- CONFIGURE_COMMAND ./configure --prefix=${installDir} --disable-libcurl +- BUILD_COMMAND $(MAKE) lib-static +-) +- +- +-# Setup boost user config so that it uses the same c++ compiler as other components: +-if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") +- set (BOOST_COMPILER_TAG "gcc") +-elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Clang") +- set (BOOST_COMPILER_TAG "clang") +- set(B2_OPTIONS ${B2_OPTIONS} "toolset=clang") +-elseif(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") +- set (BOOST_COMPILER_TAG "darwin") +- set(B2_OPTIONS ${B2_OPTIONS} "toolset=clang") +-endif() +- +-if (BOOST_COMPILER_TAG) +- set(BOOST_UCONFIG "${CMAKE_BINARY_DIR}/user-config.jam") +- file(WRITE "${BOOST_UCONFIG}" "using ${BOOST_COMPILER_TAG} : : \"${CMAKE_CXX_COMPILER}\" ;\n") +- set(BOOST_PATCH_COMMAND ${CMAKE_COMMAND} -E copy ${BOOST_UCONFIG} tools/build/src/user-config.jam) +-endif() +- +-ExternalProject_Add(Boost +- BUILD_IN_SOURCE YES +- URL https://boostorg.jfrog.io/artifactory/main/release/1.73.0/source/boost_1_73_0.tar.bz2 +- PATCH_COMMAND ${BOOST_PATCH_COMMAND} +- CONFIGURE_COMMAND ./bootstrap.sh --prefix=${installDir} +- BUILD_COMMAND ./b2 install -j8 --with-filesystem --with-system --with-program_options link=static ${B2_OPTIONS} +- INSTALL_COMMAND "" +-) +- +- +-ExternalProject_Add(spdlog +- URL https://github.com/gabime/spdlog/archive/refs/tags/v1.6.1.tar.gz +- CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${installDir} +- -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +- -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} +-) +- +- +-ExternalProject_Add(catch2 +- URL https://github.com/catchorg/Catch2/archive/refs/tags/v2.12.4.tar.gz +- CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${installDir} +- -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +- -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} +- -DBUILD_TESTING=OFF +-) +- +- + ExternalProject_Add(reviewer + SOURCE_DIR ${CMAKE_SOURCE_DIR}/reviewer + BUILD_ALWAYS YES +@@ -78,5 +23,5 @@ ExternalProject_Add(reviewer + + + ExternalProject_Add_StepDependencies(reviewer configure +- Boost spdlog htslib catch2) ++ ) + +diff --git a/reviewer/CMakeLists.txt b/reviewer/CMakeLists.txt +index c7602afa0..b7fa22539 100644 +--- a/reviewer/CMakeLists.txt ++++ b/reviewer/CMakeLists.txt +@@ -10,16 +10,12 @@ if (NOT CMAKE_BUILD_TYPE) + "Choose the type of build (default: ${DEFAULT_CMAKE_BUILD_TYPE})" FORCE) + endif () + +-set(Boost_USE_STATIC_LIBS ON) + find_package(Boost 1.73 REQUIRED COMPONENTS program_options filesystem system) + + find_package(spdlog REQUIRED) +-find_package(ZLIB REQUIRED) +-find_package(BZip2 REQUIRED) +-find_package(LibLZMA REQUIRED) +-find_package(CURL REQUIRED) + find_package(Catch2 REQUIRED) + find_package(Threads REQUIRED) ++find_package(fmt) + find_library(htslib libhts.a) + find_library(htslib hts) + +@@ -82,11 +78,8 @@ target_link_libraries(REViewer PUBLIC + Core + Metrics + ${STATIC_FLAGS} +- ${htslib} +- ${LIBLZMA_LIBRARIES} +- ${CURL_LIBRARIES} +- ZLIB::ZLIB +- BZip2::BZip2 ++ hts ++ fmt::fmt + Threads::Threads) + + diff --git a/recipes/reviewer/meta.yaml b/recipes/reviewer/meta.yaml new file mode 100644 index 0000000000000..52ae1ed20bb7f --- /dev/null +++ b/recipes/reviewer/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "0.2.7" %} +{% set sha256 = "8411c40028907b0294b1899cd20af6934325796da160511b649044ecf9a5169f" %} + +package: + name: reviewer + version: '{{ version }}' + +source: + url: https://github.com/Illumina/REViewer/archive/refs/tags/v{{ version }}.tar.gz + sha256: '{{ sha256 }}' + patches: + - cpp-fixes.patch + - external-libs.patch + +build: + number: 0 + run_exports: + - {{ pin_compatible('reviewer', max_pin="x.x") }} + ignore_run_exports: + - spdlog # This library is header-only + +requirements: + build: + - {{ compiler('cxx') }} + - make + - cmake + host: + - boost-cpp + - catch2 <3 + - fmt + - htslib + - spdlog + run: + - boost-cpp + +test: + commands: + - REViewer --help + +about: + home: https://github.com/Illumina/REViewer + license: GPL-3.0 + license_family: GPL + license_file: LICENSE.txt + summary: A tool for visualizing alignments of reads in regions containing tandem repeats + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - doi:10.1186/s13073-022-01085-z From d655bef3f213de7e19b255aca7af477b5a6c8dcb Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Sat, 23 Mar 2024 17:22:21 -0700 Subject: [PATCH 1115/1813] Update meta.yaml (#46711) --- recipes/ampliconsuite/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index 84d1fa2b1de45..12d8bf1f0fda7 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,7 +1,7 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.2.2" %} -{% set AA_version="1.3.r8" %} -{% set AC_version="1.1.2" %} +{% set AS_version="1.3.1" %} +{% set AA_version="1.4.r1" %} +{% set AC_version="1.1.3" %} package: name: {{ name }} @@ -11,12 +11,12 @@ source: # the sha256 sum is generated by doing # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: 40d3b4560fb2c9fd0cbc5166b9d136751ff16217a6228fb38b74e12207ef5b63 + sha256: b74c8201b9e53493a8f1604f6035fa9e42c0ce7d1a258f9095b037afe2d5f2d8 - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz - sha256: 44466fb4a275f5dd1a142269bb72dc53a651b9d9193e5ba799eee14f0f693f89 + sha256: d62e30999c69b994691c8a61b09255a0b223906fd76709febc0ae8387164f208 folder: ampliconarchitectlib - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz - sha256: 0f57d0775d7b68a76fab6cc375e45410fe76dd9245697855f257378bd1f21650 + sha256: 105f3d0dfd99c52bb8cd988f3fd71afb064b01167a36b72d8fe789f5dfe8c9f5 build: noarch: python @@ -41,12 +41,14 @@ requirements: - pysam - samtools - scipy + - bedtools host: - python >=3 test: commands: - AmpliconSuite-pipeline.py -v + - GroupedAnalysisAmpSuite.py -v - amplicon_classifier.py -v - feature_similarity.py -h - make_results_table.py -h From 942b4cff849858b020bb1a76e20f1488d9cb7958 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Sat, 23 Mar 2024 18:31:13 -0600 Subject: [PATCH 1116/1813] update rgi pinning for pyrodigal (#46669) * update rgi pinning for pyrodigal * bump build number --- recipes/rgi/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/rgi/meta.yaml b/recipes/rgi/meta.yaml index 8bf0c27c66e61..abfe223b51225 100644 --- a/recipes/rgi/meta.yaml +++ b/recipes/rgi/meta.yaml @@ -16,7 +16,7 @@ source: build: noarch: python - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -50,7 +50,8 @@ requirements: - lxml ==4.6.5 - wget - dask - - pyrodigal >=2.0.0 + # pyrodigal v3 renamed OrfFinder to GeneFinder, please review on future RGI releases + - pyrodigal >=2.0.0,<3 run: # RGI requires these exact versions of blast prodigal and diamond, or else --alignment_mode DIAMOND fails # - python >=3.5,<3.7 @@ -80,7 +81,8 @@ requirements: - lxml ==4.6.5 - wget - dask - - pyrodigal >=2.0.0 + # pyrodigal v3 renamed OrfFinder to GeneFinder, please review on future RGI releases + - pyrodigal >=2.0.0,<3 test: commands: From 3f6b12a2c38eca2dc4515b4c9c176fc1d40cac31 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Sat, 23 Mar 2024 18:31:36 -0600 Subject: [PATCH 1117/1813] fix issue with sistr container (#46712) * fix issue with sistr container * fix typo --- recipes/sistr_cmd/build.sh | 3 ++- recipes/sistr_cmd/meta.yaml | 6 +----- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/recipes/sistr_cmd/build.sh b/recipes/sistr_cmd/build.sh index 87f4375bf2c85..27efb5e5b1c08 100644 --- a/recipes/sistr_cmd/build.sh +++ b/recipes/sistr_cmd/build.sh @@ -1,2 +1,3 @@ #!/bin/bash -python -m pip install . --no-deps --no-build-isolation --ignore-installed --no-cache-dir -vvv \ No newline at end of file +python -m pip install . --no-deps --no-build-isolation --ignore-installed --no-cache-dir -vvv +${PREFIX}/bin/sistr_init diff --git a/recipes/sistr_cmd/meta.yaml b/recipes/sistr_cmd/meta.yaml index bec537bcae08d..ed0a38044b262 100644 --- a/recipes/sistr_cmd/meta.yaml +++ b/recipes/sistr_cmd/meta.yaml @@ -6,18 +6,15 @@ package: version: "{{ version }}" source: - #url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - #sha256: f68de3f90c2d744db1f282db82f9e4094626c1448a5dbf834ff853c760975bb5 url: https://github.com/phac-nml/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz sha256: 5acffbaeb345bb6bdea4fae3317e651c254b114b37762eeb284c5bfa928329a2 build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} - #script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --ignore-installed --no-cache-dir -vvv entry_points: - sistr=sistr.sistr_cmd:main - sistr_init=sistr.sistr_cmd:setup_sistr_dbs @@ -62,4 +59,3 @@ extra: - usegalaxy-eu:sistr_cmd - doi:10.1371/journal.pone.0147101 - biotools:SISTR - From c070ee113165969b66195d07060b0e0fa1bdb6bb Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Sat, 23 Mar 2024 18:31:57 -0600 Subject: [PATCH 1118/1813] adjust python pinning in gubbins (#46713) --- recipes/gubbins/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml index ac2bc3d57f6d7..7f27a03430d08 100644 --- a/recipes/gubbins/meta.yaml +++ b/recipes/gubbins/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [py < 38] run_exports: - {{ pin_subpackage('gubbins', max_pin="x") }} @@ -28,7 +28,7 @@ requirements: host: - perl - zlib - - python >=3.8,<3.11 + - python >=3.8,<3.10 - scipy - setuptools - dendropy @@ -36,7 +36,7 @@ requirements: - numpy <=1.23.0 - numba run: - - python >=3.8,<3.11 + - python >=3.8,<3.10 - scipy - dendropy - biopython From 98ef6b1b6903b48a03038991390e822452416306 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Sat, 23 Mar 2024 18:32:24 -0600 Subject: [PATCH 1119/1813] fix amrfinderplus pinning in abritamr (#46714) --- recipes/abritamr/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/abritamr/meta.yaml b/recipes/abritamr/meta.yaml index 6d55a4bd9bb53..26d85eddc87b6 100644 --- a/recipes/abritamr/meta.yaml +++ b/recipes/abritamr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 0 + number: 1 noarch: python entry_points: - abritamr=abritamr.abritamr:main @@ -29,7 +29,10 @@ requirements: - python >=3.9 - pandas - xlsxwriter - - ncbi-amrfinderplus =3.10.42 + # Please review ncbi-amrfinderplus pinning every release + # The version should be pinned to the database version used by abritamr + # Please see the "changes.txt" file in https://github.com/MDU-PHL/abritamr/blob/master/abritamr/db/amrfinderplus/data//changes.txt + - ncbi-amrfinderplus =3.12.8 - blast - hmmer From 1917985ea2a17d7af3692879dec6d5a3b45c1641 Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Sun, 24 Mar 2024 06:35:12 -0400 Subject: [PATCH 1120/1813] locidex v0.1.1 recipe (#46715) * locidex v0.0.1 recipe * locidex v0.0.1 recipe * locidex v0.1.1 recipe * locidex v0.1.1 recipe --- recipes/locidex/meta.yaml | 54 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 recipes/locidex/meta.yaml diff --git a/recipes/locidex/meta.yaml b/recipes/locidex/meta.yaml new file mode 100644 index 0000000000000..ea40a8732b724 --- /dev/null +++ b/recipes/locidex/meta.yaml @@ -0,0 +1,54 @@ +{% set name = "locidex" %} +{% set version = "0.1.1" %} +{% set sha256 = "39b4d4f55cc6d13bae23fce36a46f818a2d43fd7b87bbd24408633d973e62458" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/locidex-{{ version }}.tar.gz + sha256: {{ sha256 }} + + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv + entry_points: + - locidex=locidex.main:main + +requirements: + host: + - python >=3.8,<4 + - pip + run: + - python >=3.8,<4 + - {{ pin_compatible('numpy', max_pin="x") }} + - pandas >=2.0.2 + - numba >=0.57.1 + - pytables >=3.8 + - six >=1.16 + - pyrodigal + - biopython >=1.83 + - mafft + - blast >=2.9.0 + +test: + commands: + - locidex -h + - locidex search -h + - locidex extract -h + - locidex report -h + - locidex merge -h + - locidex format -h + - locidex build -h + +about: + home: 'https://pypi.org/project/locidex/' + summary: 'Locidex: Common search engine for similarity based typing applications' + license: Apache-2.0 + dev_url: 'https://github.com/phac-nml/locidex' + From 338c904307148f93632e70117dc42b0335d116f9 Mon Sep 17 00:00:00 2001 From: AntonS-bio <47866509+AntonS-bio@users.noreply.github.com> Date: Sun, 24 Mar 2024 10:36:25 +0000 Subject: [PATCH 1121/1813] Add new package for genotyping reads (#46587) * Add new package for genotyping reads * Changed python version to 3.8 * Updated python version * Updated dependencies * Updated biopython version * Removed build.sh * Update meta.yaml * Updated meta.yaml * Updated meta.yaml * Updated meta.yaml * Updated meta.yaml * Updated meta.yaml * Updated meta.yaml * Updated meta.yaml * Updated meta.yaml * Update meta.yaml * Minor changes * Minor change * Version update --- recipes/handyreadgenotyper/meta.yaml | 59 ++++++++++++++++++++++++++++ recipes/handyreadgenotyper/setup.py | 54 +++++++++++++++++++++++++ 2 files changed, 113 insertions(+) create mode 100644 recipes/handyreadgenotyper/meta.yaml create mode 100644 recipes/handyreadgenotyper/setup.py diff --git a/recipes/handyreadgenotyper/meta.yaml b/recipes/handyreadgenotyper/meta.yaml new file mode 100644 index 0000000000000..9e4c4734d3ee8 --- /dev/null +++ b/recipes/handyreadgenotyper/meta.yaml @@ -0,0 +1,59 @@ +{% set name = "HandyReadGenotyper" %} +{% set version = "0.1.9" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/AntonS-bio/HandyReadGenotyper/archive/{{ version }}.tar.gz + sha256: fdb514deaf7b9c483bef48e1f1bf955d948697e78ef128aaf41e198c0fc38f6e + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('handyreadgenotyper', max_pin="x.x") }} + number: 0 + +requirements: + build: + - python <3.9.0a0,>=3.8 + - pandas >=2.0.0 + - scikit-learn >=1.3.* + - pysam >=0.22.0 + - numpy >=1.20.* + - tqdm >=4.66.* + - biopython >=1.78 + - tqdm >=4.66.* + host: + - pip + - python <3.9.0a0,>=3.8 + run: + - python <3.9.0a0,>=3.8 + - pandas >=2.0.0 + - scikit-learn >=1.3.* + - pysam >=0.22.0 + - numpy >=1.20.* + - tqdm >=4.66.* + - biopython >=1.78 + - tqdm >=4.66.* + +test: + commands: + - train -h + - classify -h + +about: + license: GPL-3.0 + license_file: LICENSE + home: https://github.com/AntonS-bio/HandyReadGenotyper + summary: 'Tool for training model and classifying reads from environmental ONT amplicon sequencing.' + description: | + Tool for training model and classifying reads from environmental ONT amplicon sequencing. + doc_source_url: https://github.com/AntonS-bio/HandyAmpliconTool/blob/main/README.md + + +extra: + recipe-maintainers: + - AntonS-bio diff --git a/recipes/handyreadgenotyper/setup.py b/recipes/handyreadgenotyper/setup.py new file mode 100644 index 0000000000000..25c9cabb5ea92 --- /dev/null +++ b/recipes/handyreadgenotyper/setup.py @@ -0,0 +1,54 @@ +#!/usr/bin/env python3 +from setuptools import setup +from setuptools.command.install import install +import os +import sys + +__version__ = '0.1.9' + +def readme(): + with open('README.md') as f: + return f.read() + +def check_dir_write_permission(directory): + if os.path.isdir(directory) and not os.access(directory, os.W_OK): + sys.exit('Error: no write permission for ' + directory + ' ' + + 'Perhaps you need to use sudo?') + +class HandyReadGenotyperInstall(install): + + def run(self): + check_dir_write_permission(self.install_lib) + install.run(self) + + + +setup(name='HandyReadGenotyper', + version=__version__, + description='HandyReadGenotyper', + long_description=readme(), + python_requires='>=3.8,<3.9.0a0', + classifiers=['Development Status :: Beta', + 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', + 'Programming Language :: Python :: 3', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + 'Intended Audience :: Science/Research'], + keywords='PCR amplicon primers', + url='https://github.com/AntonS-bio/HandyReadGenotyper.git', + author='Anton Spadar', + author_email='', + packages=['scripts'], + include_package_data=True, + entry_points={'console_scripts': ['classify = classify:main', 'train = train:main']}, + scripts=[ + 'scripts/classify.py', + 'scripts/data_classes.py', + 'scripts/genotyper_data_classes.py', + 'scripts/input_processing.py', + 'scripts/inputs_validation.py', + 'scripts/model_manager.py', + 'scripts/read_classifier.py', + 'scripts/train.py' + ], + cmdclass={'install': HandyReadGenotyperInstall} +) From 88d4026ea1c04a119e1cb63a64d1fa6b4115da00 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 06:36:58 -0400 Subject: [PATCH 1122/1813] Update neat to 4.1.1 (#46708) * Update neat to 4.1 * Update neat to 4.1.1 --- recipes/neat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/neat/meta.yaml b/recipes/neat/meta.yaml index e302227fc03b2..f02728e585edb 100644 --- a/recipes/neat/meta.yaml +++ b/recipes/neat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "NEAT" %} -{% set version = "4.0" %} +{% set version = "4.1.1" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/ncsa/{{ name }}/archive/{{ version }}.tar.gz - sha256: 89abf23f202e4e93fc333a2b6f2a7c7b63ef3db691f8372b659d8627df3616c3 + sha256: 1f6ad3398be7e647f528a23f7d1f6470756620786b0f0331a1e41ddc1074288f build: From 5af46bfbf9ddd8998fb4c89b47c888a45a2c8c53 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 06:37:19 -0400 Subject: [PATCH 1123/1813] Update massdash to 0.0.9 (#46707) --- recipes/massdash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/massdash/meta.yaml b/recipes/massdash/meta.yaml index dcbbef4ea0961..09f269a84b383 100644 --- a/recipes/massdash/meta.yaml +++ b/recipes/massdash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "massdash" %} -{% set version = "0.0.8" %} +{% set version = "0.0.9" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 9e03e23c7f2f9c84c30ba7aef936d2f26b0284b4fa0dd330618e6fd6fb40cbef + sha256: 68d90f668312d94ec44f744376c0dad0b671fe78f01906d2e36ce43cc9c85ffa build: number: 0 From 9aedcf4abf8c205c9f6ab7153edc31477fe3fbf1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 06:37:39 -0400 Subject: [PATCH 1124/1813] Update pbfusion to 0.4.1 (#46705) --- recipes/pbfusion/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbfusion/meta.yaml b/recipes/pbfusion/meta.yaml index 8433b41fcd948..b2a63c19e6a0e 100644 --- a/recipes/pbfusion/meta.yaml +++ b/recipes/pbfusion/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbfusion" %} -{% set version = "0.4.0" %} -{% set pbfusion_sha256 = "bb6c37188288492dbcf5f1e9ddbc02492e86590e5a4567d6ded0d1ab9deb12ec" %} +{% set version = "0.4.1" %} +{% set pbfusion_sha256 = "c6abde2ee1f88355158bf1c655e5ae754f942708f7addbaef8d626fdebfcfe7a" %} package: name: {{ name }} From e5c9b822e2d07ce6fef15b330727eb7141021b71 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 06:37:57 -0400 Subject: [PATCH 1125/1813] Update hifihla to 0.3.0 (#46702) --- recipes/hifihla/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hifihla/meta.yaml b/recipes/hifihla/meta.yaml index df508026a76a4..fdf95a9243a04 100644 --- a/recipes/hifihla/meta.yaml +++ b/recipes/hifihla/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hifihla" %} -{% set version = "0.2.3" %} -{% set hifihla_sha256 = "f2c3cf24ca12b1bf1bec88dae6a30089c702077e683eb01451f216b3ee93bbe0" %} +{% set version = "0.3.0" %} +{% set hifihla_sha256 = "6d03ff73bce0c2c2805b2b3d51ec181e6aeae36a11a4cb99440914ffcecd2bb6" %} package: name: {{ name }} From e588a7175171b0ecc1bbd89a88132a88e7c73fe4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 07:14:46 -0400 Subject: [PATCH 1126/1813] Update snakemake to 8.10.0 (#46691) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake to 8.10.0 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index c103bc15844b0..a12e2aad43fbd 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.9.0" %} +{% set version = "8.10.0" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 1c36d231da92a1e37ab9f96d35346f5268949fbd1cebf4c9d429816a05538066 + sha256: abd73a2acd6741d0794bbf6e11eb1ae50cf44dc060e6dc80328fce2a4633dd78 build: number: 0 @@ -103,7 +103,7 @@ outputs: - requests >=2.8.1 - reretry - smart_open >=3.0,<4.0 - - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 + - snakemake-interface-executor-plugins >=9.0.2,<10.0.0 - snakemake-interface-common >=1.17.0,<2.0 - snakemake-interface-storage-plugins >=3.1.0,<4.0 - snakemake-interface-report-plugins >=1.0.0,<2.0.0 From acb2864b32092e74beaeefd97396f10630664c0f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 07:32:44 -0400 Subject: [PATCH 1127/1813] Update chewbbaca to 3.3.4 (#46698) --- recipes/chewbbaca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index 770e27d49c701..8dbb1f8eacb80 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,5 +1,5 @@ {% set name = 'chewBBACA' %} -{% set version = '3.3.3' %} +{% set version = '3.3.4' %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: c29e34bdca769b38f8e9c7f7bd3547563f9e1e1effe5266e7b00674d9a7ca12a + sha256: 3e9debdd29fe67741b81041ffeb3b05946018ef273b7876daf033ec433f6e293 build: number: 0 From 8188956e93c6c689f992efa735e55710c9b19018 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 07:45:44 -0400 Subject: [PATCH 1128/1813] Update fiji-simple_omero_client to 5.18.0 (#46700) --- recipes/fiji-simple_omero_client/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fiji-simple_omero_client/meta.yaml b/recipes/fiji-simple_omero_client/meta.yaml index cf97f12237bf0..98f1a97ecd7cd 100644 --- a/recipes/fiji-simple_omero_client/meta.yaml +++ b/recipes/fiji-simple_omero_client/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fiji-simple_omero_client" %} -{% set version = "5.17.0" %} +{% set version = "5.18.0" %} package: name: {{ name | lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/GReD-Clermont/simple-omero-client/releases/download/{{ version }}/simple-omero-client-{{ version }}.jar - sha256: 4dd058185368fb7511e538112bd8edc382409495ce2127ab19405c2b3dcef55a + sha256: 0b70886437e9cf6c2ab1096d6e711c7319b45bac6784ab4aac5fb8ef98e64e61 build: number: 0 From 5e9f7d9dab749ceec3ce708b8c3cb9da0517aa4c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 07:48:35 -0400 Subject: [PATCH 1129/1813] Update dxpy to 0.372.0 (#46692) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index ee21bce95daa2..0d5cbbcaf6e0a 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.371.0" %} +{% set version = "0.372.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: d264d06c9101877e5d185c9b3165a19c0d8c5af4bdaf1c42530ad316c53188ae + sha256: 6be5cf0ecd03977c2ad09d863a7de17b6b866cc280ca85dc192612b4fb87da7b build: number: 0 From d0e91e3a2988d06b992ee5864031fd0708479fcb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 07:49:16 -0400 Subject: [PATCH 1130/1813] Update dimet to 0.2.4 (#46685) --- recipes/dimet/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dimet/meta.yaml b/recipes/dimet/meta.yaml index 601dacf485321..80d5d1ce73a27 100644 --- a/recipes/dimet/meta.yaml +++ b/recipes/dimet/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dimet" %} -{% set version = "0.2.2" %} +{% set version = "0.2.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dimet-{{ version }}.tar.gz - sha256: f5d601a43994705d6bc0cd3948b57756b89dfbd8784266549929a0c8ac3368db + sha256: d394d9a9b1eab5c9cc89f9ac59ff0ee06226b3c6421a6eede001491220fb2642 build: noarch: python From 66c16d926b948e9a99f93c6bce098cb93d856124 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 07:49:40 -0400 Subject: [PATCH 1131/1813] Update viroconstrictor to 1.4.1 (#46682) --- recipes/viroconstrictor/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/viroconstrictor/meta.yaml b/recipes/viroconstrictor/meta.yaml index a1f44a2d6cd3d..9f8aefdc77b11 100644 --- a/recipes/viroconstrictor/meta.yaml +++ b/recipes/viroconstrictor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ViroConstrictor" %} -{% set version = "1.4.0" %} +{% set version = "1.4.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/RIVM-bioinformatics/ViroConstrictor/archive/v{{ version }}.tar.gz - sha256: 56944f978fc5bb4f934d8a82be3862236552b9beab090f7e61c10023b51b8b25 + sha256: fb2c80018762b5809d3b6a404c27f60b7534d4a0dc00543365a21fd1efc0dd7a build: noarch: python @@ -17,7 +17,7 @@ build: - viroConstrictor = ViroConstrictor.__main__:main - Viroconstrictor = ViroConstrictor.__main__:main script: {{ PYTHON }} -m pip install . --no-deps -vvv - number: 1 + number: 0 run_exports: - {{ pin_subpackage('viroconstrictor', max_pin="x") }} From af84aebba7097d4f5000fc80f370f6dcb2ef22f0 Mon Sep 17 00:00:00 2001 From: Jens-Uwe Ulrich <46562264+JensUweUlrich@users.noreply.github.com> Date: Sun, 24 Mar 2024 12:50:16 +0100 Subject: [PATCH 1132/1813] update taxor to version 0.1.3 (#46678) Co-authored-by: Jens-Uwe Ulrich --- recipes/taxor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxor/meta.yaml b/recipes/taxor/meta.yaml index b7846fe6d4640..767c30ea4dcda 100755 --- a/recipes/taxor/meta.yaml +++ b/recipes/taxor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: taxor @@ -6,7 +6,7 @@ package: source: url: https://github.com/JensUweUlrich/Taxor/archive/refs/tags/{{ version }}.tar.gz # [linux] - md5: 9c4ce8562b17c21035433233ceb98d66 # [linux] + md5: 7bffd64282894433b4db60af8f1052c9 # [linux] build: number: 0 From ed7d640b2189b1a22d3b3041269318cc0d58c4fc Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Sun, 24 Mar 2024 21:25:22 +0100 Subject: [PATCH 1133/1813] Update hictk to v0.0.11 (#46703) * Bump hictk to v0.0.11 * Compiler segfaults are so much fun... * WIP * WIP * WIP * WIP * Bugfix * Update URL and checksum --- recipes/hictk/conanfile.txt.patch | 16 ++++++++-------- recipes/hictk/meta.yaml | 9 ++++++--- recipes/hictk/run_test.sh | 4 +++- 3 files changed, 17 insertions(+), 12 deletions(-) diff --git a/recipes/hictk/conanfile.txt.patch b/recipes/hictk/conanfile.txt.patch index 3e89ed9ffc3b1..b2752bd88fd25 100644 --- a/recipes/hictk/conanfile.txt.patch +++ b/recipes/hictk/conanfile.txt.patch @@ -1,18 +1,18 @@ diff --git a/conanfile.txt b/conanfile.txt -index 0fc36a2..5577407 100644 +index 06a2202..a6164f6 100644 --- a/conanfile.txt +++ b/conanfile.txt -@@ -3,75 +3,11 @@ +@@ -3,75 +3,13 @@ # SPDX-License-Identifier: MIT [requires] --boost/1.84.0#774abb4a1b3702b2f7171ac6b6de777a +-boost/1.84.0#5cc9767cd47ba6b5e1b53ab4670f07fc bshoshany-thread-pool/4.0.1#b7ce99198b3a54e403393961480085c7 --catch2/3.5.2#9554dc3c4ffcab50daf8f2cac4b79308 +-catch2/3.5.3#2178a424c7c53da1e7df5fef1a051f1f -cli11/2.4.1#afacffd31f631bbb8b7c7d6425fe7a66 concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502 -eigen/3.4.0#2e192482a8acff96fe34766adca2b24c --fast_float/6.1.0#85dc5bf9d3d6e605abf536818397baf3 +-fast_float/6.1.0#d5ebf20d96102abc0f5d2d2269a317bc -fmt/10.2.1#9199a7a0611866dea5c8849a77467b25 -hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1 -highfive/2.9.0#c57477beed8b0110fadeb6da8f48bcc5 @@ -20,13 +20,13 @@ index 0fc36a2..5577407 100644 parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7 readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83 span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422 --spdlog/1.13.0#2775cc949e26b339029a852785b6b276 +-spdlog/1.13.0#8e88198fd5b9ee31d329431a6d0ccaa2 -zstd/1.5.5#b87dc3b185caa4b122979ac4ae8ef7e8 [generators] CMakeDeps -- --[options] + + [options] -boost*:system_no_deprecated=True -boost*:asio_no_deprecated=True -boost*:filesystem_no_deprecated=True diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index 6ae4433671ca6..ebcfbb7c853f1 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.10" %} -{% set sha256 = "0b2d60af73578b292317e5ab513f24965176f9852ceda29e8d02007a434588c3" %} +{% set version = "0.0.11" %} +{% set sha256 = "a06b674de2301918188d1c890a95aaa4d6164377ebaa44cc07efb77fd9eb654c" %} package: name: {{ name|lower }} @@ -61,7 +61,10 @@ test: - test/scripts/check_test_files_exist.sh - test/scripts/compare_matrix_files.sh - test/scripts/compare_plain_files.sh - - test/scripts/hictk_balance.sh + - test/scripts/compare_weights.py + - test/scripts/hictk_balance_ice.sh + - test/scripts/hictk_balance_scale.sh + - test/scripts/hictk_balance_vc.sh - test/scripts/hictk_convert_hic2cool.sh - test/scripts/hictk_convert_cool2hic.sh - test/scripts/hictk_dump_cells.sh diff --git a/recipes/hictk/run_test.sh b/recipes/hictk/run_test.sh index 9d039acef9489..40324b44eca22 100755 --- a/recipes/hictk/run_test.sh +++ b/recipes/hictk/run_test.sh @@ -20,7 +20,9 @@ hictk="$(which hictk)" # Run integration tests -test/scripts/hictk_balance.sh "$hictk" +test/scripts/hictk_balance_ice.sh "$hictk" +test/scripts/hictk_balance_scale.sh "$hictk" +test/scripts/hictk_balance_vc.sh "$hictk" test/scripts/hictk_dump_chroms.sh "$hictk" test/scripts/hictk_dump_bins.sh "$hictk" From 157dfc438c7ce56843998e2b3c73766bdaa4d088 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 21:31:47 -0400 Subject: [PATCH 1134/1813] Update dragonflye to 1.2.0 (#46721) * Update dragonflye to 1.2.0 * Update depends --------- Co-authored-by: Robert A. Petit III --- recipes/dragonflye/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/dragonflye/meta.yaml b/recipes/dragonflye/meta.yaml index e69873f01afb6..94fb87669134c 100644 --- a/recipes/dragonflye/meta.yaml +++ b/recipes/dragonflye/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dragonflye" %} -{% set version = "1.1.2" %} +{% set version = "1.2.0" %} package: name: {{ name }} @@ -13,13 +13,14 @@ build: source: url: https://github.com/rpetit3/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 0175f72233c2aa5b4f398fee8f1c17ae69ff04a17dd81ca5e105ec3b3fb4d0ab + sha256: e01f7c6ad237811fcf7719abc756c29e3751d019bac7a827ff2f5d202c150b23 requirements: run: - assembly-scan >=1.0.0 - any2fasta >=0.4.2 - bwa + - dnaapler - fastp - flye >=2.9.2 - kmc >=3.1 @@ -31,7 +32,7 @@ requirements: - perl-findbin - pigz >=2.6 - pilon - - polypolish + - polypolish >=0.6.0 - porechop - racon >=1.5.0 - rasusa >=0.7.1 From bfcff4f200bfa2a78e11d2b8ba133e8f3a7aa283 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 24 Mar 2024 22:33:32 -0400 Subject: [PATCH 1135/1813] Update bactopia-assembler to 1.0.4 (#46720) * Update bactopia-assembler to 1.0.4 * Update depends --------- Co-authored-by: Robert A. Petit III --- recipes/bactopia-assembler/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bactopia-assembler/meta.yaml b/recipes/bactopia-assembler/meta.yaml index d44aba6c79699..12a861b1cf8f4 100644 --- a/recipes/bactopia-assembler/meta.yaml +++ b/recipes/bactopia-assembler/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.3" %} +{% set version = "1.0.4" %} package: name: bactopia-assembler @@ -12,12 +12,12 @@ build: source: url: https://github.com/bactopia/bactopia-assembler/archive/v{{version}}.tar.gz - sha256: d4f318b7ba97a5c54823f7405bb79f03e0244bc7ccc52313acb4dcffbc1b7347 + sha256: fb332391d7c53db233716bfdc2adc1be25577a268bdb2b3a3fadcea168bcc816 requirements: run: - coreutils - - dragonflye >=1.1.2 + - dragonflye >=1.2.0 - importlib-metadata <5 - sed - shovill-se From d07703423c77005406d866d0429c78b91bb1d56c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 03:43:59 -0400 Subject: [PATCH 1136/1813] Update pangu to 0.2.5 (#46701) --- recipes/pangu/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangu/meta.yaml b/recipes/pangu/meta.yaml index dbf8e578c4815..ee811a1024ba7 100644 --- a/recipes/pangu/meta.yaml +++ b/recipes/pangu/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.4" %} -{% set sha256 = "1437175d891a76f71a19dc86121c08b19d81a61273cbbd09bbab6e090c42e3f2" %} +{% set version = "0.2.5" %} +{% set sha256 = "3ad9f4e93fe237d41fe2d06a1798d24dc3018a0a59f0133b3bd2cb1f79c1b0b0" %} package: name: pangu From 972fab6bba3e1cadd9b258fd782a1644a3450b3f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 03:44:25 -0400 Subject: [PATCH 1137/1813] Update bactopia to 3.0.1 (#46724) * Update bactopia to 3.0.1 * Update depends --------- Co-authored-by: Robert A. Petit III --- recipes/bactopia/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/bactopia/meta.yaml b/recipes/bactopia/meta.yaml index 8c4f438484b0b..df8f01409f6a0 100644 --- a/recipes/bactopia/meta.yaml +++ b/recipes/bactopia/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bactopia" %} -{% set version = "3.0.0" %} +{% set version = "3.0.1" %} package: name: {{ name }} @@ -13,11 +13,11 @@ build: source: url: https://github.com/bactopia/bactopia/archive/v{{version}}.tar.gz - sha256: 24a934c02cde5ab33997590e8db748d045aaec993328b2675123f531e6c6aaf6 + sha256: f3f152294555c05ec37c20041385034b02a79a709d7801b07d2115f50115fa4a requirements: run: - - bactopia-py >=1.0.8 + - bactopia-py >=1.0.9 - conda >=22.11.0 - coreutils - mamba >=1.1.0 @@ -25,7 +25,6 @@ requirements: - python >=3.9 - sed - wget - test: commands: From 77ce3947c531fca4f0f83572090c36e43aac629f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 10:51:13 -0400 Subject: [PATCH 1138/1813] Update tb-profiler to 6.2.0 (#46732) --- recipes/tb-profiler/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml index 9fc9e95ddbdeb..62489b7775eec 100644 --- a/recipes/tb-profiler/meta.yaml +++ b/recipes/tb-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "tb-profiler" %} -{% set version = "6.1.0" %} -{% set sha256 = "9ef62a6da769bdf745e70e35e02bf61fba5e1eb4d52bf228e01c4daf6ad4c910" %} +{% set version = "6.2.0" %} +{% set sha256 = "23880e0a38541629f5d2b66fd5323dc9df07fb357e359ad3dc640e4c5b77a206" %} package: name: {{name}} @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 0 run_exports: - {{ pin_subpackage('tb-profiler', max_pin="x") }} From ab394026ac3be9d50681f1487f6b890410ee50bd Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Mon, 25 Mar 2024 22:57:49 +0800 Subject: [PATCH 1139/1813] add linux-aarch64-alignoth (#46646) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * alignoth * alignoth2 * alignoth2 * alignoth2 --------- Co-authored-by: yejianbang --- recipes/alignoth/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/alignoth/meta.yaml b/recipes/alignoth/meta.yaml index 6777f87490857..452eea4bb43a6 100644 --- a/recipes/alignoth/meta.yaml +++ b/recipes/alignoth/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 # TODO fails to build on osx with # Undefined symbols for architecture x86_64: "_SSLCopyALPNProtocols", referenced from: _sectransp_connect_step2 in libcurl_sys-1f07db570920ba9f.rlib(sectransp.o) skip: true #[osx] @@ -30,6 +30,7 @@ requirements: - libcurl - openssl + test: commands: - alignoth --help @@ -43,3 +44,5 @@ extra: recipe-maintainers: - fxwiegand - johanneskoester + additional-platforms: #add aarch64 + - linux-aarch64 From a4fc286517043349787cc74addf29c7e8a94767b Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Mon, 25 Mar 2024 09:59:32 -0500 Subject: [PATCH 1140/1813] Update DRAM version (#46723) * Update dram version * Add github issue link * Add run_exports * Fix patches location * Fix patch --------- Co-authored-by: Natasha Pavlovikj --- recipes/dram/fix_setup.patch | 14 ++++++++++++++ recipes/dram/meta.yaml | 13 +++++++++---- 2 files changed, 23 insertions(+), 4 deletions(-) create mode 100644 recipes/dram/fix_setup.patch diff --git a/recipes/dram/fix_setup.patch b/recipes/dram/fix_setup.patch new file mode 100644 index 0000000000000..f8fb0fcc6f255 --- /dev/null +++ b/recipes/dram/fix_setup.patch @@ -0,0 +1,14 @@ +--- scripts/DRAM-setup.py.old 2024-03-24 22:09:07.980198244 -0500 ++++ scripts/DRAM-setup.py 2024-03-24 22:10:39.107097364 -0500 +@@ -121,10 +121,10 @@ + help='vog annotations file') # add loc to vog_annotations to match the rest + + set_db_locs_parser.add_argument('--viral_loc', default=None, ++ help='mmseqs2 database file from ref seq viral gene collection') + set_db_locs_parser.add_argument('--camper_tar_gz_loc', default=None, + help='The source for the CAMPER database files, this is a tar.gz file downloaded' + ' from the release page https://github.com/WrightonLabCSU/CAMPER/releases') +- help='mmseqs2 database file from ref seq viral gene collection') + set_db_locs_parser.add_argument('--peptidase_loc', default=None, + help='mmseqs2 database file from MEROPS database') + set_db_locs_parser.add_argument('--description_db_loc', default=None, diff --git a/recipes/dram/meta.yaml b/recipes/dram/meta.yaml index 6c93600ad8052..71f440a076c1b 100644 --- a/recipes/dram/meta.yaml +++ b/recipes/dram/meta.yaml @@ -1,7 +1,7 @@ {% set name = "DRAM" %} {% set pypi_name = "DRAM-bio" %} -{% set version = "1.4.6" %} -{% set sha256 = "f014c55d7e75433bfc029dc20092df6eb9fb5a565dc60d6e7934d0261f36f945" %} +{% set version = "1.5.0" %} +{% set sha256 = "2d4a503fa806e33b580afb6d21879b2399178e48ba3b05ada882449fee571889" %} package: name: {{ name|lower }} @@ -10,15 +10,20 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ pypi_name }}/{{ pypi_name }}-{{ version }}.tar.gz sha256: {{ sha256 }} + patches: + # https://github.com/WrightonLabCSU/DRAM/issues/339 + - fix_setup.patch build: - number: 2 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: host: - - python >=3.6 + - python >=3.8 - pip run: - python >=3.8 From d6ce8daf45b952cd5d6c2ff2b0cd249bd08b9262 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 11:00:20 -0400 Subject: [PATCH 1141/1813] Update resfinder to 4.5.0 (#46681) --- recipes/resfinder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/resfinder/meta.yaml b/recipes/resfinder/meta.yaml index d05f4a9a1a066..6614f72cec293 100644 --- a/recipes/resfinder/meta.yaml +++ b/recipes/resfinder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "resfinder" %} -{% set version = "4.4.3" %} +{% set version = "4.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/resfinder-{{ version }}.tar.gz - sha256: 8db4f9a41fd55e3f69836094fd8c101751c7a984ed2d8f4c124d756b43f26ee3 + sha256: 7c2ad096c2f5f746607c4433d327f890776aba996f86112dc4527fc3c2bc0ec4 patches: - python_path.patch From 4a1b31c27714a3e3874dce94a3120204b0ef2a4d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 11:00:38 -0400 Subject: [PATCH 1142/1813] Update rmats to 4.3.0 (#46695) --- recipes/rmats/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml index fb7233b0e8977..7e19cc620dc0d 100644 --- a/recipes/rmats/meta.yaml +++ b/recipes/rmats/meta.yaml @@ -1,12 +1,12 @@ {% set name = "rmats" %} -{% set version = "4.2.0" %} +{% set version = "4.3.0" %} package: name: {{ name }} version: {{ version }} source: - sha256: 7d5b56623e684c460a33b1709e0e2dc3ad13288d7db2be6c55c61f4fef880444 + sha256: c78e6411b7c6634cc31511b69d37a6a3da2e2e076e87609679818debd513aa7a url: https://github.com/Xinglab/rmats-turbo/releases/download/v{{ version }}/rmats_turbo_v{{ version|replace(".","_") }}.tar.gz build: From df2dafb71930b8330361d24c037d87283edce6de Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 11:01:21 -0400 Subject: [PATCH 1143/1813] Update pybiolib to 1.1.1909 (#46688) * Update pybiolib to 1.1.1890 * Update pybiolib to 1.1.1892 * Update pybiolib to 1.1.1896 * Update pybiolib to 1.1.1909 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 30221cbc876d2..d9a1f6089c3d0 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1881" %} +{% set version = "1.1.1909" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: beceb650d8708f7c2c2d537ac6f04acf3ed55818ed0df4a6512d6fdc4e119a94 + sha256: e73d45300253e2dcd147b4cb85ee07d33cdd28e17095e6209ec0a9997fddbeda build: noarch: python From 70d879491155b906c6ad899680c95e436314e38a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 11:02:03 -0400 Subject: [PATCH 1144/1813] Update gnparser to 1.9.1 (#46683) --- recipes/gnparser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml index 6c8f65f4ec4df..be751375ed4df 100644 --- a/recipes/gnparser/meta.yaml +++ b/recipes/gnparser/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.9.0" %} -{% set sha256 = "c326fe0398fafde9048f67962064cce741996a533e48180b27c5548e4b7289ab" %} +{% set version = "1.9.1" %} +{% set sha256 = "90090b57eb7b1c3f21cdb9abc37151d87e3f03268ddb82c0fd948c2403352501" %} package: name: "gnparser" From 1ff020bf16cdea16c65fc7fd44b5ec428d5573cc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 11:02:24 -0400 Subject: [PATCH 1145/1813] Update cazy_webscraper to 2.3.0.3 (#46725) --- recipes/cazy_webscraper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cazy_webscraper/meta.yaml b/recipes/cazy_webscraper/meta.yaml index 4e856fcf1d133..e46ee87c652f9 100644 --- a/recipes/cazy_webscraper/meta.yaml +++ b/recipes/cazy_webscraper/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cazy_webscraper" %} -{% set version = "2.3.0.2" %} -{% set sha256 = "4edd7f8f121bcab1c85af649c40c497490e8b5d5769e748536ce4c965daf5297" %} +{% set version = "2.3.0.3" %} +{% set sha256 = "82af3a5c13c1f3254bcbc9967c85d38f085c88f18834fb5a84155d5f13e669d9" %} package: name: {{ name|lower }} From 7ebd0d87a77592f2649ea1f265ce30ee1a74ef51 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 11:02:33 -0400 Subject: [PATCH 1146/1813] Update influx-si-data-manager to 1.0.1 (#46737) --- recipes/influx-si-data-manager/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/influx-si-data-manager/meta.yaml b/recipes/influx-si-data-manager/meta.yaml index dade7d4fe4c17..d61b76f9bbfd8 100644 --- a/recipes/influx-si-data-manager/meta.yaml +++ b/recipes/influx-si-data-manager/meta.yaml @@ -1,5 +1,5 @@ {% set name = "influx-si-data-manager" %} -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/influx_si_data_manager-{{ version }}.tar.gz - sha256: 0cea604084022f74b0886a7ce088cd1966f29cc35b2854b33b62545bafe84eb9 + sha256: 0deebc0d3359ffe00cea599ffaac69a1736ce2c7a9e9770e9cbf3eddd54fbdeb build: entry_points: From 0ae702a355a7b20023aec9b57c6bfe3286e60bef Mon Sep 17 00:00:00 2001 From: Bryce Kille Date: Mon, 25 Mar 2024 10:14:16 -0500 Subject: [PATCH 1147/1813] Add lemur v1.0.0 (#46666) * Add lemur v1.0.0 * Add run_exports --- recipes/lemur/meta.yaml | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 recipes/lemur/meta.yaml diff --git a/recipes/lemur/meta.yaml b/recipes/lemur/meta.yaml new file mode 100644 index 0000000000000..731b4749ab532 --- /dev/null +++ b/recipes/lemur/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "lemur" %} +{% set version = "1.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: 'https://github.com/treangenlab/lemur/archive/refs/tags/v{{version}}.tar.gz' + sha256: 591cc3d1d8a7ebb8b51486cb9c74b61dc39aeb8d8e3baf4d318e04278f9f6459 + +build: + run_exports: + - {{ pin_subpackage('lemur', max_pin="x") }} + noarch: generic + number: 0 + script: mkdir -p ${PREFIX}/bin && cp lemur ${PREFIX}/bin + +requirements: + run: + - python >=3.7 + - pysam >=0.15 + - numpy >=1.11 + - pandas >=1.1.3 + - minimap2 >=2.22 + +test: + commands: + - lemur --help + +about: + home: https://github.com/treangenlab/lemur + license: MIT + license_file: LICENSE + summary: Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets From 596e8c153bf0059b390f04223a2e196252c713de Mon Sep 17 00:00:00 2001 From: April Shen Date: Mon, 25 Mar 2024 15:39:29 +0000 Subject: [PATCH 1148/1813] Add eva-sub-cli recipe (#45929) * add eva-sub-cli recipe * fix indentation * add unzip * quiet unzip * add preserve_egg_dir * add node to run requirements * update meta with new conda dependencies * trigger pipeline --- recipes/eva-sub-cli/build.sh | 21 ++++++++++++ recipes/eva-sub-cli/meta.yaml | 60 +++++++++++++++++++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 recipes/eva-sub-cli/build.sh create mode 100644 recipes/eva-sub-cli/meta.yaml diff --git a/recipes/eva-sub-cli/build.sh b/recipes/eva-sub-cli/build.sh new file mode 100644 index 0000000000000..aa7198453931d --- /dev/null +++ b/recipes/eva-sub-cli/build.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +BIOVALIDATOR_VERSION=2.2.1 + +EVA_SUB_CLI="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}" +mkdir -p ${PREFIX}/bin ${EVA_SUB_CLI} + +# Install eva-sub-cli +$PYTHON -m pip install . +cp bin/* ${PREFIX}/bin +echo "Done with eva-sub-cli" + +cd ${EVA_SUB_CLI} + +# Install biovalidator from source +curl -Lo biovalidator.zip https://github.com/elixir-europe/biovalidator/archive/refs/tags/v${BIOVALIDATOR_VERSION}.zip \ + && unzip -q biovalidator.zip && rm biovalidator.zip \ + && cd biovalidator-${BIOVALIDATOR_VERSION} \ + && npm install && npm install -g \ + && cd .. +echo "Done with biovalidator" diff --git a/recipes/eva-sub-cli/meta.yaml b/recipes/eva-sub-cli/meta.yaml new file mode 100644 index 0000000000000..d60fc92c71c34 --- /dev/null +++ b/recipes/eva-sub-cli/meta.yaml @@ -0,0 +1,60 @@ +{% set name = "eva-sub-cli" %} +{% set version = "0.2" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/EBIvariation/eva-sub-cli/archive/v{{version}}.tar.gz + sha256: c997f72a93f13f03485274bf5f0468bfc9d5ed3082a9b81742eb21133aa35bff + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - nextflow >=21.10.0 + - python >=3.8 + - nodejs >=10.19.1 + - vcf-validator >=0.9.6 + - ebi-eva-common-pyutils >=0.6.1 + - pyyaml + - jinja2 + - openpyxl + - requests + - jsonschema + - unzip + run: + - nextflow >=21.10.0 + - python >=3.8 + - nodejs >=10.19.1 + - vcf-validator >=0.9.6 + - ebi-eva-common-pyutils >=0.6.1 + - pyyaml + - jinja2 + - openpyxl + - requests + - jsonschema + +test: + imports: + - eva_sub_cli + commands: + - biovalidator --help + - eva-sub-cli.py --help + +about: + home: https://github.com/EBIvariation/eva-sub-cli + summary: EVA Submission Command Line Interface + license: Apache-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - apriltuesday + - tcezard + - ebi-variation \ No newline at end of file From 5577b36f19fd138eda3905e1b3694b0d976405c5 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 25 Mar 2024 17:40:16 +0200 Subject: [PATCH 1149/1813] bamtools: add linux-aarch64 build (#46734) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bamtools/meta.yaml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/bamtools/meta.yaml b/recipes/bamtools/meta.yaml index 4b1e918f5bfae..803497b6c9a4b 100644 --- a/recipes/bamtools/meta.yaml +++ b/recipes/bamtools/meta.yaml @@ -1,7 +1,8 @@ +{% set name = "bamtools" %} {% set version = "2.5.2" %} package: - name: bamtools + name: {{ name }} version: {{ version }} source: @@ -11,7 +12,9 @@ source: # - 0001-Const-qualify-all-functors-operator-member-functions.patch build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: build: @@ -32,5 +35,7 @@ about: summary: C++ API & command-line toolkit for working with BAM data extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:bamtools From b1a5bf6547a6aac1668b23a5e54abc7d43279ad5 Mon Sep 17 00:00:00 2001 From: Bob <55469084+yhhan19@users.noreply.github.com> Date: Mon, 25 Mar 2024 11:48:15 -0400 Subject: [PATCH 1150/1813] Update TREE-QMC to 3.0.1 (#46738) * tqmc * build.sh fixed * "folder_and_package_name_must_match" fixed * missing_run_exports fixed * g++ not found fix * build error fixed * build error fix * build.sh fix * osx compilation fix * made the name and version number consistent * minor * tree-qmc 3.0.0 updates * tree-qmc 3.0.0 updates * build.sh fixed * build.sh fixed * build.sh fixed * build.sh * build.sh * debug * build * v3.0.1 --- recipes/tree-qmc/build.sh | 6 +++--- recipes/tree-qmc/meta.yaml | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/tree-qmc/build.sh b/recipes/tree-qmc/build.sh index 1577713af44f0..34621c3bee530 100644 --- a/recipes/tree-qmc/build.sh +++ b/recipes/tree-qmc/build.sh @@ -4,10 +4,10 @@ make cd ../.. $CXX -std=c++11 -O2 \ -I external/MQLib/include -I external/toms743 \ - -o TREE-QMC \ + -o tree-qmc \ src/*.cpp external/toms743/toms743.cpp \ external/MQLib/bin/MQLib.a -lm \ -DVERSION=\"$(cat version.txt)\" mkdir -p $PREFIX/bin -cp TREE-QMC $PREFIX/bin/ -chmod a+x $PREFIX/bin/TREE-QMC +cp tree-qmc $PREFIX/bin/ +chmod a+x $PREFIX/bin/tree-qmc diff --git a/recipes/tree-qmc/meta.yaml b/recipes/tree-qmc/meta.yaml index a4d3178e290d8..2925ea75e649c 100644 --- a/recipes/tree-qmc/meta.yaml +++ b/recipes/tree-qmc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "TREE-QMC" %} -{% set version = "3.0.0" %} +{% set version = "3.0.1" %} package: @@ -7,8 +7,8 @@ package: version: "{{ version }}" source: - url: https://github.com/molloy-lab/{{ name|upper }}/archive/refs/tags/v3-f40cc44.zip - sha256: cdabdc24b2f2f203fe0c075227d61d66e78155fca91e7fe3a32d162abb6216f0 + url: https://github.com/molloy-lab/{{ name|upper }}/archive/refs/tags/v{{ version }}.zip + sha256: 0fc11b22d981cbf62ee3d832ed79ac7dbf526669231b0137fd4e4756a0af506c build: number: 0 @@ -24,7 +24,7 @@ requirements: test: commands: - - TREE-QMC -h + - tree-qmc -h about: home: https://github.com/molloy-lab/TREE-QMC From 8e8fdddd85bdf750da7d0366787f5f8c50375c7d Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 25 Mar 2024 18:03:09 +0200 Subject: [PATCH 1151/1813] seqtk: add linux-aarch64 build (#46730) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/seqtk/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/seqtk/meta.yaml b/recipes/seqtk/meta.yaml index df6b2e5bb7c06..6425b4714964d 100644 --- a/recipes/seqtk/meta.yaml +++ b/recipes/seqtk/meta.yaml @@ -12,7 +12,9 @@ source: - 0001-makefile.patch build: - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage('seqtk', max_pin="x.x") }} requirements: build: @@ -33,5 +35,7 @@ about: summary: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:seqtk From 7c034124870bce2d3fcdabb3cff113d44eea84af Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 12:15:59 -0400 Subject: [PATCH 1152/1813] Update dajin2 to 0.4.2 (#46722) --- recipes/dajin2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index 2c1bd818cfbc1..5ffd4d0f18afd 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: 5a0c360cf52d506c1c60ba94a13f408a2789c66443ba92f3d2a6f1a7acd0aa3e + sha256: 34f25000f2f2d0c7ff40163cd68f2702549b7ae703cf9c665f3a208601f549fa build: entry_points: From 6b6d811cd531ffcb0f25053ba0c3ce753038b4da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 25 Mar 2024 17:40:43 +0100 Subject: [PATCH 1153/1813] update dimet for Ben (#46739) --- recipes/dimet/meta.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/recipes/dimet/meta.yaml b/recipes/dimet/meta.yaml index 80d5d1ce73a27..3dbed3022c530 100644 --- a/recipes/dimet/meta.yaml +++ b/recipes/dimet/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python script: {{ PYTHON }} -m pip install . -vv - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -28,15 +28,15 @@ requirements: - coverage - hydra-colorlog >=1.2.0,<1.3.0 - hydra-core >=1.3.2,<1.4.0 - - matplotlib-base >=3.7.1,<3.8.0 - - numpy >=1.23.1,<1.24.0 - - pandas >=1.5.3,<1.6.0 - - pydantic >=1.10.8,<2.0.0 + - matplotlib-base >=3.8.3 + - numpy >=1.26.4 + - pandas >=2.2.0 + - pydantic >=2.6.1 - python-dotenv >=1.0,<2.0 - pyyaml >=6.0,<7.0 - - scikit-learn >=1.1.1,<1.2.0 + - scikit-learn >=1.4.0 - scipy >=1.9.1,<1.10.0 - - seaborn >=0.11.2,<0.12.0 + - seaborn >=0.13.2 - statsmodels >=0.13.5,<0.14.0 test: @@ -44,7 +44,7 @@ test: - dimet about: home: https://github.com/cbib/DIMet.git - summary: A tool for Differential Isotope-labeled targeted Metabolomics + summary: A tool for Differential Isotope-labeled targeted Metabolomics data license: MIT license_file: LICENSE From fb0d1e40a9691ec24e79ed379d1e18ac8a7fcb47 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 13:58:43 -0400 Subject: [PATCH 1154/1813] Update bioconda-utils to 2.13.0 (#46740) * Update bioconda-utils to 2.13.0 * update requirements to match bioconda-utils repo --------- Co-authored-by: aliciaaevans --- recipes/bioconda-utils/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index e6f5a9ee840bb..565f668029366 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.12.0" %} -{% set sha256 = "b481f5232f55e53decc732856604d4e949a85522804efe1ec8f9edb45f065ca5" %} +{% set version = "2.13.0" %} +{% set sha256 = "cee55582cc6f0f9a489e90d5f43e4171700f6140360031899e057a13c183a745" %} package: name: bioconda-utils @@ -52,12 +52,12 @@ requirements: - aiohttp-security - aiofiles 0.8.* - aioftp 0.12.* - - backoff 1.6.* + - backoff 2.2.* - cachetools 3.0.* - gitpython >=3.0.8,3.0.* - gidgethub 3.0.* - pyjwt >=2.4.0 - - beautifulsoup4 4.8.* + - beautifulsoup4 4.12.* - galaxy-lib >=18.9.1 - jinja2 >2.10.1,<3 - markupsafe <2.1 @@ -68,7 +68,7 @@ requirements: - docutils - markdown - graphviz - - requests 2.22.* + - requests 2.29.* - pygithub 1.* - diskcache 5.* - appdirs 1.* From d7c029cab51dbe8db66702e1f55195a009a68bb3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 14:07:40 -0400 Subject: [PATCH 1155/1813] Update influx-si-data-manager to 1.0.2 (#46741) --- recipes/influx-si-data-manager/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/influx-si-data-manager/meta.yaml b/recipes/influx-si-data-manager/meta.yaml index d61b76f9bbfd8..5165c63acd2c4 100644 --- a/recipes/influx-si-data-manager/meta.yaml +++ b/recipes/influx-si-data-manager/meta.yaml @@ -1,5 +1,5 @@ {% set name = "influx-si-data-manager" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/influx_si_data_manager-{{ version }}.tar.gz - sha256: 0deebc0d3359ffe00cea599ffaac69a1736ce2c7a9e9770e9cbf3eddd54fbdeb + sha256: 5bac948f0c781e50a7e47f746cb7fc71f1f5de1182356a8b6952f0a622bd8fe8 build: entry_points: From cbbd362f2f2a64210be212fad539d37eb259ec31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 14:07:52 -0400 Subject: [PATCH 1156/1813] Update vcfdist to 2.5.1 (#46743) --- recipes/vcfdist/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vcfdist/meta.yaml b/recipes/vcfdist/meta.yaml index 855ce4f6f418c..7936d92329652 100644 --- a/recipes/vcfdist/meta.yaml +++ b/recipes/vcfdist/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.5.0" %} -{% set sha256 = "d48c95902c9a700049003018ae28a9684d6b320235cf152f418a544f63aa6e7d" %} +{% set version = "2.5.1" %} +{% set sha256 = "25d7d8c8613cfcfb1c582edbe09d20d1d3cb7de6fd6d18c0b83ac4d8195637a3" %} package: name: vcfdist From 6973c753c1ee2293bc7ad26c1667a80852183969 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Tue, 26 Mar 2024 03:00:41 +0800 Subject: [PATCH 1157/1813] linux-aarch64 build for alignstats (#46635) * linux-aarch64 build for alignstats * linux-aarch64 build for alignstats * Update meta.yaml --------- Co-authored-by: yejianbang Co-authored-by: yejianbang <145335562+yejianbang@users.noreply.github.com> --- recipes/alignstats/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/alignstats/meta.yaml b/recipes/alignstats/meta.yaml index 009b1ec52d685..645cec41b08ca 100644 --- a/recipes/alignstats/meta.yaml +++ b/recipes/alignstats/meta.yaml @@ -10,7 +10,9 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage("alignstats", max_pin="x.x.x") }} requirements: build: @@ -33,3 +35,7 @@ about: home: https://github.com/jfarek/alignstats license: BSD-3-Clause summary: Comprehensive alignment, whole-genome coverage, and capture coverage statistics. + +extra: + additional-platforms: + - linux-aarch64 From 43526016a9c8af7c7d3e2f880deae820ae3cd4b3 Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Mon, 25 Mar 2024 20:02:13 +0100 Subject: [PATCH 1158/1813] update umi_tools adding new platform (#46598) --- recipes/umi_tools/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/umi_tools/meta.yaml b/recipes/umi_tools/meta.yaml index 8a309583a61c8..c7f05cab66524 100644 --- a/recipes/umi_tools/meta.yaml +++ b/recipes/umi_tools/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256hash }} build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" skip: True # [py27] entry_points: @@ -47,3 +47,7 @@ about: summary: 'Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs)' dev_url: https://github.com/CGATOxford/UMI-tools + +extra: + additional-platforms: + - linux-aarch64 From 8c6c87657a53e8454accc66009ff58316b7348b6 Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Mon, 25 Mar 2024 15:08:18 -0400 Subject: [PATCH 1159/1813] updated pyrodigal >=3.0 due to new feature for locidex (#46742) --- recipes/locidex/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/locidex/meta.yaml b/recipes/locidex/meta.yaml index ea40a8732b724..19946a13bd778 100644 --- a/recipes/locidex/meta.yaml +++ b/recipes/locidex/meta.yaml @@ -12,7 +12,7 @@ source: build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -31,7 +31,7 @@ requirements: - numba >=0.57.1 - pytables >=3.8 - six >=1.16 - - pyrodigal + - pyrodigal >=3.0 - biopython >=1.83 - mafft - blast >=2.9.0 From 2460065848419e00202db53141f6a980974009dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 15:15:18 -0400 Subject: [PATCH 1160/1813] Update condiga to 0.2.2 (#46675) * Update condiga to 0.2.2 * add run_exports --------- Co-authored-by: mencian --- recipes/condiga/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/condiga/meta.yaml b/recipes/condiga/meta.yaml index 49725a4d226b7..bc43a45207ab8 100644 --- a/recipes/condiga/meta.yaml +++ b/recipes/condiga/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ConDiGA" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/metagentools/{{ name }}/archive/v{{ version }}.tar.gz" - sha256: adde1cc9808f3d1b174309affc385464880968a33434f2de411e099686c1aec2 + sha256: 492bcf86bfceff50af12c230e98284f9422330d6d2840280c0eb3fed3fd843ed build: number: 0 @@ -15,14 +15,16 @@ build: entry_points: - convert=condiga_utils.support.convert:main script: - - "{{ PYTHON }} -m pip install . -vv" + - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('condiga', max_pin="x.x") }} requirements: host: - pip - - python + - python >=3.8 run: - - python + - python >=3.8 - click - biopython - xlsxwriter From 847bf816cc94cd8e234613eef959840407f97353 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 15:16:08 -0400 Subject: [PATCH 1161/1813] Update anvio-minimal to 8 (#43417) * Update anvio-minimal to 8 * Update anvio-minimal to 8 * add run_exports * edit dependencies * Update anvio-minimal to 8 * Update anvio-minimal to 8 * Update anvio-minimal to 8 * add multiprocess * add rich-argparse --------- Co-authored-by: joshuazhuang7 Co-authored-by: Thanh Lee Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/anvio-minimal/meta.yaml | 31 +++++++++++++++++++++---------- 1 file changed, 21 insertions(+), 10 deletions(-) diff --git a/recipes/anvio-minimal/meta.yaml b/recipes/anvio-minimal/meta.yaml index 4c1d381c9b90f..8cd80ff415df2 100644 --- a/recipes/anvio-minimal/meta.yaml +++ b/recipes/anvio-minimal/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "7.1" %} -{% set sha256 = "5ff729ba392a530b200378cd55e0dd85032152da44dce0260daef2ddc3122c99" %} +{% set version = "8" %} +{% set sha256 = "4ced91773648d9ca27a20b725ab64bc213d80b33726940f5f818240033912c04" %} package: name: anvio-minimal @@ -12,7 +12,9 @@ source: build: number: 0 noarch: python - script: python -m pip install --no-deps --ignore-installed -vv . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir -vvv . + run_exports: + - {{ pin_subpackage('anvio-minimal', max_pin="x.x") }} requirements: host: @@ -20,18 +22,18 @@ requirements: - pip run: - python >=3 - - numpy + - numpy <=1.24 - bottle - pysam - ete3 - scipy - - scikit-learn <0.21 + - scikit-learn ==1.2.2 - django - requests - - psutil ==5.4.3 + - psutil - mistune - six - - pandas ==0.25.1 + - pandas ==1.4.4 - matplotlib-base - statsmodels - colored @@ -40,24 +42,33 @@ requirements: - numba - sqlite >=3.31.1 - paste + - multiprocess + - rich-argparse + - plotext + - networkx # these three are critical versions. any changes must be # tested with extra attention: - pyani ==0.2.10 - snakemake-minimal ==5.10.0 + test: commands: - anvi-pan-genome --help - anvi-script-reformat-fasta --help about: - home: http://merenlab.org/software/anvio/ + home: https://merenlab.org/software/anvio/ license: GPL-3.0-or-later license_family: GPL3 license_file: LICENSE.txt summary: "An interactive analysis and visualization platform for omics data" - dev_url: https://github.com/merenlab/anvio - + dev_url: https://github.com/merenlab/anvio + doc_url: https://anvio.org/learn/ + extra: container: # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly extended-base: True + identifiers: + - biotools:anvio + - doi:10.1038/s41564-020-00834-3 From d50dd6275bf75a22dd4f85adc06e59f99710bd3e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 15:37:34 -0400 Subject: [PATCH 1162/1813] Update hapog to 1.3.8 (#46680) * Update hapog to 1.3.8 * add zlib --------- Co-authored-by: mencian --- recipes/hapog/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/hapog/meta.yaml b/recipes/hapog/meta.yaml index 525046c08f7e6..295b5552dc1d6 100644 --- a/recipes/hapog/meta.yaml +++ b/recipes/hapog/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.7" %} +{% set version = "1.3.8" %} package: name: hapog @@ -12,7 +12,7 @@ build: source: url: https://github.com/institut-de-genomique/HAPO-G/archive/refs/tags/{{ version }}.tar.gz - sha256: "727ff2a712b046c7787ac2bb599a7e3808f70219d6b7e22ddfc5942ba38c5841" + sha256: "822f4c7e688ae2b3004ac444911b592beaa25db6800b766503c1d41f0290af4b" requirements: build: @@ -22,11 +22,10 @@ requirements: host: - python - htslib - - setuptools + - zlib run: - htslib - python - - setuptools - biopython - bwa - samtools @@ -45,6 +44,8 @@ about: license_family: OTHER license_file: LICENSE.md summary: Haplotype-Aware Polishing of Genomes + doc_url: https://www.genoscope.cns.fr/hapog/ + dev_url: https://github.com/institut-de-genomique/HAPO-G extra: identifiers: From d4009e29d92f9d2390c15d5ae32e83a0d627a5a4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 15:45:11 -0400 Subject: [PATCH 1163/1813] Update magus-msa to 0.2.0 (#46726) * Update magus-msa to 0.2.0 * edit tests * edit tests --------- Co-authored-by: mencian --- recipes/magus-msa/meta.yaml | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/recipes/magus-msa/meta.yaml b/recipes/magus-msa/meta.yaml index feb4112d6441e..93ad68e11ed02 100644 --- a/recipes/magus-msa/meta.yaml +++ b/recipes/magus-msa/meta.yaml @@ -1,6 +1,6 @@ {% set name = "magus-msa" %} -{% set version = "0.1.3" %} -{% set sha256 = "de96170bd768a15d07e03724fc4f32b6c7cb8992e2cd259a45f1371363b6a7c1" %} +{% set version = "0.2.0" %} +{% set sha256 = "4152ab0d5cedfe0691dc1a3fce2cd38e3549bcd0883227a346cc47f093570141" %} package: name: {{ name }} @@ -13,15 +13,16 @@ source: build: noarch: python number: 0 - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv + entry_points: + - magus = magus.main:main run_exports: - - {{ pin_subpackage('magus-msa', max_pin="x") }} + - {{ pin_subpackage('magus-msa', max_pin="x.x") }} requirements: host: - python >=3.6 - pip - - setuptools run: - python >=3.6 - dendropy >=4.5.2 @@ -32,23 +33,20 @@ requirements: - hmmer test: - imports: - - magus_align - - magus_align.decompose - - magus_align.merge - - magus_align.merge.graph_build - - magus_align.merge.graph_cluster - - magus_align.merge.graph_trace - - magus_helpers - - magus_tasks - - magus_tools commands: - magus --help about: home: "https://github.com/vlasmirnov/MAGUS" license: MIT + license_family: MIT + license_file: LICENSE.txt summary: "Multiple Sequence Alignment using Graph Clustering" doc_url: "https://github.com/vlasmirnov/MAGUS/blob/master/README.md" dev_url: "https://github.com/vlasmirnov/MAGUS" + +extra: + identifiers: + - biotools:magus + - doi:10.1093/bioinformatics/btaa992 From 81931613f78e32fed008a5a1f728b1a13e327d89 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 16:14:22 -0400 Subject: [PATCH 1164/1813] Update treeqmc to 3.0.1 (#46696) * Update treeqmc to 3.0.1 * Update treeqmc to 3.0.3 * update meta.yaml * add recipe to blacklist --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian Co-authored-by: Robert A. Petit III --- build-fail-blacklist | 3 +++ recipes/treeqmc/build.sh | 22 ++++++++++++++-------- recipes/treeqmc/meta.yaml | 12 ++++++------ 3 files changed, 23 insertions(+), 14 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 8f4d12ec4436f..73519fd680f0d 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1061,3 +1061,6 @@ recipes/mudskipper # md5 mismatch when downloading source recipes/komb + +# duplicate recipe +recipes/treemqc diff --git a/recipes/treeqmc/build.sh b/recipes/treeqmc/build.sh index afeec38073355..56130c62a04c3 100644 --- a/recipes/treeqmc/build.sh +++ b/recipes/treeqmc/build.sh @@ -1,9 +1,15 @@ -cd MQLib -make \ - GXX="${CXX}" \ - AR="${AR}" -cd .. -$CXX -std=c++11 -O2 -I MQLib/include -o TREE-QMC src/*.cpp MQLib/bin/MQLib.a +#!/bin/bash + +cd external/MQLib +sed -i.bak "s#g++#${CXX}#" Makefile +make +cd ../.. +$CXX -std=c++11 -O2 \ + -I external/MQLib/include -I external/toms743 \ + -o tree-qmc \ + src/*.cpp external/toms743/toms743.cpp \ + external/MQLib/bin/MQLib.a -lm \ + -DVERSION=\"$(cat version.txt)\" mkdir -p $PREFIX/bin -cp TREE-QMC $PREFIX/bin/ -chmod a+x $PREFIX/bin/TREE-QMC +cp tree-qmc $PREFIX/bin/ +chmod a+x $PREFIX/bin/tree-qmc diff --git a/recipes/treeqmc/meta.yaml b/recipes/treeqmc/meta.yaml index 2af0d99783ba1..47e3e64294ac8 100644 --- a/recipes/treeqmc/meta.yaml +++ b/recipes/treeqmc/meta.yaml @@ -1,13 +1,13 @@ {% set name = "TREEQMC" %} -{% set version = "2.0.0" %} +{% set version = "3.0.1" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/molloy-lab/TREE-QMC/releases/download/2.0.0/TREE-QMC-2.0.0.zip - sha256: f8530dd6d106c63ffde0d728eeef835b8bded16e69620e78bd45f562129f86a9 + url: https://github.com/molloy-lab/TREE-QMC/archive/refs/tags/v{{ version }}.zip + sha256: 0fc11b22d981cbf62ee3d832ed79ac7dbf526669231b0137fd4e4756a0af506c build: number: 0 @@ -18,14 +18,14 @@ requirements: build: - make - {{ compiler('cxx') }} - host: - run: test: commands: - - TREE-QMC -h + - tree-qmc -h about: home: https://github.com/molloy-lab/TREE-QMC license: MIT + license_family: MIT summary: TREE-QMC is a quartet-based method for estimating species trees from gene trees. + dev_url: https://github.com/molloy-lab/TREE-QMC From c6e5c80d0de43c982d63b383b1cad4ec11674e4d Mon Sep 17 00:00:00 2001 From: pabloaledo <112545720+pabloaledo@users.noreply.github.com> Date: Mon, 25 Mar 2024 21:16:32 +0100 Subject: [PATCH 1165/1813] update ucsc-bedclip (#46686) * remove specific cpu flag * bump build number --------- Co-authored-by: mencian --- recipes/ucsc-bedclip/build.sh | 4 ++-- recipes/ucsc-bedclip/meta.yaml | 3 +-- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/ucsc-bedclip/build.sh b/recipes/ucsc-bedclip/build.sh index d77ce6d815f3a..a0d9457e75286 100644 --- a/recipes/ucsc-bedclip/build.sh +++ b/recipes/ucsc-bedclip/build.sh @@ -2,8 +2,8 @@ if [ $(arch) = "aarch64" ] then - export CFLAGS+=" -O3 -mcpu=neoverse-n1 " - export CPPFLAGS+=" -O3 -mcpu=neoverse-n1 " + export CFLAGS+=" -O3 " + export CPPFLAGS+=" -O3 " else export MACHTYPE=x86_64 fi diff --git a/recipes/ucsc-bedclip/meta.yaml b/recipes/ucsc-bedclip/meta.yaml index 6501ba30fd427..b985207becc8a 100644 --- a/recipes/ucsc-bedclip/meta.yaml +++ b/recipes/ucsc-bedclip/meta.yaml @@ -16,7 +16,7 @@ source: build: skip: True # [osx] - number: 3 + number: 4 run_exports: - {{ pin_subpackage("ucsc-bedclip", max_pin=None) }} @@ -30,7 +30,6 @@ requirements: - mysql-connector-c - openssl - zlib - run: - libpng - libuuid From 67a79f3fe7b946814b859ea5526079ff2ce2859a Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Mon, 25 Mar 2024 14:41:12 -0600 Subject: [PATCH 1166/1813] add treeqmc to blacklist (#46746) --- build-fail-blacklist | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 73519fd680f0d..94d6a11bd8263 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1063,4 +1063,4 @@ recipes/mudskipper recipes/komb # duplicate recipe -recipes/treemqc +recipes/treeqmc From d2b9f213020f9986ea1b989ea90246f4bfe5ad34 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 25 Mar 2024 17:45:36 -0500 Subject: [PATCH 1167/1813] Update gmap to 2024.03.15 (#46745) * Update gmap to 2024.03.15 * edit build.sh * revert to skipping OSX & enable aarch64 build * revert to linux only --- recipes/gmap/build.sh | 4 ++++ recipes/gmap/meta.yaml | 4 ++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/gmap/build.sh b/recipes/gmap/build.sh index f8c4331734fc6..2597b241bce1d 100644 --- a/recipes/gmap/build.sh +++ b/recipes/gmap/build.sh @@ -12,6 +12,10 @@ if [ "$(uname)" == "Darwin" ]; then export CFLAGS="${CFLAGS} -m64" fi +export LANGUAGE=en_US.UTF-8 +export LANG=en_US.UTF-8 +export LC_ALL=en_US.UTF-8 + autoreconf -if ./configure CC="${CC}" CFLAGS="${CFLAGS}" \ CPPFLAGS="${CPPFLAGS}" \ diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index c4d1ffcb146e2..89862ec6db554 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GMAP" %} -{% set version = "2024.02.22" %} -{% set sha256 = "d528c2d9554cb5f98f805eebb412c58297125edb1e7164dba6bbc2f72ff2204c" %} +{% set version = "2024.03.15" %} +{% set sha256 = "b3004175a06e3111d93021f0cd4d826ffa40ac4d069a2fa5db19fdaaa09fab3d" %} package: name: {{ name|lower }} From cff90c7a75dfd3ff648e5e7339f9b33097feb944 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 18:56:32 -0400 Subject: [PATCH 1168/1813] Update arcs to 1.2.7 (#46749) --- recipes/arcs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/arcs/meta.yaml b/recipes/arcs/meta.yaml index e32cd8699d69f..761927d7f9309 100644 --- a/recipes/arcs/meta.yaml +++ b/recipes/arcs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.6" %} +{% set version = "1.2.7" %} package: name: arcs @@ -11,7 +11,7 @@ build: source: url: https://github.com/bcgsc/arcs/releases/download/v{{ version }}/arcs-{{ version }}.tar.gz - sha256: 6efc120d55212bfb0483a262731827318ec0a5f037d4984da8445cc3788ba297 + sha256: 3162cff3286a033b494ace8050abc96d4083f846cafe921bb0122170f705eca8 requirements: build: From b5a7e782a2456f3b7eae28082b5329637f545570 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 25 Mar 2024 18:34:54 -0500 Subject: [PATCH 1169/1813] Update scib recipe (#46748) --- recipes/scib/meta.yaml | 32 +++++++++++++++++++------------- 1 file changed, 19 insertions(+), 13 deletions(-) diff --git a/recipes/scib/meta.yaml b/recipes/scib/meta.yaml index a8598ccf3891c..f33f37de8a644 100644 --- a/recipes/scib/meta.yaml +++ b/recipes/scib/meta.yaml @@ -1,31 +1,29 @@ {% set name = "scib" %} {% set version = "1.1.4" %} - package: name: "{{ name|lower }}" version: "{{ version }}" build: - number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + number: 1 + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" skip: True # [ py < 37 or py > 311] run_exports: - - {{ pin_subpackage(name, max_pin='x.x') }} + - {{ pin_subpackage(name, max_pin='x') }} source: - url: https://github.com/theislab/scib/archive/v{{ version }}.tar.gz - sha256: aebdad725b58a0bf8f3660a57e1ab81a06845632bb1b6cf9c64f6378d191154b + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/scib-{{ version }}.tar.gz + sha256: b7800f308cd6acc36db6e159a53b0432adb2f48e9b7b434240bc5d696df10bfb patches: - setup_compiler.patch requirements: + build: + - {{ compiler('cxx') }} host: - python - pip - - setuptools - build: - - {{ compiler('cxx') }} run: - anndata >=0.7.2 - deprecated @@ -35,7 +33,7 @@ requirements: - llvmlite - matplotlib-base - numpy - - pandas + - pandas <2 - pydot - python - scanpy >=1.5 @@ -46,10 +44,18 @@ requirements: - umap-learn test: - commands: - - python3 -c "import scib; print(scib.__version__)" + imports: + - scib about: home: https://github.com/theislab/scib license: MIT - summary: "Evaluating single-cell data integration methods" \ No newline at end of file + license_family: MIT + license_file: LICENSE.txt + summary: "Evaluating single-cell data integration methods" + doc_url: https://scib.readthedocs.io/en/latest/ + dev_url: https://github.com/theislab/scib + +extra: + identifiers: + - doi:10.1038/s41592-021-01336-8 From 0e10ab13c539c403e593ccc05abc9bb0022cfaf2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 22:33:22 -0400 Subject: [PATCH 1170/1813] Update phold to 0.1.4 (#46751) --- recipes/phold/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phold/meta.yaml b/recipes/phold/meta.yaml index 44650fb63f6e9..fd6985bdd47e0 100644 --- a/recipes/phold/meta.yaml +++ b/recipes/phold/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phold" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: a89c24d063784fa3a318ccc795fff3c5d2d8c00b4ed22bb8ee188052871778e7 + sha256: 660283dae06b866a0b903d098252288a382cb2d72a8adcc1e9a5e38a5547d9b3 build: number: 0 From fcddf016cccd9228ebc18a40be5c700a81dfe1fc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 25 Mar 2024 23:45:36 -0400 Subject: [PATCH 1171/1813] Update pangu to 0.2.6 (#46752) --- recipes/pangu/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangu/meta.yaml b/recipes/pangu/meta.yaml index ee811a1024ba7..17fe86f5d9ce6 100644 --- a/recipes/pangu/meta.yaml +++ b/recipes/pangu/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.5" %} -{% set sha256 = "3ad9f4e93fe237d41fe2d06a1798d24dc3018a0a59f0133b3bd2cb1f79c1b0b0" %} +{% set version = "0.2.6" %} +{% set sha256 = "0484e73185bbed3d54e7a000cf2f0749871589d694dfe7b7d276aaad2892f9a3" %} package: name: pangu From 7614da4368a1007c10cb7d242b7f4b96ba35f792 Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" <19176506+pdimens@users.noreply.github.com> Date: Tue, 26 Mar 2024 00:20:15 -0400 Subject: [PATCH 1172/1813] Harpy 0.8.0 + recipe change (#46658) * update build recipe * specify current version --- recipes/harpy/meta.yaml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index 811932262d836..8c458665b2709 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.3" %} -{% set sha256 = "0ed76b2be37bbb6529f3cefbd3b8587f33ddb90afdd53931d99230b8af642668" %} +{% set version = "0.8.0" %} +{% set sha256 = "40314dba83fc20e7f57bcacc706eed3bd6c52391327c1b10b5ba41aa5ae0d4f0" %} package: name: harpy @@ -20,16 +20,14 @@ build: requirements: host: - - python =3.10 + - python =3.12 - pip run: - bcftools =1.19 - - multiqc - pandas - - pysam =0.22 - - python =3.10 + - python >3.10 - rich-click - - snakemake-minimal + - snakemake-minimal >7 - samtools - seqtk - tabix From 5230b11688d6613fcabebc695e1535d066c6ab07 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 26 Mar 2024 06:27:20 +0200 Subject: [PATCH 1173/1813] raxml: add linux-aarch64 build (#46469) * raxml: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Disable the tests which are x86_64/AVX specific Signed-off-by: Martin Tzvetanov Grigorov * try build selector * try build selector --------- Signed-off-by: Martin Tzvetanov Grigorov Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/raxml/build.sh | 7 +++++++ recipes/raxml/meta.yaml | 8 +++++--- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/recipes/raxml/build.sh b/recipes/raxml/build.sh index 7a51b016595ca..6dd8706245751 100644 --- a/recipes/raxml/build.sh +++ b/recipes/raxml/build.sh @@ -6,10 +6,17 @@ Linux) SUF=.gcc;; *) echo "Unknown architecture"; exit 1;; esac +ARCH=$(uname -m) + mkdir -p $PREFIX/bin for PTHREADS in "" .PTHREADS; do for OPT in "" .SSE3 .AVX2; do + + if [ "${ARCH}" == "aarch64" -a "${OPT}" == ".AVX2" ]; then + continue + fi + echo "######## Building Flags opt=$OPT pthread=$PTHREADS os=$SUF ######" MAKEFILE=Makefile${OPT}${PTHREADS} if [ -e ${MAKEFILE}${SUF} ]; then diff --git a/recipes/raxml/meta.yaml b/recipes/raxml/meta.yaml index 87550af90f582..b98b2551cc414 100644 --- a/recipes/raxml/meta.yaml +++ b/recipes/raxml/meta.yaml @@ -3,7 +3,7 @@ package: version: "8.2.13" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('raxml', max_pin="x") }} @@ -22,8 +22,8 @@ test: - raxmlHPC-PTHREADS -h > /dev/null - raxmlHPC-SSE3 -h > /dev/null - raxmlHPC-PTHREADS-SSE3 -h > /dev/null - - raxmlHPC-AVX2 -h > /dev/null - - raxmlHPC-PTHREADS-AVX2 -h > /dev/null + - 'raxmlHPC-AVX2 -h > /dev/null' # [not aarch64] + - 'raxmlHPC-PTHREADS-AVX2 -h > /dev/null' # [not aarch64] about: home: http://sco.h-its.org/exelixis/web/software/raxml/index.html @@ -31,6 +31,8 @@ about: summary: Phylogenetics - Randomized Axelerated Maximum Likelihood. extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:raxml - doi:10.1093/bioinformatics/btu033 From af4414b0d6751a0c0324cfee29e785d53cea4d24 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 26 Mar 2024 00:49:35 -0500 Subject: [PATCH 1174/1813] wfa2-lib: enable linux-aarch64 build (#46753) * wfa2-lib: enable linux-aarch64 build * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh --- recipes/wfa2-lib/build.sh | 12 ++++++++++-- recipes/wfa2-lib/meta.yaml | 6 +++++- recipes/wfa2-lib/patches/1-macOS_endian.patch | 10 +++++----- 3 files changed, 20 insertions(+), 8 deletions(-) diff --git a/recipes/wfa2-lib/build.sh b/recipes/wfa2-lib/build.sh index 523f810bac3b2..c8b9552cd5b41 100644 --- a/recipes/wfa2-lib/build.sh +++ b/recipes/wfa2-lib/build.sh @@ -5,13 +5,21 @@ export C_INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +ARCH=$(uname -m) + +if [ "${ARCH}" == "aarch64" ]; then + export EXTRA_FLAGS="-ftree-vectorize" +else + export EXTRA_FLAGS="-ftree-vectorize -msse2 -mfpmath=sse" +fi + cmake -S . -B build \ -DCMAKE_CXX_COMPILER="${CXX}" \ -DCMAKE_C_COMPILER="${CC}" \ -DCMAKE_CXX_FLAGS="-O3 -D_FILE_OFFSET_BITS=64 -I${PREFIX}/include ${LDFLAGS}" \ - -DEXTRA_FLAGS="-ftree-vectorize -msse2 -mfpmath=sse" \ + -DEXTRA_FLAGS="${EXTRA_FLAGS}" \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ - -DBUILD_SHARED_LIBS=ON + -DOPENMP=TRUE cmake --build build/ --target install -v diff --git a/recipes/wfa2-lib/meta.yaml b/recipes/wfa2-lib/meta.yaml index d5ceb2b683486..82dd47e20f99c 100644 --- a/recipes/wfa2-lib/meta.yaml +++ b/recipes/wfa2-lib/meta.yaml @@ -13,7 +13,7 @@ source: - patches/1-macOS_endian.patch # [osx] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -25,6 +25,8 @@ requirements: host: - pkg-config - rhash # [osx] + - libgomp # [linux or aarch64] + - llvm-openmp # [osx] test: commands: @@ -42,3 +44,5 @@ extra: identifiers: - doi:10.1093/bioinformatics/btaa777 - doi:10.1101/2022.04.14.488380 + additional-platforms: + - linux-aarch64 diff --git a/recipes/wfa2-lib/patches/1-macOS_endian.patch b/recipes/wfa2-lib/patches/1-macOS_endian.patch index 5e6f8206b8b9b..309ffb4a13a45 100644 --- a/recipes/wfa2-lib/patches/1-macOS_endian.patch +++ b/recipes/wfa2-lib/patches/1-macOS_endian.patch @@ -6,11 +6,11 @@ index 7600442..a1fab79 100644 */ -#include -+#ifdef __APPLE__ || defined(__FreeBSD__) -+ #include // __BYTE_ORDER -+ #else -+ #include // __BYTE_ORDER -+ #endif ++#if defined(__APPLE__) || defined(__FreeBSD__) ++#include // __BYTE_ORDER ++#else ++#include // __BYTE_ORDER ++#endif #include "wavefront_extend_kernels.h" #include "wavefront_termination.h" From 865249ff4b809f8b3740d1527bcacac5332e176c Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 26 Mar 2024 02:18:58 -0500 Subject: [PATCH 1175/1813] tabixpp: enable linux-aarch64 build (#46754) * tabixpp: enable linux-aarch64 build * try without patch * try without patch 2 --- recipes/tabixpp/meta.yaml | 8 +++++--- recipes/tabixpp/shared_lib.patch | 5 +++-- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/tabixpp/meta.yaml b/recipes/tabixpp/meta.yaml index db6ce10c381fa..b8f8488b7f72c 100644 --- a/recipes/tabixpp/meta.yaml +++ b/recipes/tabixpp/meta.yaml @@ -12,12 +12,12 @@ source: patches: - shared_lib.patch - pkg-config.patch # [osx] -- url: https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2 - sha256: 763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f +- url: https://github.com/samtools/htslib/releases/download/1.19.1/htslib-1.19.1.tar.bz2 + sha256: 222d74d3574fb67b158c6988c980eeaaba8a0656f5e4ffb76b5fa57f035933ec folder: htslib build: - number: 1 + number: 2 run_exports: # Observed ABI version increase from 1.1.0 to 1.1.2. # Hence, we pin to the patch version even. @@ -53,3 +53,5 @@ extra: - biotools:tabixpp recipe-maintainers: - jpuritz + additional-platforms: + - linux-aarch64 diff --git a/recipes/tabixpp/shared_lib.patch b/recipes/tabixpp/shared_lib.patch index 819773b164a42..da684d327f915 100644 --- a/recipes/tabixpp/shared_lib.patch +++ b/recipes/tabixpp/shared_lib.patch @@ -38,9 +38,10 @@ index f2ba44e..7718d76 100644 DFLAGS = -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE BIN = tabix++ -LIB = libtabix.a -+LIB = libtabixpp.a - SOVERSION = 1 +-SOVERSION = 1 -SLIB = libtabix.so.$(SOVERSION) ++LIB = libtabixpp.a ++SOVERSION = 0 +SLIB = libtabixpp.so.$(SOVERSION) OBJS = tabix.o SUBDIRS = . From 15106f38c6acef264f0eaf20d7c0f76c4eeca39f Mon Sep 17 00:00:00 2001 From: DuyenLe2000 <128071771+DuyenLe2000@users.noreply.github.com> Date: Tue, 26 Mar 2024 11:19:30 +0100 Subject: [PATCH 1176/1813] update from 0.2.0 to 0.3.0 (#46756) * update from 0.2.0 to 0.3.0 * add run_exports --- recipes/rsv-typer/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/rsv-typer/meta.yaml b/recipes/rsv-typer/meta.yaml index a022aa258f893..4a2d0f8a78d4f 100644 --- a/recipes/rsv-typer/meta.yaml +++ b/recipes/rsv-typer/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: rsv-typer @@ -6,7 +6,7 @@ package: source: url: https://github.com/DiltheyLab/RSVTyper/archive/refs/tags/v{{ version }}.tar.gz - sha256: ca302df7eb22f4d8cb0e5e6b9eb78b0e236714f95ab136c35d2afd05552d1229 + sha256: d91607ebe37c305fb3aba4871161d51c6fa2bd7aa43d5d6defcca8d9def74431 build: number: 0 @@ -14,6 +14,8 @@ build: script: python -m pip install . entry_points: - rsv-typer = rsv_typer.process_RSV_sample:main + run_exports: + - {{ pin_subpackage("rsv-typer", max_pin="x.x") }} requirements: host: - python From 0024afe5a29e90911822251dc2f1cb8208a9bdb5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Mar 2024 10:39:25 -0400 Subject: [PATCH 1177/1813] Update vembrane to 1.0.5 (#46766) --- recipes/vembrane/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vembrane/meta.yaml b/recipes/vembrane/meta.yaml index 753f85df6c5f3..5b3851289ab76 100644 --- a/recipes/vembrane/meta.yaml +++ b/recipes/vembrane/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: vembrane @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/v/vembrane/vembrane-{{ version }}.tar.gz - sha256: 8d0892c61e4172440390f89cbda16ba2fccd0c519a3e763a0e3950479869673c + sha256: c0afc7dc69dd32ac95c45ba679b5751c2d63170e4876dbc0ce860d44f6b6c18e build: number: 0 From b079eb67ee2eef6052889d7cfdd4b6f1571d35e7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Mar 2024 12:00:13 -0400 Subject: [PATCH 1178/1813] Update tissuumaps to 3.2.1.4 (#46760) * Update tissuumaps to 3.2.1.4 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/tissuumaps/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index ee3fe1375a10d..f5db72adfd1e0 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.1.3" %} +{% set version = "3.2.1.4" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: b15b12bcac2005ef9d2c542e8275324680ae93f981e5ddd4860cf89be0463f9f + sha256: 765decbd743ffae399ad35ffff1f925defc26969a1db3512183c7fcb64c9ceb2 build: number: 0 @@ -42,7 +42,8 @@ test: about: home: https://tissuumaps.research.it.uu.se/ - license: GPLv3 + license: MIT + license_file: LICENSE summary: > TissUUmaps is a lightweight viewer that uses basic web tools to visualize gene expression data or any kind of point data on top of whole slide images From c23dc7b67e850eabd8a51f85df49ead0782315a0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Mar 2024 12:40:33 -0400 Subject: [PATCH 1179/1813] Update earlgrey to 4.1.1 (#46759) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index f7fcf4ea41de7..b2caab5f88b65 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.1.0" %} -{% set sha256 = "682fe5115294b48ac663c3ebe3260811d490d011565f4ad876218ca0417a33cd" %} +{% set version = "4.1.1" %} +{% set sha256 = "499b39f0887f6b258a0fc7ac8eb4aa1abbc3fbe2e22d412be245c21e2c896381" %} package: name: {{ name|lower }} From 0fc59ae356aa66e809ee17bcca9ba350a788aa73 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Mar 2024 12:40:42 -0400 Subject: [PATCH 1180/1813] Update pybiolib to 1.1.1917 (#46758) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index d9a1f6089c3d0..55245a3b2e076 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1909" %} +{% set version = "1.1.1917" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: e73d45300253e2dcd147b4cb85ee07d33cdd28e17095e6209ec0a9997fddbeda + sha256: 66deac3428c03197c956bb734aff867bc08a14d112c1940ac257e07d0e51ced4 build: noarch: python From bf75de1d35291e522f1a13d7452d553208f48304 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Mar 2024 12:42:29 -0400 Subject: [PATCH 1181/1813] Update pydeseq2 to 0.4.8 (#46767) --- recipes/pydeseq2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml index b2931dd3b81b1..cab0312268fa3 100644 --- a/recipes/pydeseq2/meta.yaml +++ b/recipes/pydeseq2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydeseq2" %} -{% set version = "0.4.7" %} +{% set version = "0.4.8" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz - sha256: acdd7911d47128c1d58203cbd161a8c1c5bec8062ebd4724d5dbc63bd2f4f78c + sha256: ae6cb09ce921d866b1d79f2a54bcc6acc61e22d832f1c16e56716ff18e4d35fc build: noarch: python From 7471b5e23a8b8be59de6992b5ba62c01247f7481 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Mar 2024 16:30:56 -0400 Subject: [PATCH 1182/1813] Update tree-qmc to 3.0.4 (#46773) --- recipes/tree-qmc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tree-qmc/meta.yaml b/recipes/tree-qmc/meta.yaml index 2925ea75e649c..e000a16bf22e1 100644 --- a/recipes/tree-qmc/meta.yaml +++ b/recipes/tree-qmc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "TREE-QMC" %} -{% set version = "3.0.1" %} +{% set version = "3.0.4" %} package: @@ -8,7 +8,7 @@ package: source: url: https://github.com/molloy-lab/{{ name|upper }}/archive/refs/tags/v{{ version }}.zip - sha256: 0fc11b22d981cbf62ee3d832ed79ac7dbf526669231b0137fd4e4756a0af506c + sha256: d7490fb79d23d5aa8c24c661e070c150421b0991464c4a8ae6cc694cd124f83e build: number: 0 From bc4c298dd574d0565362ce56bb00e5cd5668e366 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Mar 2024 16:31:27 -0400 Subject: [PATCH 1183/1813] Update snakemake-interface-executor-plugins to 9.1.0 (#46770) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 27912ce5814d8..0f2ccd84a1dd2 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "9.0.2" %} +{% set version = "9.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: aea5544fda5affc899ec3c6f580cd3f839aa88f10123af341c40019f2c04ef10 + sha256: 26da734f7399f5963c5bc7cbcbb51f2d61e3c76298010418d76c48dda92aeb2f build: noarch: python From 522f60822caef8cb81cdaf1f5e646532b548b2a9 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 26 Mar 2024 22:32:09 +0200 Subject: [PATCH 1184/1813] vcftools: add linux-aarch64 build (#46764) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/vcftools/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/vcftools/meta.yaml b/recipes/vcftools/meta.yaml index 296c3146b59a1..fc5557f5b5c3b 100644 --- a/recipes/vcftools/meta.yaml +++ b/recipes/vcftools/meta.yaml @@ -13,7 +13,9 @@ source: - patch build: - number: 9 + number: 10 + run_exports: + - {{ pin_subpackage('vcftools', max_pin='x.x') }} requirements: build: @@ -41,5 +43,7 @@ about: summary: A set of tools written in Perl and C++ for working with VCF files. extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:vcftools From 9d904757f2b2d95b8138699989e55d21f0d83f69 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 27 Mar 2024 02:09:10 +0200 Subject: [PATCH 1185/1813] prodigal: add linux-aarch64 build (#46763) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/prodigal/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/prodigal/meta.yaml b/recipes/prodigal/meta.yaml index abb4fd87c74b2..70e320ad05502 100644 --- a/recipes/prodigal/meta.yaml +++ b/recipes/prodigal/meta.yaml @@ -13,7 +13,7 @@ source: - sd_motif_B.patch build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage('prodigal', max_pin=None) }} @@ -22,7 +22,6 @@ requirements: - make - {{ compiler('c') }} - unzip - run: test: commands: @@ -33,3 +32,7 @@ about: dev_url: https://github.com/hyattpd/Prodigal license: GPL v3 summary: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 3fc7d1879c90801bec9b570659877a0c74dae4b7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Mar 2024 20:10:12 -0400 Subject: [PATCH 1186/1813] Update cytoscape to 3.10.2 (#46777) --- recipes/cytoscape/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cytoscape/meta.yaml b/recipes/cytoscape/meta.yaml index 6fc7e23fbb204..068d4c8f5ba8c 100644 --- a/recipes/cytoscape/meta.yaml +++ b/recipes/cytoscape/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cytoscape" %} -{% set version = "3.10.1" %} -{% set sha256 = "93373f75143822a2162c4db5b0b0b614fdf2e34c1a0300ab915cadfd1b148418" %} +{% set version = "3.10.2" %} +{% set sha256 = "561380f7429aa806941027897fd1ca902597c4dadf4bf1bbd3141a39f2bd3f3e" %} package: name: {{ name }} From 7ec6cbe3b1491a37ae19dc2022415bd478168828 Mon Sep 17 00:00:00 2001 From: Ilya Shlyakhter Date: Tue, 26 Mar 2024 20:11:13 -0400 Subject: [PATCH 1187/1813] Update IGV to 2.17.3 (#46718) * updated IGV to 2.17.3 * added run_exports * fix pin_subpackage * changed jdk requirement to exactly 17. added strict bash mode to build script --- recipes/igv/build.sh | 2 ++ recipes/igv/meta.yaml | 10 ++++++---- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/igv/build.sh b/recipes/igv/build.sh index b156b5aa9d4df..2dcf09d8be126 100644 --- a/recipes/igv/build.sh +++ b/recipes/igv/build.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -eux -o pipefail + mkdir -p ${PREFIX}/lib/igv # Build diff --git a/recipes/igv/meta.yaml b/recipes/igv/meta.yaml index f3a127e2f9d6b..f6b4328bcb2b3 100644 --- a/recipes/igv/meta.yaml +++ b/recipes/igv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "IGV" %} -{% set version = "2.16.2" %} -{% set sha256 = "d08e785d9d44f4e3c16dfe22514133fa0a80d067b677c0cc3c64d2e3d2c12d21" %} +{% set version = "2.17.3" %} +{% set sha256 = "81ab0164014612ff37eea6c7673072fb38ba65b527c05c1197f605c3e9cf3c39" %} package: name: {{ name|lower }} @@ -13,12 +13,14 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: build: - - openjdk 11 + - openjdk 17 run: - - openjdk 11 + - openjdk 17 test: commands: From f1a733f7179c6e88759a61f970b88ff4452d477e Mon Sep 17 00:00:00 2001 From: Julie Lao Date: Wed, 27 Mar 2024 01:12:26 +0100 Subject: [PATCH 1188/1813] Update abromics_galaxy_json_extractor to 0.8.3.5 (#46772) * Update abromics_galaxy_json_extractor to 0.8.3.5 * Update sha256 --- recipes/abromics_galaxy_json_extractor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abromics_galaxy_json_extractor/meta.yaml b/recipes/abromics_galaxy_json_extractor/meta.yaml index ab4d067298934..83137b0abfd9e 100644 --- a/recipes/abromics_galaxy_json_extractor/meta.yaml +++ b/recipes/abromics_galaxy_json_extractor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.3.4" %} +{% set version = "0.8.3.5" %} context: {} @@ -8,7 +8,7 @@ package: source: url: https://gitlab.com/ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/archive/{{ version }}/abromics-galaxy-json-extractor-{{ version }}.tar.gz - sha256: '4106ed76eb759f3bd3fcb866d18fdafce64f4ef6d364967f7ccee29b6af06d19' + sha256: '4736daff2927da5d27afd4b5b944f56ee1f8858a2c247fd5987f0307044989b3' build: noarch: python From b7363708a5e9a6f0b3320045807473552c832e45 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Mar 2024 20:24:27 -0400 Subject: [PATCH 1189/1813] Update checkv to 1.0.2 (#46778) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update checkv to 1.0.2 * Update CheckV requirements * Add `flit-core` as a host dependency --------- Co-authored-by: Antônio Camargo --- recipes/checkv/meta.yaml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/checkv/meta.yaml b/recipes/checkv/meta.yaml index 50aa0beb676aa..4b9f1b39e073d 100644 --- a/recipes/checkv/meta.yaml +++ b/recipes/checkv/meta.yaml @@ -1,5 +1,5 @@ {% set name = "checkv" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: "{{ name|lower }}" @@ -7,27 +7,31 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c32b93e67ba92cd64e9214754d96c527152bda4cd06cc8214afe68130c33ea6e + sha256: 5ad43702b8a326946a7151d325de87bfe1955ee1c744005e6c79dfd9e0da92b3 build: number: 0 noarch: python + script: "{{ PYTHON }} -m pip install . -vv" entry_points: - checkv=checkv.cli:cli - script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage("checkv", max_pin="x") }} requirements: host: - python >=3.6 - pip + - flit-core >=3.2,<4 run: - python >=3.6 - biopython - importlib-metadata >=0.12 - numpy - psutil + - requests - kcounter - - diamond + - diamond <=2.1.8 - hmmer - prodigal-gv From 257cafaea71e7e651e4e0645040e43dae1dddb2b Mon Sep 17 00:00:00 2001 From: Leon Rauschning <99650940+lrauschning@users.noreply.github.com> Date: Wed, 27 Mar 2024 02:05:51 +0100 Subject: [PATCH 1190/1813] fix tests for magus, bump version (#46761) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/magus-msa/meta.yaml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/recipes/magus-msa/meta.yaml b/recipes/magus-msa/meta.yaml index 93ad68e11ed02..cde6aeeb6ad37 100644 --- a/recipes/magus-msa/meta.yaml +++ b/recipes/magus-msa/meta.yaml @@ -33,6 +33,17 @@ requirements: - hmmer test: + imports: + - magus + - magus.align + - magus.align.decompose + - magus.align.merge + - magus.align.merge.graph_build + - magus.align.merge.graph_cluster + - magus.align.merge.graph_trace + - magus.helpers + - magus.tasks + - magus.tools commands: - magus --help From 0160f4d8434293e3887febb097c7d3773705079c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Mar 2024 04:34:22 -0400 Subject: [PATCH 1191/1813] Update checkv to 1.0.3 (#46788) --- recipes/checkv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/checkv/meta.yaml b/recipes/checkv/meta.yaml index 4b9f1b39e073d..544e4afbcee9f 100644 --- a/recipes/checkv/meta.yaml +++ b/recipes/checkv/meta.yaml @@ -1,5 +1,5 @@ {% set name = "checkv" %} -{% set version = "1.0.2" %} +{% set version = "1.0.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 5ad43702b8a326946a7151d325de87bfe1955ee1c744005e6c79dfd9e0da92b3 + sha256: 2438516f270191267a9860dfe31bf596d64a4fbc16be922b46fb6a4fd98d762a build: number: 0 From dce713f1318182a49b397c6166834477581f6535 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Mar 2024 09:51:35 -0400 Subject: [PATCH 1192/1813] Update bioconda-utils to 2.13.2 (#46791) * Update bioconda-utils to 2.13.1 * Update bioconda-utils to 2.13.2 * bioconda-utils: Update anaconda-client=1.12 --------- Co-authored-by: Marcel Bargull --- recipes/bioconda-utils/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 565f668029366..3ca830e56ace9 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.13.0" %} -{% set sha256 = "cee55582cc6f0f9a489e90d5f43e4171700f6140360031899e057a13c183a745" %} +{% set version = "2.13.2" %} +{% set sha256 = "da2b1d2a816c3b647c684fd389f941463e5c37bd502fc7cb650f8db8e2458232" %} package: name: bioconda-utils @@ -41,7 +41,7 @@ requirements: - jsonschema 3.2.* - pyopenssl >=22.1 - conda-forge-pinning 2023.05.06.13.08.41 - - anaconda-client 1.6.* + - anaconda-client 1.12.* - involucro 1.1.* - skopeo 1.11.* - git 2.* From 10d59e47e59de5a1202a95aab5918bc8f5b657fd Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 27 Mar 2024 17:57:44 +0200 Subject: [PATCH 1193/1813] usher & ucsc-fatovcf: add linux-aarch64 build (#46765) * usher: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * ucsc-fatovcf: add linux-aarch64 build Needed by 'usher' Signed-off-by: Martin Tzvetanov Grigorov * ucsc-fatovcf: patch htmshell.c Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-fatovcf/build.sh | 2 +- recipes/ucsc-fatovcf/htmshell.patch | 11 +++++++++++ recipes/ucsc-fatovcf/meta.yaml | 9 ++++++++- recipes/usher/meta.yaml | 4 +++- 4 files changed, 23 insertions(+), 3 deletions(-) create mode 100644 recipes/ucsc-fatovcf/htmshell.patch diff --git a/recipes/ucsc-fatovcf/build.sh b/recipes/ucsc-fatovcf/build.sh index 1074509ead921..2f2c83808ef5c 100644 --- a/recipes/ucsc-fatovcf/build.sh +++ b/recipes/ucsc-fatovcf/build.sh @@ -7,7 +7,7 @@ export CFLAGS="${CFLAGS} -I${PREFIX}/include ${LDFLAGS}" export USE_HIC=0 mkdir -p "${PREFIX}/bin" -export MACHTYPE=x86_64 +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export L="${LDFLAGS}" mkdir -p "${BINDIR}" diff --git a/recipes/ucsc-fatovcf/htmshell.patch b/recipes/ucsc-fatovcf/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-fatovcf/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-fatovcf/meta.yaml b/recipes/ucsc-fatovcf/meta.yaml index 1d2de4903514d..36c44e98dcd56 100644 --- a/recipes/ucsc-fatovcf/meta.yaml +++ b/recipes/ucsc-fatovcf/meta.yaml @@ -12,10 +12,13 @@ source: sha256: {{ sha256 }} patches: - include.patch + - htmshell.patch build: - number: 0 + number: 1 skip: True # [osx] + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -45,3 +48,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "Extract VCF from a multi-sequence FASTA alignment" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file diff --git a/recipes/usher/meta.yaml b/recipes/usher/meta.yaml index 63b3f108e082f..107664cd88018 100644 --- a/recipes/usher/meta.yaml +++ b/recipes/usher/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 95aba8f748599915f21f7bdf883c2e532f2d821138f06cb2e4e58d7323019946 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('usher', max_pin="x.x") }} @@ -51,5 +51,7 @@ about: doc_url: https://usher-wiki.readthedocs.io/en/latest/ extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1038/s41588-021-00862-7 From d4164104abac6b0da39a4c3f94f9f1df68c1d547 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 27 Mar 2024 23:59:23 +0800 Subject: [PATCH 1194/1813] linux-aarch64 build for allegro (#46672) * linux-aarch64 build for allegro * linux-aarch64 build for allegro * fix --------- Co-authored-by: yejianbang --- recipes/allegro/build.sh | 4 ++++ recipes/allegro/meta.yaml | 7 ++++++- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/recipes/allegro/build.sh b/recipes/allegro/build.sh index f8dc625177f65..193897e45693d 100644 --- a/recipes/allegro/build.sh +++ b/recipes/allegro/build.sh @@ -1,4 +1,8 @@ #!/bin/bash +rm -rf src/config.guess +rm -rf src/config.sub +wget "http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD" -O src/config.guess +wget "http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD" -O src/config.sub ./configure make CXXFLAGS="${CXXFLAGS} -std=c++03" diff --git a/recipes/allegro/meta.yaml b/recipes/allegro/meta.yaml index 72183ae9d3512..8a98f890cce1a 100644 --- a/recipes/allegro/meta.yaml +++ b/recipes/allegro/meta.yaml @@ -18,7 +18,9 @@ source: build: skip: True # [osx] - number: 7 + number: 8 + run_exports: + - {{ pin_subpackage("allegro", max_pin="x.x.x") }} requirements: build: @@ -27,6 +29,7 @@ requirements: host: - zlib - patch + - wget run: - zlib @@ -43,3 +46,5 @@ about: extra: skip-lints: - should_not_be_noarch_source + additional-platforms: + - linux-aarch64 From bfdf3f1ff4400fdbb817a3838ed0542da4353d6c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Mar 2024 12:00:28 -0400 Subject: [PATCH 1195/1813] Update varlociraptor to 8.4.6 (#46815) --- recipes/varlociraptor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index c7c24a4b76bf6..393782477f7c8 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.5" %} +{% set version = "8.4.6" %} package: name: varlociraptor @@ -11,7 +11,7 @@ build: source: url: https://github.com/varlociraptor/varlociraptor/archive/v{{ version }}.tar.gz - sha256: 96141350ba0eeaf57731f654f2c33b7044a3b64a433d863e6c659b82d1ca3526 + sha256: b734b322a6ff96ba5f074947505bce0166907afd448350731c9eb1dd453a5311 requirements: build: From 6ed9eba55ceaaea26f5dc12e64044c6a694e15a2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Mar 2024 14:43:09 -0400 Subject: [PATCH 1196/1813] Update wgd to 2.0.29 (#46799) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index d0b37b6c04f8f..ccd95f04a20aa 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.28" %} +{% set version = "2.0.29" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: d63d0eed83a633b0281553d0f26c4804a2538ed6bba70e7bd04918f2d30f128d + sha256: e1d3e08540c9ba88f10f0cefc636225ac31ea9300c318757eb860df954dc153a build: number: 0 From 965b89344c2b612faf954afbd30b08e9e0755ca0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Mar 2024 14:43:37 -0400 Subject: [PATCH 1197/1813] Update pybiolib to 1.1.1921 (#46810) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 55245a3b2e076..ea2d2a355045b 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1917" %} +{% set version = "1.1.1921" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 66deac3428c03197c956bb734aff867bc08a14d112c1940ac257e07d0e51ced4 + sha256: 264482522ffa2b571c06421489c78b4bc9dddee95a402c6cc37e74f2cba66531 build: noarch: python From c9978983e5117e26e11b35e7a7d5d397b178fa52 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Mar 2024 14:48:30 -0400 Subject: [PATCH 1198/1813] Update tksm to 0.6.0 (#46782) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update tksm to 0.6.0 * Added missing JSON requirement --------- Co-authored-by: Baraa Orabi /baraːʔ ʕraːbi/ --- recipes/tksm/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/tksm/meta.yaml b/recipes/tksm/meta.yaml index df1add61a6a93..57e521aca272d 100644 --- a/recipes/tksm/meta.yaml +++ b/recipes/tksm/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.5.0" %} -{% set sha256 = "d2e0abc0ca378945fc2165d489dbe189c71fe0fc7d50bf8fb3be1bd9ce1e7bf3" %} +{% set version = "0.6.0" %} +{% set sha256 = "53f53f0038ee29a3c46b5eb314a731b1067045224ad9a0037551dd7cf4187eef" %} package: name: tksm @@ -22,9 +22,11 @@ requirements: - make - vim - lld + - nlohmann_json host: - python - zlib + - nlohmann_json - cxxopts >=3.1.0 - fmt >=9.1.0 run: From 6688156269fcbdab08c4592597fd1bcbdf199f01 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Mar 2024 16:04:27 -0400 Subject: [PATCH 1199/1813] Update hificnv to 1.0.0 (#46825) --- recipes/hificnv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hificnv/meta.yaml b/recipes/hificnv/meta.yaml index b95edc171d3b1..e6d3537158283 100644 --- a/recipes/hificnv/meta.yaml +++ b/recipes/hificnv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hificnv" %} -{% set version = "0.1.7" %} -{% set sha256 = "db74f665c5aeab59d02bb33b86bfe7f0023f4069af8729920faf1b088e5a0d73" %} +{% set version = "1.0.0" %} +{% set sha256 = "276afe35d34171f17a5f30e7aa35eb156765156536ae7411171376565d63cfe5" %} package: name: {{ name }} From 9bd47ed3d71046e724002dd53528499ee3ffd18f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Mar 2024 19:02:37 -0400 Subject: [PATCH 1200/1813] Update r-acidsinglecell to 0.4.2 (#46827) --- recipes/r-acidsinglecell/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidsinglecell/meta.yaml b/recipes/r-acidsinglecell/meta.yaml index ad35a25f806b7..962ac75f917b7 100644 --- a/recipes/r-acidsinglecell/meta.yaml +++ b/recipes/r-acidsinglecell/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} {% set github = "https://github.com/acidgenomics/r-acidsinglecell" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 69b81a103280720ac91f05056b81c8a485e5a70cc5802cfb39a23db7ebdc2487 + sha256: cc3068a1653e99a218607a9a994d8ee13490ebe162c403a6a7805ba10bfc50b0 build: number: 0 From f73afdd2c072ab95fffc1ea7cf9d90694dc2a6a4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Mar 2024 19:46:33 -0400 Subject: [PATCH 1201/1813] Update minimap2 to 2.28 (#46818) --- recipes/minimap2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/minimap2/meta.yaml b/recipes/minimap2/meta.yaml index 6a9b301cd30f3..8962090b3324b 100644 --- a/recipes/minimap2/meta.yaml +++ b/recipes/minimap2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.27" %} +{% set version = "2.28" %} package: name: minimap2 @@ -6,10 +6,10 @@ package: source: url: https://github.com/lh3/minimap2/archive/v{{ version }}.tar.gz - sha256: ca9ceb07e3b388858ebc2d7d91a6c74e996659402d16aa759ecedd63588b1ef7 + sha256: 5ea6683b4184b5c49f6dbaef2bc5b66155e405888a0790d1b21fd3c93e474278 build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('minimap2', max_pin="x") }} From c1e7efdde7eeeaff46a59f18ce06f29d2568a956 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Mar 2024 19:47:13 -0400 Subject: [PATCH 1202/1813] Update mappy to 2.28 (#46819) --- recipes/mappy/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mappy/meta.yaml b/recipes/mappy/meta.yaml index e26e609345c22..422595563dc9d 100644 --- a/recipes/mappy/meta.yaml +++ b/recipes/mappy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mappy" %} -{% set version = "2.27" %} +{% set version = "2.28" %} package: name: {{ name }} @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mappy-{{ version }}.tar.gz - sha256: 47df11e7cecee9138680d6d2312e44397d0484a02ecf1f5908dea50d94a0efe4 + sha256: 0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('mappy', max_pin="x") }} From 69e80d8f6c8deac75d8ba0f14852dc4c1514a145 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 06:11:31 -0400 Subject: [PATCH 1203/1813] Update slow5curl to 0.2.1 (#46846) --- recipes/slow5curl/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/slow5curl/meta.yaml b/recipes/slow5curl/meta.yaml index 4830b0486ce78..3c6270698f1c6 100644 --- a/recipes/slow5curl/meta.yaml +++ b/recipes/slow5curl/meta.yaml @@ -1,5 +1,5 @@ {% set name = "slow5curl" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/BonsonW/slow5curl/releases/download/v{{ version }}/slow5curl-v{{ version }}-release.tar.gz - sha256: 11eac212e3452fb91e158999d0c5b186ac238d5580e3a9696a87590c21206bd3 + sha256: 6c062e59dc3e8bd65612613da7ac9a2518544061f1ef81d159e938e717393d3e build: number: 0 From d15a7dc7175c5a5329c18ab0ea3a6bf050ac4f67 Mon Sep 17 00:00:00 2001 From: Julie Lao Date: Thu, 28 Mar 2024 12:30:54 +0100 Subject: [PATCH 1204/1813] Update to 0.8.3.6 (#46834) * Update to 0.8.3.6 * Update sha256 for abromics_galaxy_json_extractor version 0.8.3.6 --- recipes/abromics_galaxy_json_extractor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abromics_galaxy_json_extractor/meta.yaml b/recipes/abromics_galaxy_json_extractor/meta.yaml index 83137b0abfd9e..ffb7d367e33e6 100644 --- a/recipes/abromics_galaxy_json_extractor/meta.yaml +++ b/recipes/abromics_galaxy_json_extractor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.3.5" %} +{% set version = "0.8.3.6" %} context: {} @@ -8,7 +8,7 @@ package: source: url: https://gitlab.com/ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/archive/{{ version }}/abromics-galaxy-json-extractor-{{ version }}.tar.gz - sha256: '4736daff2927da5d27afd4b5b944f56ee1f8858a2c247fd5987f0307044989b3' + sha256: '364997088a29c30cdc45d2c66af40a3d6b8e3398efe1d7eb242d31b0e68abd77' build: noarch: python From 4f0da573eaa54ffd21455f1896a52fe0703ce00a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 08:54:58 -0400 Subject: [PATCH 1205/1813] Update r-acidplots to 0.7.3 (#46830) --- recipes/r-acidplots/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidplots/meta.yaml b/recipes/r-acidplots/meta.yaml index c34dc6a9b5aa5..491f5b79bb3d1 100644 --- a/recipes/r-acidplots/meta.yaml +++ b/recipes/r-acidplots/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.2" %} +{% set version = "0.7.3" %} {% set github = "https://github.com/acidgenomics/r-acidplots" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 29edee3a481384cb4b3593e07f87cde2c7313f6d3318c7747ec3bfa1c933376a + sha256: d329072ba00d062ccef15a510aac73fc918b6f9db2d47dbfd5ffd82afc70c548 build: noarch: generic From c1eca2f84384c2e9fa40116e5ae4275980b6c29c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 10:04:02 -0400 Subject: [PATCH 1206/1813] Update agat to 1.3.3 (#46855) --- recipes/agat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/agat/meta.yaml b/recipes/agat/meta.yaml index 87f39ec90c60c..a1bae16c77a83 100755 --- a/recipes/agat/meta.yaml +++ b/recipes/agat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "AGAT" %} -{% set version = "1.3.2" %} -{% set sha256 = "f5ceadceca0ad8b423e51c199a6ae66921b88021ebf969c971da59df53b72fc5" %} +{% set version = "1.3.3" %} +{% set sha256 = "08fa159f7badb418a681a514d471d7233bb1cc09a5e41d875118eaec4c2ec813" %} package: name: "{{ name|lower }}" From 8cdd9987977a4c0b2d2ed36fa9b1ebcb3f734425 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 10:11:53 -0400 Subject: [PATCH 1207/1813] Update r-deseqanalysis to 0.7.1 (#46829) --- recipes/r-deseqanalysis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-deseqanalysis/meta.yaml b/recipes/r-deseqanalysis/meta.yaml index 4f0912b12277e..c946b43612c5b 100644 --- a/recipes/r-deseqanalysis/meta.yaml +++ b/recipes/r-deseqanalysis/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} {% set github = "https://github.com/acidgenomics/r-deseqanalysis" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: cf5b1cae6fa44e0db16cba3aab8de0d738ab26af7326f9ff24ee42ffb05574d6 + sha256: b5e77ddd1d2109069c6ad5ed01f073c904e5cf164c1c5a418853c554263b0e97 build: noarch: generic From 596e2ebdf55e20cf1c8d0f16964e640bcca034a2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 11:35:51 -0400 Subject: [PATCH 1208/1813] Update phykit to 1.19.1 (#46831) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index ae6066f0ad672..c0cfae8640d07 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.19.0" %} +{% set version = "1.19.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: da276adaf07f65a1d693db5f3f3c790ddc77610436a1178f49f6d3ab57b4c44b + sha256: 09dcc2649d9a217d5afdefc151568d68beec3cfdc5789cfc3ec255610677cc5c build: noarch: python From 8c6259c76606930f0d61bc2de4408963768659c9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 11:36:00 -0400 Subject: [PATCH 1209/1813] Update pyhmmer to 0.10.11 (#46832) --- recipes/pyhmmer/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 035907bda7054..586e1db28ee9c 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.10" %} +{% set version = "0.10.11" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 2c7bda6f5c5520d708c7886a6303229a275791fe4e7074a716dbb63fec16804b + sha256: c45a2335e6dc5b7d3f3db424e234c398b21b6063ad48b19c90abde0120c3d866 build: - number: 1 + number: 0 skip: True # [py2k or win] script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" run_exports: From 5e5003be9ee50221276db0f41fd3eeff7377a05b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 11:41:37 -0400 Subject: [PATCH 1210/1813] Update physiofit to 3.3.6 (#46817) --- recipes/physiofit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/physiofit/meta.yaml b/recipes/physiofit/meta.yaml index 1452c97491f6f..aec1c034ed92d 100644 --- a/recipes/physiofit/meta.yaml +++ b/recipes/physiofit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "physiofit" %} -{% set version = "3.3.5" %} +{% set version = "3.3.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/physiofit-{{ version }}.tar.gz - sha256: 40f3484b8f70ea13ef38fe29c847aa0b76030f580091c227398e8598835ab328 + sha256: 6d6aa155ec16ca1da9bb04548b506adfd70b8b1000cd6eb3aa1ee4634a738af1 build: entry_points: From 1d7157e1fcf5afb6d946e4cd62e9a99bbd1fbdf1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 11:46:35 -0400 Subject: [PATCH 1211/1813] Update gxf2bed to 0.2.2 (#46822) --- recipes/gxf2bed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gxf2bed/meta.yaml b/recipes/gxf2bed/meta.yaml index 914c92ba00eb3..a0b0d0160416c 100644 --- a/recipes/gxf2bed/meta.yaml +++ b/recipes/gxf2bed/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gxf2bed" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} package: name: gxf2bed @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 139efd9c4294d92a27f058db2bc58dfbcaaab8be45ca1022794a4f3780cd962f + sha256: ee500e08e8c94b2663ea511482d6520300cb81c9cbbb05a288563e4a808f5377 build: number: 0 From 38b64a5e7fdcc88bdf7e437ea395745c4e1374fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 11:46:44 -0400 Subject: [PATCH 1212/1813] Update psm-utils to 0.8.0 (#46820) --- recipes/psm-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index ed079a377b69a..7620a67085e42 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.7.4" %} -{% set sha256 = "bf36ad6246568841a5c4b658fdbbb0bf3a70f6f3b24b31b141f6018de24d4ad8" %} +{% set version = "0.8.0" %} +{% set sha256 = "735f44dce1f99ac7821d61fe87df955fa935cb06377cdfa7fd18ead464850c49" %} package: name: {{ name|lower }} From 8ba979315a37e9452df7a04560ce197c7d725261 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 12:53:21 -0400 Subject: [PATCH 1213/1813] Update r-bcbiornaseq to 0.6.2 (#46856) --- recipes/r-bcbiornaseq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-bcbiornaseq/meta.yaml b/recipes/r-bcbiornaseq/meta.yaml index bcf9df357c9d3..5438c656df52d 100644 --- a/recipes/r-bcbiornaseq/meta.yaml +++ b/recipes/r-bcbiornaseq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.1" %} +{% set version = "0.6.2" %} {% set github = "https://github.com/hbc/bcbioRNASeq" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 75399d753cd0fbef5f644e43fc1e30b7ccd3a56b754b999b5ce9086de0259596 + sha256: 01c7848a13e5eb5bb043725fbdcec2de9e545dd37c2995bcbbfde73a8632ede8 build: number: 0 From 131a728898f33757eb2671f0befc5aaa2e9e35b7 Mon Sep 17 00:00:00 2001 From: Joe Wirth <71667025+dr-joe-wirth@users.noreply.github.com> Date: Thu, 28 Mar 2024 13:05:46 -0400 Subject: [PATCH 1214/1813] Add primerforge (#46858) * added primerforge conda installation * fixed name of matplotlib to comply with linter * update exports and pip params --------- Co-authored-by: Robert A. Petit III --- recipes/primerforge/meta.yaml | 39 +++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 recipes/primerforge/meta.yaml diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml new file mode 100644 index 0000000000000..5c666d4ec97ee --- /dev/null +++ b/recipes/primerforge/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "primerForge" %} +{% set version = "0.7.4" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 6409887f69d20d7ec86609997f55c9df0ae1e5f3e890b0f9d6f95be97d9fbdc6 + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + run_exports: + - {{ pin_subpackage('primerforge', max_pin="x.x") }} + +requirements: + host: + - python >=3.11 + - pip + run: + - biopython + - matplotlib-base >=3.7 + - numpy + - primer3-py >=2.0 + - scipy >=1.10 + +test: + commands: + - primerForge --help + +about: + home: https://github.com/dr-joe-wirth/{{ name }} + license: Apache-2.0 + license_family: Apache + license_file: LICENSE + summary: "primerForge: software to identify primers that can be used to distinguish genomes" From 6d9d73867e07a89ab659be674f5a4544dac1bd4a Mon Sep 17 00:00:00 2001 From: Lee Katz Date: Thu, 28 Mar 2024 13:28:36 -0400 Subject: [PATCH 1215/1813] Update mashpit version 0.9.3 (#46664) * Bump mashpit version 0.9.3 * add run_exports * add requests * add more libraries in meta.yaml Based on what I see here: https://github.com/tongzhouxu/mashpit/blame/52f8901f96e793068a2d215b52ffd26b49ad8169/setup.py#L30 * added pyqt5-sip in meta.yaml * Update ncbi-datasets-pylib version to 16.6.0 * Update meta.yaml * loosened scipy version * update to 0.9.31 * bump versions for pyqt, pyqt5-sip, and ete3 * loosen versions fo pyqt, pyqt5-sip, and ete3 * added libGL runtime library * mashpit v0.9.32 * Force a rerun of the tests * rerun test Quay timed out??? https://dev.azure.com/bioconda/bioconda-recipes/_build/results?buildId=54269&view=logs&j=e14e69ff-a0ae-55c4-b71d-229b239cfb2f&t=4dddc55b-10bc-50fc-ac68-7ff899b7a030&l=11 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update subpackage pin for pre-v1 --------- Co-authored-by: Robert A. Petit III Co-authored-by: Tongzhou Xu --- recipes/mashpit/meta.yaml | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/recipes/mashpit/meta.yaml b/recipes/mashpit/meta.yaml index 59823e05bd435..16a7f9b314a25 100644 --- a/recipes/mashpit/meta.yaml +++ b/recipes/mashpit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9.2" %} +{% set version = "0.9.6" %} package: name: mashpit @@ -6,12 +6,14 @@ package: source: url: https://github.com/tongzhouxu/mashpit/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8556e02af3d2478bff6cc83f0446690d77c171e7fd6f7d071eec19e70e8ef75b + sha256: 94754449251e51fff771c5d9579ef7016cf1d2984dfcdc5f01a558ceac772d14 build: noarch: python script: python -m pip install --no-deps --ignore-installed . number: 0 + run_exports: + - {{ pin_subpackage("mashpit", max_pin="x.x") }} requirements: host: @@ -19,14 +21,19 @@ requirements: - pip run: - biopython =1.78 + - dask >=2024.1 + - flask >=3.0 + - ncbi-datasets-cli >=16.10 + - ncbi-datasets-pylib >=16.6.0 - numpy >=1.19.5 - python >=3.8 - - python-dotenv - pandas >=1.1.5 - - scipy =1.7.3 + - requests + - scikit-bio + - scipy >=1.0 - screed >=1.0.5 - - sourmash >=4.2.2 - - sra-tools >=2.10.8 + - sourmash >=4.6.1 + - tqdm test: commands: From 36b27ab6227ef39aa6f35fe69aae57bbdcdc670a Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 03:06:31 +0800 Subject: [PATCH 1216/1813] linux-aarch64 build for selam (#46794) Co-authored-by: yejianbang --- recipes/selam/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/selam/meta.yaml b/recipes/selam/meta.yaml index 8a34616bd07a0..befd25c006cac 100644 --- a/recipes/selam/meta.yaml +++ b/recipes/selam/meta.yaml @@ -11,7 +11,9 @@ source: sha256: {{sha256}} build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage("selam", max_pin="x.x.x") }} requirements: build: @@ -45,3 +47,5 @@ about: extra: identifiers: - doi:10.1093/bioinformatics/btw365 # Paper in Bioinformatics + additional-platforms: + - linux-aarch64 From 6da4fb4ab23be726a0e32c660c701c0bc7f6f016 Mon Sep 17 00:00:00 2001 From: Joerg Fallmann Date: Thu, 28 Mar 2024 20:17:50 +0100 Subject: [PATCH 1217/1813] version bump, dependency cleanup, snakemake>8 support (#46806) * version bump, dependency cleanup, snakemake>8 support * Update meta.yaml Linting fix, space before version, forgot again * Update meta.yaml reset build number, again * Update meta.yaml pruned too many * Update meta.yaml relaxed perl version * Update meta.yaml versioneer * Version bump --- recipes/monsda/meta.yaml | 43 ++++++++++++++++++++++------------------ 1 file changed, 24 insertions(+), 19 deletions(-) diff --git a/recipes/monsda/meta.yaml b/recipes/monsda/meta.yaml index 68ab0c3b3a547..d0a07177d343b 100644 --- a/recipes/monsda/meta.yaml +++ b/recipes/monsda/meta.yaml @@ -1,6 +1,6 @@ {% set name = "MONSDA" %} -{% set version = "1.2.2" %} -{% set sha256 = "677ce6d6c880f022dfd70b5dddb62d2ffdb21c2816a0930ec2a712e786adc4c3" %} +{% set version = "1.2.4" %} +{% set sha256 = "7a2830bf7ccc90afdb8aa2b3d15985865109f14ac24f12ddfc3a4345031a73fb" %} package: name: "{{ name|lower }}" @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --use-pep517 --no-deps --ignore-installed -vvv" entry_points: - monsda = MONSDA.RunMONSDA:main @@ -22,26 +22,31 @@ build: requirements: host: - - python >=3.11 + - python >=3.12 - pip - pytest-runner - run: - - python >=3.11 - - biopython >=1.78 - - more-itertools >=8.8.0 - - natsort >=7.1.1 - - nextflow >=23.04.1 - - numpy >=1.21.0 - - pandas >=1.4.1 - - perl >=5.32.1 - - scipy >=1.7.0 - - snakemake >=7.32.3,<8.0.0 - versioneer >=0.20 - - yaml >=0.2.5 + run: + - python >=3.12 + - biopython >=1.83 - black >=21.5b2 - flake8 >=3.8.3 - - isort >=5.9.2 - - sphinx >=4.1.0 + - natsort >=8.4.0 + - nextflow >=23.10.1 + - numpy >=1.26.4 + - pandas >=2.2.1 + - perl >=5.32.0 + - pyyaml >=6.0.1 + - scipy >=1.12.0 + - snakemake >=8.10.0 + - snakemake-executor-plugin-slurm =0.4.2 + - snakemake-executor-plugin-cluster-generic =1.0.9 + - snakemake-interface-common =1.17.1 + - snakemake-interface-executor-plugins =9.0.2 + - snakemake-interface-report-plugins =1.0.0 + - snakemake-interface-storage-plugins =3.1.1 + - snakemake-storage-plugin-s3 =0.2.10 + - versioneer >=0.20 test: commands: @@ -54,7 +59,7 @@ about: license: GPL-3.0-or-later license_family: GPL3 license_file: LICENSE - summary: MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis + summary: MONSDA, Modular Organizer of Nextflow and Snakemake driven HTS Data Analysis doc_url: https://monsda.readthedocs.io/en/latest/ extra: From a9332c0060842823ac8cb285cf3679285a8ce2b1 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Thu, 28 Mar 2024 13:23:28 -0600 Subject: [PATCH 1218/1813] pinn macsyfinder version in defense-finder (#46824) --- recipes/defense-finder/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/defense-finder/meta.yaml b/recipes/defense-finder/meta.yaml index 8b03555254ce6..80a8fee131a79 100644 --- a/recipes/defense-finder/meta.yaml +++ b/recipes/defense-finder/meta.yaml @@ -11,7 +11,7 @@ source: # patches: 0001-fix-no-results.patch build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv run_exports: @@ -24,7 +24,9 @@ requirements: run: - click >=8.0.3 - colorlog >=6.3.0a1 - - macsyfinder + # macsyfinder pinned based notes at https://github.com/mdmparis/defense-finder/releases/tag/v1.2.2 + # Please review macsyfinder version in future release + - macsyfinder 2.1.1 - python >=3.7 - pyhmmer - pyrodigal From b78799c8f1b6cb1bcdcbaab63670deba684364bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 15:24:02 -0400 Subject: [PATCH 1219/1813] Update strainr2 to 1.0.1 (#46864) --- recipes/strainr2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/strainr2/meta.yaml b/recipes/strainr2/meta.yaml index 48ea5f5ae72aa..588aa7c636683 100644 --- a/recipes/strainr2/meta.yaml +++ b/recipes/strainr2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: strainr2 @@ -6,10 +6,10 @@ package: source: url: https://github.com/BisanzLab/StrainR2/archive/v{{ version }}.tar.gz - sha256: 6ed9671c875ec6388960dbac02a73629d58ad20adad1fe297d905d8969ec0489 + sha256: 943121e54a386bf3cf6e8278b6d443d0d3d2b0edfaff795bcc25777ad3879abb build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage("strainr2", max_pin="x") }} From 0fe8d92c99c3e6e9d00db4162dbd35af376fc0ba Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 15:24:13 -0400 Subject: [PATCH 1220/1813] Update pyensembl to 2.3.12 (#46863) --- recipes/pyensembl/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index 0a9814354ab74..b6fdac41746f5 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PyEnsembl" %} -{% set version = "2.3.11" %} -{% set sha256 = "e3283514218b93b0626165ad3aa34b6487198b715555394e026a48aed7ff0901" %} +{% set version = "2.3.12" %} +{% set sha256 = "bfa3de35a47fe85afa5f8ff39fddd86e2cca6c14c238029c1525b3d3aa8bb089" %} package: name: {{ name|lower }} From 36236ae37c016978e23f23913695a1c92cecbf58 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 15:24:20 -0400 Subject: [PATCH 1221/1813] Update omamer to 2.0.3 (#46862) --- recipes/omamer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/omamer/meta.yaml b/recipes/omamer/meta.yaml index d7a0f90833459..9bbc65251e0ac 100644 --- a/recipes/omamer/meta.yaml +++ b/recipes/omamer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "omamer" %} -{% set version = "2.0.2" %} +{% set version = "2.0.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/omamer-{{ version }}.tar.gz - sha256: 2cd75d7771333c9a611b274285eb662c19ea50c38a2ae0a2748a3b821be67dae + sha256: c29fcaf5aa39fc3a3f2ff860159ce4df1832229751a6a623ef9af4eba503b525 build: entry_points: From 9997b02d650f8c824997d14be8d58172ea7df0cc Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 03:36:57 +0800 Subject: [PATCH 1222/1813] linux-aarch64 build for annonars (#46783) Co-authored-by: yejianbang --- recipes/annonars/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 5d652eb89c8e3..c07360cdd3eb2 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("annonars", max_pin="x.x") }} @@ -45,3 +45,5 @@ about: extra: recipe-maintainers: - holtgrewe + additional-platforms: + - linux-aarch64 From 0f2dc6906d2ad004ddc0f9d01f364b10964007de Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 15:46:08 -0400 Subject: [PATCH 1223/1813] Update soda-gallery to 1.2.0 (#46828) * Update soda-gallery to 1.2.0 * add run_exports --------- Co-authored-by: mencian --- recipes/soda-gallery/meta.yaml | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/recipes/soda-gallery/meta.yaml b/recipes/soda-gallery/meta.yaml index 018c0cf1d077c..195229557cff0 100644 --- a/recipes/soda-gallery/meta.yaml +++ b/recipes/soda-gallery/meta.yaml @@ -1,5 +1,5 @@ {% set name = "soda-gallery" %} -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} package: name: "{{ name|lower }}" @@ -7,33 +7,28 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7b505ef8283e04fb381ad566b488aab3bd995641cf2b5c5380739d414ea6472e + sha256: dc71f503ecdf3d54ad00c9648176e98c0a1db37a18fe6fe7d5d1ea763340e92c build: noarch: python number: 0 entry_points: - soda = soda.soda:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('soda-gallery', max_pin="x") }} requirements: host: - - beautifulsoup4 >=4.9.3 - - certifi >=2021.5.30 - - jinja2 >=3.0.1 - - pdfminer >=20191125 - - pdfrw >=0.4 - pip - - python - - requests >=2.25.1 - - requests-kerberos >=0.12.0 + - python >=3 run: - beautifulsoup4 >=4.9.3 - - certifi >=2021.5.30 + - certifi >=2024.2.2 - jinja2 >=3.0.1 - pdfminer >=20191125 - pdfrw >=0.4 - - python + - python >=3 - requests >=2.25.1 - requests-kerberos >=0.12.0 From bbd557ad0e0b62d8b686153113bd7403a09c48c8 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Thu, 28 Mar 2024 20:53:12 +0100 Subject: [PATCH 1224/1813] Update hictkpy to v0.0.4 (#46768) * Update patch * Bump version * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Try to compile using a single thread * Remove unused deps * Build arm64 packages * Update test imports * Bugfix * Bugfix --- recipes/hictkpy/CMakeLists.txt.patch | 13 +++++++++++++ recipes/hictkpy/build.sh | 14 ++++++-------- recipes/hictkpy/conanfile.txt.patch | 28 ++++++++++++++-------------- recipes/hictkpy/meta.yaml | 12 ++++++------ recipes/hictkpy/pyproject.toml.patch | 13 +++++++++++++ 5 files changed, 52 insertions(+), 28 deletions(-) create mode 100644 recipes/hictkpy/CMakeLists.txt.patch create mode 100644 recipes/hictkpy/pyproject.toml.patch diff --git a/recipes/hictkpy/CMakeLists.txt.patch b/recipes/hictkpy/CMakeLists.txt.patch new file mode 100644 index 0000000000000..a5c3cb5839689 --- /dev/null +++ b/recipes/hictkpy/CMakeLists.txt.patch @@ -0,0 +1,13 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 01a1413..b0dcdb4 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -17,6 +17,8 @@ set(CMAKE_C_STANDARD 11) + # -std=gnu++20 for example when compiling with PCH enabled + set(CMAKE_CXX_EXTENSIONS OFF) + ++set(CMAKE_OSX_DEPLOYMENT_TARGET 10.15) ++ + project( + hictkpy + LANGUAGES C CXX diff --git a/recipes/hictkpy/build.sh b/recipes/hictkpy/build.sh index 8b2e7f66b8bd2..a6d756aa71a09 100755 --- a/recipes/hictkpy/build.sh +++ b/recipes/hictkpy/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -export CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT} +# export CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT} scratch=$(mktemp -d) export CONAN_HOME="$scratch/conan" @@ -22,22 +22,20 @@ fi mkdir -p "$CONAN_HOME/profiles/" ln -s "${RECIPE_DIR}/conan_profiles/$conan_profile" "$CONAN_HOME/profiles/default" +# explicitly set CMAKE_OSX_DEPLOYMENT_TARGET +patch CMakeLists.txt < "${RECIPE_DIR}/CMakeLists.txt.patch" + # Remove unnecessary dependencies from conanfile.txt patch conanfile.txt < "${RECIPE_DIR}/conanfile.txt.patch" -# Install header-only deps -conan install conanfile.txt \ - --build="*" \ - --output-folder=build/ +# Build hictkpy as a shared library +patch pyproject.toml < "${RECIPE_DIR}/pyproject.toml.patch" -CMAKE_ARGS="-DCMAKE_PREFIX_PATH=$PWD/build" -CMAKE_ARGS+=" ${CMAKE_PLATFORM_FLAGS[*]}" CMAKE_ARGS+=" -DPython_EXECUTABLE=$PYTHON" echo "$CMAKE_ARGS" export CMAKE_ARGS -HICTKPY_SETUP_SKIP_CONAN=1 \ SETUPTOOLS_SCM_PRETEND_VERSION="$PKG_VERSION" \ "$PYTHON" -m pip install "$SRC_DIR" -vv diff --git a/recipes/hictkpy/conanfile.txt.patch b/recipes/hictkpy/conanfile.txt.patch index 34865b8af6ab4..081aa3aa249c4 100644 --- a/recipes/hictkpy/conanfile.txt.patch +++ b/recipes/hictkpy/conanfile.txt.patch @@ -1,27 +1,26 @@ diff --git a/conanfile.txt b/conanfile.txt -index 3bea10b..444d3d1 100644 +index af68e77..276b37f 100644 --- a/conanfile.txt +++ b/conanfile.txt -@@ -4,30 +4,9 @@ - +@@ -5,30 +5,12 @@ [requires] - bshoshany-thread-pool/3.5.0#5aaea7ccf37107d3c1ba9ca9ab246e42 --fast_float/5.3.0#efd9bda97d5f77fa5a98981e014092a0 --fmt/10.1.1#cd63809a79574a2f9eb73ca35f16a243 --hdf5/1.14.2#1e12ccecd5ebc9b5191433862e196743 --highfive/2.8.0#19e1a6e78d9329851aa9da409f07d29a + bshoshany-thread-pool/4.0.1#b7ce99198b3a54e403393961480085c7 + concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502 +-fast_float/6.1.0#85dc5bf9d3d6e605abf536818397baf3 +-fmt/10.2.1#9199a7a0611866dea5c8849a77467b25 +-hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1 +-highfive/2.9.0#c57477beed8b0110fadeb6da8f48bcc5 -libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602 parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7 --pybind11/2.11.1#e24cefefdb5561ba8d8bc34ab5ba1607 - span-lite/0.10.3#1967d71abb32b314387c2ab9c558dd22 --spdlog/1.12.0#0e390a2f5c3e96671d0857bc734e4731 --xxhash/0.8.2#03fd1c9a839b3f9cdf5ea9742c312187 + readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83 + span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422 +-spdlog/1.13.0#2775cc949e26b339029a852785b6b276 -zstd/1.5.5#b87dc3b185caa4b122979ac4ae8ef7e8 [generators] CMakeDeps --[options] + [options] -fmt*:header_only=True -hdf5*:enable_cxx=False -hdf5*:hl=False @@ -32,4 +31,5 @@ index 3bea10b..444d3d1 100644 -highfive*:with_opencv=False -highfive*:with_xtensor=False -spdlog*:header_only=True --xxhash*:utility=False +-zstd*:build_programs=False + diff --git a/recipes/hictkpy/meta.yaml b/recipes/hictkpy/meta.yaml index 390777733a8ef..552b88f866780 100644 --- a/recipes/hictkpy/meta.yaml +++ b/recipes/hictkpy/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictkpy" %} -{% set version = "0.0.3" %} -{% set sha256 = "5f08caebedd88a389329549722b9f34b3fcb526c5be30c6eb793b855a26806cc" %} +{% set version = "0.0.4" %} +{% set sha256 = "5fdbe2bb59643fcc084f1576a7557dbd949bfd5f14981e16dda50a8e8f49eb8f" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: build: number: 0 - skip: True # [py < 37] + skip: True # [py < 39] run_exports: - {{ pin_subpackage('hictkpy', max_pin='x.x') }} @@ -27,14 +27,12 @@ requirements: - fast_float >=5 - fmt >=10 - highfive >=2.7 - - pybind11 >=2.11 - spdlog >=1.12 host: - python - hdf5 >=1.12 - libdeflate - - xxhash >=0.8 - - setuptools + - scikit-build-core - setuptools_scm - zstd >=1.5 @@ -70,3 +68,5 @@ extra: identifiers: - biotools:hictkpy - doi:10.5281/zenodo.8220300 + additional-platforms: + - linux-aarch64 diff --git a/recipes/hictkpy/pyproject.toml.patch b/recipes/hictkpy/pyproject.toml.patch new file mode 100644 index 0000000000000..6763068194b11 --- /dev/null +++ b/recipes/hictkpy/pyproject.toml.patch @@ -0,0 +1,13 @@ +diff --git a/pyproject.toml b/pyproject.toml +index 1a03623..36102d0 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -49,7 +49,7 @@ HICTK_BUILD_EXAMPLES = "OFF" + HICTK_BUILD_BENCHMARKS = "OFF" + HICTK_BUILD_TOOLS = "OFF" + HICTK_ENABLE_GIT_VERSION_TRACKING = "OFF" +-BUILD_SHARED_LIBS = "OFF" ++BUILD_SHARED_LIBS = "ON" + CONAN_INSTALL_ARGS = "--settings=compiler.cppstd=17;--build=missing;--update;--options=*/*:shared=False" + + [tool.setuptools_scm] From bece85447495bf3039fb33be9c44762376bb72e6 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Thu, 28 Mar 2024 13:00:41 -0700 Subject: [PATCH 1225/1813] Add ntroot recipe (#46747) * Add ntroot recipe * Ancestry inference using genomic data * Remove extra btllib * Remove btllib imports check * ntHits version pin * Add another test * Move cmake to host * Add llvm-openmp (osx) to run * Add patch for meson linker --- recipes/ntroot/build.sh | 9 +++++++ recipes/ntroot/meta.yaml | 50 +++++++++++++++++++++++++++++++++++++ recipes/ntroot/ntroot.patch | 10 ++++++++ 3 files changed, 69 insertions(+) create mode 100644 recipes/ntroot/build.sh create mode 100644 recipes/ntroot/meta.yaml create mode 100644 recipes/ntroot/ntroot.patch diff --git a/recipes/ntroot/build.sh b/recipes/ntroot/build.sh new file mode 100644 index 0000000000000..8f8449ef386d5 --- /dev/null +++ b/recipes/ntroot/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" + +# Build ntRoot +mkdir -p ${PREFIX}/bin +meson setup build --prefix ${PREFIX} +cd build +ninja install diff --git a/recipes/ntroot/meta.yaml b/recipes/ntroot/meta.yaml new file mode 100644 index 0000000000000..af7861de8eb89 --- /dev/null +++ b/recipes/ntroot/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "ntRoot" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/bcgsc/ntRoot/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.gz + sha256: 0de1e98bc9ac4a3eb1d3265358ac866d031190dd2375fa644ac5b34bb71f4795 + patches: + - ntroot.patch + +build: + number: 0 + run_exports: + - {{ pin_subpackage("ntroot", max_pin="x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - cmake + host: + - python + - meson + - ninja + - llvm-openmp # [osx] + - libgomp # [linux] + - btllib >=1.7.0 + - boost-cpp + - cmake + run: + - python + - btllib + - snakemake + - samtools + - ntcard + - nthits >=1.0.2 + - perl + +test: + commands: + - ntroot -h + - make_genome_bf -h + +about: + home: https://github.com/bcgsc/ntroot + license: GPL-3.0 + license_file: LICENSE + summary: 'Ancestry inference from genomic data' diff --git a/recipes/ntroot/ntroot.patch b/recipes/ntroot/ntroot.patch new file mode 100644 index 0000000000000..927f59539c481 --- /dev/null +++ b/recipes/ntroot/ntroot.patch @@ -0,0 +1,10 @@ +--- subprojects/ntEdit/meson.build 2024-03-26 15:01:23.000000000 -0700 ++++ subprojects/ntEdit/meson.build.patch 2024-03-26 15:03:25.000000000 -0700 +@@ -32,6 +32,7 @@ + 'ntedit.cpp', + dependencies: dependencies, + include_directories: 'lib', ++ link_args : link_args, + install: true, + ) + From 656f078e6bc98f22db0e6ead59783536b0101de9 Mon Sep 17 00:00:00 2001 From: Martin Larralde Date: Thu, 28 Mar 2024 21:02:22 +0100 Subject: [PATCH 1226/1813] Add `gb-io` Python package (#46744) * Add build recipe for `gb-io` Python package * Add `build.sh` to `gb-io` recipe * Fix dependencies in `meta.yaml` --- recipes/gb-io/build.sh | 12 ++++++++++++ recipes/gb-io/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 recipes/gb-io/build.sh create mode 100644 recipes/gb-io/meta.yaml diff --git a/recipes/gb-io/build.sh b/recipes/gb-io/build.sh new file mode 100644 index 0000000000000..a8f3305257de7 --- /dev/null +++ b/recipes/gb-io/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash -e + +set -ex + +# Use a custom temporary directory as home on macOS. +# (not sure why this is useful, but people use it in bioconda recipes) +if [ `uname` == Darwin ]; then + export HOME=`mktemp -d` +fi + +# build statically linked binary with Rust +$PYTHON -m pip install . --no-deps --no-build-isolation -vvv diff --git a/recipes/gb-io/meta.yaml b/recipes/gb-io/meta.yaml new file mode 100644 index 0000000000000..fb3e7f98f0014 --- /dev/null +++ b/recipes/gb-io/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "gb-io" %} +{% set version = "0.3.0" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +build: + number: 0 + run_exports: + - {{ pin_subpackage('gb-io', max_pin="x.x") }} + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 210e41ab8bf732883a242e78284c57ed3854829589559cb939dad757f652cb3b + +requirements: + build: + - {{ compiler('rust') }} + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - pip + - python + - setuptools-rust + run: + - python + +test: + imports: + - gb_io + +about: + home: https://github.com/althonos/gb-io.py + license: MIT + license_file: COPYING + summary: A Python interface to gb-io, a fast GenBank parser and serializer written in Rust. From 515e1e02b599f59fa4d5b91b37c6f7fbbef64407 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 28 Mar 2024 22:03:01 +0200 Subject: [PATCH 1227/1813] ViennaRNA: add linux-aarch64 build (#46733) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * ViennaRNA: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * viennarna: Disable openmp for MacOS https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/install.html#macos-x-users Signed-off-by: Martin Tzvetanov Grigorov * viennarna: Disable 'naview' for Mac OS The build fails with: ``` 08:41:36.0304210Z 08:41:14 ␛[32mBIOCONDA INFO␛[0m (OUT) Making all in plotting/naview␛[0m 2024-03-26T08:41:36.0305220Z 08:41:14 ␛[32mBIOCONDA INFO␛[0m (OUT) make[4]: Entering directory '$SRC_DIR/src/ViennaRNA/plotting/naview'␛[0m 2024-03-26T08:41:36.0306020Z 08:41:14 ␛[32mBIOCONDA INFO␛[0m (OUT) CC naview.lo␛[0m 2024-03-26T08:41:36.0307370Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) RNA_wrap.cpp:72350:24: error: use of undeclared identifier 'SWIG_Python_str_AsChar'; did you mean 'SWIG_Python_str_FromChar'?␛[0m 2024-03-26T08:41:36.0308460Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) symbolset = strdup(SWIG_Python_str_AsChar(_val));␛[0m 2024-03-26T08:41:36.0309200Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) ^~~~~~~~~~~~~~~~~~~~~~␛[0m 2024-03-26T08:41:36.0310060Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) SWIG_Python_str_FromChar␛[0m 2024-03-26T08:41:36.0311170Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) RNA_wrap.cpp:857:1: note: 'SWIG_Python_str_FromChar' declared here␛[0m 2024-03-26T08:41:36.0311960Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) SWIG_Python_str_FromChar(const char *c)␛[0m 2024-03-26T08:41:36.0312640Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) ^␛[0m 2024-03-26T08:41:36.0313490Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) RNA_wrap.cpp:72350:47: error: cannot initialize a parameter of type 'const char *' with an lvalue of type 'PyObject *' (aka '_object *')␛[0m 2024-03-26T08:41:36.0315290Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) symbolset = strdup(SWIG_Python_str_AsChar(_val));␛[0m 2024-03-26T08:41:36.0316080Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) ^~~~␛[0m 2024-03-26T08:41:36.0316860Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) RNA_wrap.cpp:857:38: note: passing argument to parameter 'c' here␛[0m 2024-03-26T08:41:36.0317600Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) SWIG_Python_str_FromChar(const char *c)␛[0m 2024-03-26T08:41:36.0319140Z 08:41:31 ␛[32mBIOCONDA INFO␛[0m (ERR) ^␛[0m 2024-03-26T08:41:36.0319850Z 08:41:35 ␛[32mBIOCONDA INFO␛[0m (ERR) 2 errors generated.␛[0m 2024-03-26T08:41:36.0320690Z 08:41:35 ␛[32mBIOCONDA INFO␛[0m (ERR) make[3]: *** [Makefile:867: _RNA_la-RNA_wrap.lo] Error 1␛[0m 2024-03-26T08:41:36.0322000Z 08:41:35 ␛[32mBIOCONDA INFO␛[0m (ERR) make[2]: *** [Makefile:670: all-recursive] Error 1␛[0m 2024-03-26T08:41:36.0322800Z 08:41:35 ␛[32mBIOCONDA INFO␛[0m (ERR) make[1]: *** [Makefile:747: all-recursive] Error 1␛[0m ``` Signed-off-by: Martin Tzvetanov Grigorov * viennarna: Skip build for OSX because of compilation problems with naview `--without-naview` breaks with: ``` 2024-03-26T09:58:55.7422620Z 09:58:55 ␛[32mBIOCONDA INFO␛[0m (ERR) Undefined symbols for architecture x86_64:␛[0m 2024-03-26T09:58:55.7424070Z 09:58:55 ␛[32mBIOCONDA INFO␛[0m (ERR) "_naview_xy_coordinates", referenced from:␛[0m 2024-03-26T09:58:55.7425890Z 09:58:55 ␛[32mBIOCONDA INFO␛[0m (ERR) _initStacks in libRNA_special_const.a(ugly_bt.o)␛[0m 2024-03-26T09:58:55.7427900Z 09:58:55 ␛[32mBIOCONDA INFO␛[0m (ERR) ld: symbol(s) not found for architecture x86_64␛[0m 2024-03-26T09:58:55.7429230Z 09:58:55 ␛[32mBIOCONDA INFO␛[0m (ERR) clang-15: error: linker command failed with exit code 1 (use -v to see invocation)␛[0m ``` Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/viennarna/meta.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/viennarna/meta.yaml b/recipes/viennarna/meta.yaml index 50fd571203462..e8213a5142c1e 100644 --- a/recipes/viennarna/meta.yaml +++ b/recipes/viennarna/meta.yaml @@ -6,7 +6,8 @@ package: version: {{ version }} build: - number: 0 + skip: True # [osx] + number: 1 run_exports: # Ronny said VRNA is stable in x.x releases - {{ pin_subpackage('viennarna', max_pin='x.x') }} @@ -45,3 +46,7 @@ about: license: custom license_file: COPYING summary: ViennaRNA package -- RNA secondary structure prediction and comparison + +extra: + additional-platforms: + - linux-aarch64 From cb95b171bcf8f34017194acff0026c200a1ac84a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 16:11:49 -0400 Subject: [PATCH 1228/1813] Update methylartist to 1.3.0 (#46816) * Update methylartist to 1.3.0 * add tqdm --------- Co-authored-by: mencian --- recipes/methylartist/meta.yaml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/methylartist/meta.yaml b/recipes/methylartist/meta.yaml index 43fa87877feaf..13807dcfdbdd1 100644 --- a/recipes/methylartist/meta.yaml +++ b/recipes/methylartist/meta.yaml @@ -1,5 +1,5 @@ {% set name = "methylartist" %} -{% set version = "1.2.11" %} +{% set version = "1.3.0" %} package: name: "{{ name|lower }}" @@ -7,12 +7,12 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 63c3493e65352471836b54eda82ce5678e676bf7c2557c2bb56ab34ae04cf29e + sha256: 955f2ca5b0ba0d2c28e7421140e90555a8ef867ecedb41788c83132b29410329 build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -23,7 +23,7 @@ test: requirements: host: - pip - - python >=3.8 + - python >=3.7 run: - bx-python >=0.8.11 - matplotlib-base >=3.4.3 @@ -35,11 +35,13 @@ requirements: - scikit-bio >=0.5.6 - scipy >=1.7.1 - seaborn >=0.11.2 + - tqdm about: home: "https://github.com/adamewing/methylartist" license: MIT license_family: MIT + license_file: LICENSE summary: "Tools for parsing and plotting nanopore methylation data" extra: @@ -47,3 +49,5 @@ extra: - adamewing container: extended-base: True + identifiers: + - doi:10.1093/bioinformatics/btac292 From 566c77872e9f70c7adc5625905e3992b0322844b Mon Sep 17 00:00:00 2001 From: Ryan Wick Date: Fri, 29 Mar 2024 07:13:28 +1100 Subject: [PATCH 1229/1813] Update trycycler to 0.5.5 (#46843) --- recipes/trycycler/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/trycycler/meta.yaml b/recipes/trycycler/meta.yaml index 6a2dc9921ee6a..54af9c6a1546c 100644 --- a/recipes/trycycler/meta.yaml +++ b/recipes/trycycler/meta.yaml @@ -1,5 +1,5 @@ {% set name="trycycler" %} -{% set version="0.5.4" %} +{% set version="0.5.5" %} package: name: {{ name }} @@ -9,17 +9,19 @@ build: noarch: python number: 0 script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage('trycycler', max_pin="x.x") }} source: url: https://github.com/rrwick/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 6880e6920a5e4f3764fc3c7dd1dfc7ec4c9106eb5eb2ed90ae292e73c74893df + sha256: 5794a4520c3b8673adc69c975cee06d7658cd74ac6d9378d1fc7af860bec1a89 requirements: host: - - python >=3.6 + - python >=3.6,<3.11 - pip run: - - python >=3.6 + - python >=3.6,<3.11 - python-edlib - scipy - numpy From 2ed792d98c9693f3c9dc4bfc70c4990d8002bc26 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 16:15:58 -0400 Subject: [PATCH 1230/1813] Update nanocaller to 3.5.0 (#46835) * Update nanocaller to 3.5.0 * add run_exports * lower whatshap to >=2.2 --------- Co-authored-by: mencian --- recipes/nanocaller/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/nanocaller/meta.yaml b/recipes/nanocaller/meta.yaml index c0060cef2152f..9b41a43016d16 100644 --- a/recipes/nanocaller/meta.yaml +++ b/recipes/nanocaller/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanocaller" %} -{% set version = "3.4.1" %} +{% set version = "3.5.0" %} package: name: {{ name }} @@ -7,11 +7,13 @@ package: source: url: https://github.com/WGLab/NanoCaller/archive/refs/tags/v{{ version }}.zip - sha256: bce44e9a1c33c929032312e506fab64b3b9186e200be2de58db91913e5728faf + sha256: fcdcec8a64d75db376ce4671eaee353b6356547c6a7f43f6e13b058a2803337e build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('nanocaller', max_pin="x") }} requirements: run: @@ -23,8 +25,8 @@ requirements: - tensorflow >=2.4 - pysam - intervaltree - - muscle >=3.8, <4 - - whatshap >=1.4 + - muscle >=3.8,<4 + - whatshap >=2.2 - parasail-python - tqdm - rtg-tools From 23c56859b701806236f3ac8b9a2d6140148aba40 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 04:17:35 +0800 Subject: [PATCH 1231/1813] Linux-aarch64 build for assembly-stats (#46840) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * fix * Linux-aarch64 build for assembly-stats * fix * Update subpackage max_pin --------- Co-authored-by: yejianbang Co-authored-by: HWsunqian0027 Co-authored-by: dingronghua Co-authored-by: Robert A. Petit III --- recipes/assembly-stats/meta.yaml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/assembly-stats/meta.yaml b/recipes/assembly-stats/meta.yaml index 482798649fd68..9513521d7e277 100644 --- a/recipes/assembly-stats/meta.yaml +++ b/recipes/assembly-stats/meta.yaml @@ -12,8 +12,10 @@ source: - 0001-Fix-macOS-compilation.patch build: - number: 7 - + number: 8 + run_exports: + - {{ pin_subpackage("assembly-stats", max_pin="x") }} + requirements: build: - make @@ -30,3 +32,6 @@ about: home: https://github.com/sanger-pathogens/assembly-stats license: GPL-3.0 summary: 'Get assembly statistics from FASTA and FASTQ files' +extra: + additional-platforms: + - linux-aarch64 From 33ba2711b47f7c9ec6a4439c38740f68fd3138f8 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 04:19:34 +0800 Subject: [PATCH 1232/1813] linux-aarch64 build for anise_basil (#46785) Co-authored-by: yejianbang --- recipes/anise_basil/meta.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/anise_basil/meta.yaml b/recipes/anise_basil/meta.yaml index 6eb293b43fae4..39ee6a2a7275f 100644 --- a/recipes/anise_basil/meta.yaml +++ b/recipes/anise_basil/meta.yaml @@ -18,7 +18,9 @@ source: build: skip: True # [py27] - number: 6 + number: 7 + run_exports: + - {{ pin_subpackage("anise_basil", max_pin="x.x.x") }} requirements: build: @@ -29,6 +31,7 @@ requirements: host: - boost-cpp - python + - zlib run: - python @@ -51,3 +54,5 @@ about: extra: identifiers: - doi:10.1093/bioinformatics/btv051 + additional-platforms: + - linux-aarch64 From 1d3e8881d221e3ff70c0ef7614f233cbc7a31c60 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 04:20:41 +0800 Subject: [PATCH 1233/1813] linux-aarch64 build for bamcmp (#46852) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * linux-aarch64 build for bamcmp * fix * Update recipes/bamcmp/meta.yaml Co-authored-by: Martin Grigorov --------- Co-authored-by: yejianbang Co-authored-by: root Co-authored-by: Robert A. Petit III Co-authored-by: Martin Grigorov --- recipes/bamcmp/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/bamcmp/meta.yaml b/recipes/bamcmp/meta.yaml index e9798a1a41ca0..6972f19620ab3 100644 --- a/recipes/bamcmp/meta.yaml +++ b/recipes/bamcmp/meta.yaml @@ -7,7 +7,9 @@ source: md5: 05e583af007f86b275bcf95eceea7ba7 build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("bamcmp", max_pin="x") }} script_env: - HTSLIBDIR=$PREFIX @@ -28,3 +30,7 @@ about: home: https://github.com/CRUKMI-ComputationalBiology/bamcmp license: GPL-3 summary: Tools for deconvolving host and graft reads using full-length alignments and their scores. + +extra: + additional-platforms: + - linux-aarch64 From f0ab332996faa6730b0186e4ccc0b9ff42753128 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 04:20:55 +0800 Subject: [PATCH 1234/1813] linux-aarch64 build for balrog (#46849) * fix * Update recipes/balrog/meta.yaml Co-authored-by: Martin Grigorov --------- Co-authored-by: Robert A. Petit III Co-authored-by: Martin Grigorov --- recipes/balrog/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/balrog/meta.yaml b/recipes/balrog/meta.yaml index 0811762f8e566..b9157d536a298 100644 --- a/recipes/balrog/meta.yaml +++ b/recipes/balrog/meta.yaml @@ -6,7 +6,9 @@ package: version: {{ version }} build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("balrog", max_pin="x.x") }} source: url: https://github.com/salzberg-lab/BalrogCPP/archive/v{{ version }}.tar.gz @@ -35,3 +37,7 @@ about: license: MIT license_file: LICENSE summary: "Balrog: A universal protein model for prokaryotic gene prediction" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 8980a21e32854ef745e046811d46417eafe9c137 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 04:21:23 +0800 Subject: [PATCH 1235/1813] Linux-aarch64 build for aster (#46851) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * fix * Linux-aarch64 build for aster --------- Co-authored-by: yejianbang Co-authored-by: HWsunqian0027 Co-authored-by: dingronghua --- recipes/aster/build.sh | 5 +++-- recipes/aster/meta.yaml | 5 ++++- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/aster/build.sh b/recipes/aster/build.sh index ef017cb87c7ae..0dbd5f0bcda22 100644 --- a/recipes/aster/build.sh +++ b/recipes/aster/build.sh @@ -5,8 +5,9 @@ do mkdir -p "${PREFIX}/etc/conda/${CHANGE}.d" cp "${RECIPE_DIR}/${CHANGE}.sh" "${PREFIX}/etc/conda/${CHANGE}.d/${PKG_NAME}_${CHANGE}.sh" done - -sed -i.bak1 's/-march=native/-march=x86-64 -mtune=generic/g' makefile +if [ `uname -m` != "aarch64" ]; then + sed -i.bak1 's/-march=native/-march=x86-64 -mtune=generic/g' makefile +fi if [ "$(uname)" == "Darwin" ]; then sed -i.bak2 's/g++/${CXX}/g' makefile diff --git a/recipes/aster/meta.yaml b/recipes/aster/meta.yaml index 261c0d86b4a8b..19c285b795681 100644 --- a/recipes/aster/meta.yaml +++ b/recipes/aster/meta.yaml @@ -7,7 +7,7 @@ package: version: "{{ version }}" build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('aster', max_pin="x") }} @@ -37,3 +37,6 @@ about: summary: | Accurate Species Tree EstimatoR series; a family of optimation algorithms for species tree inference implemented in C++ +extra: + additional-platforms: + - linux-aarch64 From 62fdfad74fa82bf21f7deb06fcd01533309f8aef Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 04:21:31 +0800 Subject: [PATCH 1236/1813] Linux-aarch64 build for atac (#46850) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * fix * Linux-aarch64 build for atac * fix * Update recipes/atac/meta.yaml Co-authored-by: Martin Grigorov --------- Co-authored-by: yejianbang Co-authored-by: HWsunqian0027 Co-authored-by: dingronghua Co-authored-by: Robert A. Petit III Co-authored-by: Martin Grigorov --- recipes/atac/build.sh | 11 +++++++++-- recipes/atac/meta.yaml | 9 ++++++--- 2 files changed, 15 insertions(+), 5 deletions(-) diff --git a/recipes/atac/build.sh b/recipes/atac/build.sh index b4a949f10528c..bcc44e6a711ac 100644 --- a/recipes/atac/build.sh +++ b/recipes/atac/build.sh @@ -3,8 +3,11 @@ make \ CC="${CC} ${CFLAGS} ${CPPFLAGS}" \ CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} -std=c++03" \ CLDFLAGS="${LDFLAGS}" \ - CXXLDFLAGS="${LDFLAGS}" \ - install + CXXLDFLAGS="${LDFLAGS}" +if [ `uname -m` == "aarch64" ]; then + sed -i "s/Linux-i686/Linux-aarch64/" ${SRC_DIR}/Make.compilers +fi +make install mkdir -p $PREFIX @@ -12,6 +15,10 @@ if [ `uname` == Darwin ]; then cp Darwin-amd64/bin/* $PREFIX/bin/ cp Darwin-amd64/include/* $PREFIX/include/ cp Darwin-amd64/lib/* $PREFIX/lib/ +elif [ `uname -m` == "aarch64" ]; then + cp Linux-aarch64/bin/* $PREFIX/bin/ + cp Linux-aarch64/include/* $PREFIX/include/ + cp Linux-aarch64/lib/* $PREFIX/lib/ else cp Linux-amd64/bin/* $PREFIX/bin/ cp Linux-amd64/include/* $PREFIX/include/ diff --git a/recipes/atac/meta.yaml b/recipes/atac/meta.yaml index b2610cc218ce7..f0650d89f2dc5 100644 --- a/recipes/atac/meta.yaml +++ b/recipes/atac/meta.yaml @@ -9,9 +9,10 @@ source: md5: e23ef1d41836b29332b70271b7c9eb74 build: - number: 4 - skip: True # [py>=30] - + number: 5 + run_exports: + - {{ pin_subpackage("atac", max_pin=None) }} + requirements: build: - make @@ -37,3 +38,5 @@ about: extra: identifiers: - biotools:atac + additional-platforms: + - linux-aarch64 From ffb85ca30cf09b5f1a8b9549083ea5bdb234a9ce Mon Sep 17 00:00:00 2001 From: stuber Date: Thu, 28 Mar 2024 14:22:29 -0600 Subject: [PATCH 1237/1813] vsnp3 version 3.20 (#46860) --- recipes/vsnp3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsnp3/meta.yaml b/recipes/vsnp3/meta.yaml index 7daba8dea3820..2e02a9566043c 100644 --- a/recipes/vsnp3/meta.yaml +++ b/recipes/vsnp3/meta.yaml @@ -1,7 +1,7 @@ {% set user = "USDA-VS" %} {% set name = "vsnp3" %} -{% set version = "3.19" %} -{% set sha256 = "cc1c282094fc4cfcf8fdf865a954807eabe5f45a9cd1218041bd03ce2e13648d" %} +{% set version = "3.20" %} +{% set sha256 = "cb255d9e5381dcfe516bc92e35ecd3735b5447bfae74323392462579997c7a77" %} package: name: {{ name|lower }} From 05d38956fb6dca9e84e0b544b8735b25216f9bf7 Mon Sep 17 00:00:00 2001 From: farchaab <116543129+farchaab@users.noreply.github.com> Date: Thu, 28 Mar 2024 21:23:14 +0100 Subject: [PATCH 1238/1813] Update assembly_finder to v0.6.0 (#46814) * Updated recipe * clean up recipe --------- Co-authored-by: mencian --- recipes/assembly_finder/meta.yaml | 38 +++++++++++++++++-------------- 1 file changed, 21 insertions(+), 17 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index d54840930f3be..fc5c7bdc74dc3 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,44 +1,48 @@ {% set name = "assembly_finder" %} -{% set version = "0.4.2" %} +{% set version = "0.6.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - - url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 6f035d34e562c0727fa0a43172de61b879714c3a1d964b6a5952afb49301129b + url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: fe5dbe825730852005c382b88e3d89ac88f16e74cb0d6a5f26ad8c566df07119 + build: number: 0 - entry_points: - - assembly_finder = assembly_finder.assembly_finder:cli noarch: python - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv + script: {{ PYTHON }} -m pip install . -vvv + entry_points: + - assembly_finder = assembly_finder.__main__:cli run_exports: - {{ pin_subpackage('assembly_finder', max_pin="x.x") }} requirements: host: - - python >=3.9,<3.12 + - python >=3.9,<=3.12 - pip - run: - - python >=3.9,<3.12 - - snakemake-minimal >=7.32.4 - - click >=7 - - biopython >=1.78 - - pandas >=2.0.3 - - ete3 >=3.1.3 - - aspera-cli >=4.14.0 + - python >=3.9,<=3.12 + - snakemake-minimal >=7.32.4,<8 + - pulp <2.8 + - pandas >=2.2.1 + - rich-click >=1.7.4 + - ncbi-datasets-cli >=16.10.1 + test: commands: - assembly_finder -h - assembly_finder -v + about: home: https://github.com/metagenlab/assembly_finder - license: GPL-3.0-or-later + license: MIT + license_family: MIT license_file: LICENSE - summary: Snakemake pipeline to download assemblies from NCBI. + summary: "Snakemake-powered cli pipeline to download genomes with NCBI datasets" + dev_url: https://github.com/metagenlab/assembly_finder + doc_url: https://metagenlab.github.io/assembly_finder extra: container: From 475c345fd3fc3c51d1871ac667d59fbc9a7205a3 Mon Sep 17 00:00:00 2001 From: Andrew Robbins Date: Thu, 28 Mar 2024 16:30:56 -0400 Subject: [PATCH 1239/1813] clean dependencies for liger (#46845) --- recipes/r-liger/meta.yaml | 53 +++++++++++++++------------------------ 1 file changed, 20 insertions(+), 33 deletions(-) diff --git a/recipes/r-liger/meta.yaml b/recipes/r-liger/meta.yaml index b2dc397fdbd31..4d150e4e9dfbd 100644 --- a/recipes/r-liger/meta.yaml +++ b/recipes/r-liger/meta.yaml @@ -12,7 +12,7 @@ source: sha256: a189285513e5a11d658056de55670fe877bcf2f52ce65837f9b8a4b3ff7bab2f build: - number: 0 + number: 1 script: R CMD INSTALL --build . rpaths: - lib/R/lib/ @@ -26,72 +26,58 @@ requirements: - make host: - r-base - - r-fnn - - r-hmisc - - r-rann.l1 - r-rcpp >=0.12.10 - r-rcpparmadillo - r-rcppprogress - r-rtsne - r-cowplot - - r-dosnow - r-dplyr - - r-foreach - r-ggplot2 - - r-ggrepel - r-ica - r-irlba - r-mclust - - r-patchwork - - r-doparallel - r-uwot - r-hdf5r - - r-plyr - - r-snow - - r-psych - - r-rcppeigen - r-rann - - r-scattermore >=0.7 - r-circlize - bioconductor-complexheatmap - r-leidenalg >=1.1.1 - bioconductor-s4vectors + - r-cli + - r-rlang + - r-matrix + - r-lifecycle + - r-magrittr + - r-scales + - r-rcolorbrewer + - r-viridis run: - r-base - - r-fnn - - r-hmisc - - r-rann.l1 - r-rcpp >=0.12.10 - r-rcpparmadillo - r-rcppprogress - r-rtsne - r-cowplot - - r-doparallel - - r-uwot - - r-hdf5r - - r-dosnow - r-dplyr - - r-foreach - r-ggplot2 - - r-ggrepel - r-ica - r-irlba - r-mclust - - r-patchwork - - r-plyr - - r-snow - - r-psych - - r-rcppeigen + - r-uwot + - r-hdf5r - r-rann - - r-reticulate - - r-scattermore >=0.7 - - openjdk >=6 - - umap-learn - r-circlize - bioconductor-complexheatmap - r-leidenalg >=1.1.1 - bioconductor-s4vectors - + - r-cli + - r-rlang + - r-matrix + - r-lifecycle + - r-magrittr + - r-scales + - r-rcolorbrewer + - r-viridis test: commands: - $R -e "library('rliger')" @@ -111,6 +97,7 @@ about: extra: recipe-maintainers: + - theAeon - raivivek identifiers: - doi:10.1016/j.cell.2019.05.006 From 8f4327e37e4ccebe955a156fc25d49d35f81f58a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 16:45:26 -0400 Subject: [PATCH 1240/1813] Update msgf_plus to 2024.03.26 (#46781) * Update msgf_plus to 2024.03.26 * add run_exports --------- Co-authored-by: mencian --- recipes/msgf_plus/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/msgf_plus/meta.yaml b/recipes/msgf_plus/meta.yaml index 7bd4fc1fe9d28..228a710889f02 100644 --- a/recipes/msgf_plus/meta.yaml +++ b/recipes/msgf_plus/meta.yaml @@ -1,14 +1,16 @@ package: name: msgf_plus - version: 2023.01.1202 + version: 2024.03.26 build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('msgf_plus', max_pin=None) }} source: - url: https://github.com/MSGFPlus/msgfplus/releases/download/v2023.01.12/MSGFPlus_v20230112.zip - sha256: ae9eb564b119ce54e5182fa9a9cc9b1d1c3e43489e81ed80279a442b55d5607c + url: https://github.com/MSGFPlus/msgfplus/releases/download/v2024.03.26/MSGFPlus_v20240326.zip + sha256: 01bacb4e74077f84c206f6f91eba67a29433d07d649f438b013a77217b0bfaac requirements: host: @@ -33,7 +35,7 @@ about: spectra, different configurations of MS instruments and different experimental protocols). -extra: +extra: identifiers: - biotools:MSGFplus - doi:10.1038/ncomms6277 From 45651ed44da8cbbee2e01d7532d4b1e7f82295d6 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 05:02:20 +0800 Subject: [PATCH 1241/1813] linux-aarch64 build for ancestry_hmm (#46790) Co-authored-by: yejianbang Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ancestry_hmm/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/ancestry_hmm/meta.yaml b/recipes/ancestry_hmm/meta.yaml index ade1fb5b597eb..c1dc3d738c45c 100644 --- a/recipes/ancestry_hmm/meta.yaml +++ b/recipes/ancestry_hmm/meta.yaml @@ -11,7 +11,9 @@ source: sha256: {{sha256}} build: - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage("ancestry_hmm", max_pin="x.x.x") }} requirements: build: @@ -39,3 +41,5 @@ about: extra: identifiers: - doi:10.1371/journal.pgen.1006529 + additional-platforms: + - linux-aarch64 From a12c3f3b87369f33b91f5300748d18a56f69889e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 17:03:24 -0400 Subject: [PATCH 1242/1813] Update snakemake to 8.10.4 (#46774) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake to 8.10.1 * Update meta.yaml * Update meta.yaml * Update snakemake to 8.10.4 --------- Co-authored-by: Johannes Köster Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index a12e2aad43fbd..0f6be51be0208 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.10.0" %} +{% set version = "8.10.4" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: abd73a2acd6741d0794bbf6e11eb1ae50cf44dc060e6dc80328fce2a4633dd78 + sha256: 8228185f85a1e861c3e8a828f405d575a37dcdcf80b82fc681958a0e85a9ebe6 build: number: 0 @@ -103,7 +103,7 @@ outputs: - requests >=2.8.1 - reretry - smart_open >=3.0,<4.0 - - snakemake-interface-executor-plugins >=9.0.2,<10.0.0 + - snakemake-interface-executor-plugins >=9.1.0,<10.0.0 - snakemake-interface-common >=1.17.0,<2.0 - snakemake-interface-storage-plugins >=3.1.0,<4.0 - snakemake-interface-report-plugins >=1.0.0,<2.0.0 From d2e0fee49c8f2f1f43bc5d9f47bd5cc35e721b74 Mon Sep 17 00:00:00 2001 From: Ilya Shlyakhter Date: Thu, 28 Mar 2024 17:05:06 -0400 Subject: [PATCH 1243/1813] Update igvtools to 2.17.3 (#46719) * updated igvtools to 2.17.3 * added run_exports * fix pin_subpackage --- recipes/igvtools/igvtools.sh | 9 --------- recipes/igvtools/meta.yaml | 10 ++++++---- 2 files changed, 6 insertions(+), 13 deletions(-) diff --git a/recipes/igvtools/igvtools.sh b/recipes/igvtools/igvtools.sh index 08f3849b0afa5..a2702832d9ce0 100644 --- a/recipes/igvtools/igvtools.sh +++ b/recipes/igvtools/igvtools.sh @@ -16,13 +16,4 @@ while [[ -h "$SOURCE" ]]; do # resolve $SOURCE until the file is no longer a sym done DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" -# Check whether or not to use the bundled JDK -if [ -d "${DIR}/jdk-11" ]; then - echo echo "Using bundled JDK." - JAVA_HOME="${DIR}/jdk-11" - PATH=$JAVA_HOME/bin:$PATH -else - echo "Using system JDK." -fi - java -Djava.awt.headless=true --module-path="${DIR}/lib" -Xmx1500m --module=org.igv/org.broad.igv.tools.IgvTools "$@" diff --git a/recipes/igvtools/meta.yaml b/recipes/igvtools/meta.yaml index 63dc7743ed394..55cc6343b6e61 100644 --- a/recipes/igvtools/meta.yaml +++ b/recipes/igvtools/meta.yaml @@ -1,22 +1,24 @@ {% set name = "IGVtools" %} -{% set version = "2.16.2" %} -{% set sha256 = "489d34ed4e807a3d32a3720f11248d2ddf1e21d264b06bea44fbe1ccb74b3aa2" %} +{% set version = "2.17.3" %} +{% set sha256 = "58369ad1e156dc27a7cd2861c238049563396be605a2ab1b172a008a69ad7cb4" %} package: name: {{ name|lower }} version: {{ version }} source: - url: http://data.broadinstitute.org/igv/projects/downloads/2.16/IGV_{{ version }}.zip + url: http://data.broadinstitute.org/igv/projects/downloads/2.17/IGV_{{ version }}.zip sha256: {{ sha256 }} build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: run: - - openjdk 11 + - openjdk >=17 test: commands: From 2961fff1aaedb52937e41c813c16365416043c0d Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 28 Mar 2024 23:54:26 +0200 Subject: [PATCH 1244/1813] last: add linux-aarch64 build (#46808) Signed-off-by: Martin Tzvetanov Grigorov Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/last/build.sh | 11 +++++++++++ recipes/last/meta.yaml | 5 +++-- 2 files changed, 14 insertions(+), 2 deletions(-) create mode 100644 recipes/last/build.sh diff --git a/recipes/last/build.sh b/recipes/last/build.sh new file mode 100644 index 0000000000000..869569e244d1f --- /dev/null +++ b/recipes/last/build.sh @@ -0,0 +1,11 @@ +#!/usr/bin/env bash + +set -xe + +ARCH=$(uname -m) +case ${ARCH} in + x86_64) ARCH_FLAGS="-msse4" ;; + *) ARCH_FLAGS="" ;; +esac + +make install CXXFLAGS="$CXXFLAGS ${ARCH_FLAGS} -pthread" prefix=$PREFIX \ No newline at end of file diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 8c7b6b9fae609..7f57e5ad79a0a 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -10,10 +10,9 @@ source: sha256: ee26e762fe76d167241f7e85b5e72ef8d17ed243c405e38dbbd06de97003596a build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('last', max_pin=None) }} - script: make install CXXFLAGS="$CXXFLAGS -msse4 -pthread" prefix=$PREFIX requirements: build: @@ -59,6 +58,8 @@ about: description: "LAST finds & aligns related regions of sequences. It is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially good at: finding rearrangements and recombinations; finding DNA-versus-protein related regions; unusual data like AT-rich DNA; sensitive DNA-DNA search." extra: + additional-platforms: + - linux-aarch64 container: extended-base: True identifiers: From d62ab257cad68f06762e8d74fc2388a3f035a34c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 17:55:19 -0400 Subject: [PATCH 1245/1813] Update gb-io to 0.3.1 (#46865) --- recipes/gb-io/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gb-io/meta.yaml b/recipes/gb-io/meta.yaml index fb3e7f98f0014..c546baf02d07b 100644 --- a/recipes/gb-io/meta.yaml +++ b/recipes/gb-io/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gb-io" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: "{{ name }}" @@ -12,7 +12,7 @@ build: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 210e41ab8bf732883a242e78284c57ed3854829589559cb939dad757f652cb3b + sha256: 4400d9b9864402b410ee1753e0cd8c405f692bfee4032fe8ab8ce4d50bef80ce requirements: build: From 8c3c750d091ee09874ccae034895c89a53be5e58 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 17:55:35 -0400 Subject: [PATCH 1246/1813] Update ntlink to 1.3.10 (#46867) --- recipes/ntlink/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ntlink/meta.yaml b/recipes/ntlink/meta.yaml index 5a3753c1f1796..576cbcab302c5 100644 --- a/recipes/ntlink/meta.yaml +++ b/recipes/ntlink/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.9" %} +{% set version = "1.3.10" %} package: name: ntlink @@ -6,10 +6,10 @@ package: source: url: https://github.com/bcgsc/ntLink/releases/download/v{{ version }}/ntLink-{{ version }}.tar.gz - sha256: 3a6fe7ca9c7a0226cf51b7e55804e235ac2b959e82a30f9bce55b9caea5bb03b + sha256: 248ccae217dd7ed2e4664c6b48235f8db2ba24d8896b8315f6e657f19d5f7085 build: - number: 4 + number: 0 noarch: generic run_exports: - {{ pin_subpackage('ntlink', max_pin="x") }} From 592f41189821ca4c29401488e1db0e8faf8908b8 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 29 Mar 2024 00:04:12 +0200 Subject: [PATCH 1247/1813] freebayes: add linux-aarch64 build (#46736) * freebayes: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Add linux-aarch64 builds for tabixpp, vcflib and wfa2-lib freebayes depends on them Signed-off-by: Martin Tzvetanov Grigorov * freebayes: Add zlib as a host/run dependency Signed-off-by: Martin Tzvetanov Grigorov * Add zig for Linux aarch64 Signed-off-by: Martin Tzvetanov Grigorov * Re-trigger CI --------- Signed-off-by: Martin Tzvetanov Grigorov Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/freebayes/meta.yaml | 19 +++++++++++++------ recipes/vcflib/build.sh | 23 +++++++++-------------- recipes/vcflib/meta.yaml | 13 +++++++++---- 3 files changed, 31 insertions(+), 24 deletions(-) diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index 150a384c7f12c..e6a3953d98e42 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -12,7 +12,7 @@ source: - 0002-fix-intervaltree-include-path.patch build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage("freebayes", max_pin="x") }} @@ -31,25 +31,32 @@ requirements: - tabixpp - vcflib - simde + - zlib run: - parallel - samtools - tabixpp - vcflib - + - zlib + test: commands: - freebayes --version - freebayes-parallel - + about: - home: https://github.com/ekg/freebayes + home: https://github.com/freebayes/freebayes license: MIT license_file: LICENSE license_family: MIT summary: Bayesian haplotype-based polymorphism discovery and genotyping - maintainers: jpuritz + dev_url: https://github.com/freebayes/freebayes extra: - identifiers: + additional-platforms: + - linux-aarch64 + identifiers: - biotools:freebayes + - usegalaxy-eu:freebayes + recipe-maintainers: + - jpuritz diff --git a/recipes/vcflib/build.sh b/recipes/vcflib/build.sh index c282330d8bd3e..ac929087a86e7 100644 --- a/recipes/vcflib/build.sh +++ b/recipes/vcflib/build.sh @@ -1,12 +1,15 @@ #!/bin/bash set -ex -if [ `uname` == Darwin ]; then +OS=$(uname) +ARCH=$(uname -m) + +if [ "${OS}" == "Darwin" ]; then echo $(pwd)/zig-macos-x86_64-* export PATH="$(pwd)/zig-macos-x86_64-0.10.1:${PATH}" - else - echo $(pwd)/zig-linux-x86_64-* - export PATH="$(pwd)/zig-linux-x86_64-0.10.1:${PATH}" +else + echo $(pwd)/zig-linux-${ARCH}-* + export PATH="$(pwd)/zig-linux-${ARCH}-0.10.1:${PATH}" fi export INCLUDES="-I${PREFIX}/include -I. -Ihtslib -Itabixpp -I\$(INC_DIR)" @@ -24,7 +27,7 @@ sed -i.bak 's/g++/$(CXX) $(CXXFLAGS)/g' contrib/multichoose/Makefile sed -i.bak 's/g++/$(CXX) $(CXXFLAGS)/g' contrib/intervaltree/Makefile # MacOSX Build fix: https://github.com/chapmanb/homebrew-cbl/issues/14 -if [ "$(uname)" == "Darwin" ]; then +if [ "${OS}" == "Darwin" ]; then sed -i.bak 's/LDFLAGS=-Wl,-s/LDFLAGS=/' contrib/smithwaterman/Makefile export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib" export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_ENABLE_CXX17_REMOVED_FEATURES" @@ -36,15 +39,7 @@ pkg-config --list-all cmake -S . -B build \ -DZIG=ON -DOPENMP=ON -DWFA_GITMODULE=OFF \ -DCMAKE_BUILD_TYPE=Release \ - -DBUILD_SHARED_LIBS=ON \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ - -DCMAKE_CXX_COMPILER="${CXX}" \ - -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ - -DCMAKE_C_COMPILER="${CC}" \ - -DCMAKE_INCLUDE_PATH="${PREFIX}/include" \ - -DCMAKE_LIBRARY_PATH="${PREFIX}/lib" + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" cmake --build build/ --target install -j 4 -v - -#cp -n ../scripts/* $PREFIX/bin -#cp -n -r ../src/simde $PREFIX/include/ diff --git a/recipes/vcflib/meta.yaml b/recipes/vcflib/meta.yaml index aa3a495dd30c3..7b67cbff59f6c 100644 --- a/recipes/vcflib/meta.yaml +++ b/recipes/vcflib/meta.yaml @@ -14,15 +14,18 @@ source: - shared_lib.patch - backport_pr_394.patch # TODO remove once PR https://github.com/vcflib/vcflib/pull/394 is merged and released - tabix.patch -- url: https://ziglang.org/download/0.10.1/zig-linux-x86_64-0.10.1.tar.xz # [linux] - sha256: 6699f0e7293081b42428f32c9d9c983854094bd15fee5489f12c4cf4518cc380 # [linux] - folder: zig-linux-x86_64-0.10.1 # [linux] +- url: https://ziglang.org/download/0.10.1/zig-linux-x86_64-0.10.1.tar.xz # [linux and x86_64] + sha256: 6699f0e7293081b42428f32c9d9c983854094bd15fee5489f12c4cf4518cc380 # [linux and x86_64] + folder: zig-linux-x86_64-0.10.1 # [linux and x86_64] +- url: https://ziglang.org/download/0.10.1/zig-linux-aarch64-0.10.1.tar.xz # [linux and aarch64] + sha256: db0761664f5f22aa5bbd7442a1617dd696c076d5717ddefcc9d8b95278f71f5d # [linux and aarch64] + folder: zig-linux-aarch64-0.10.1 # [linux and aarch64] - url: https://ziglang.org/download/0.10.1/zig-macos-x86_64-0.10.1.tar.xz # [osx] sha256: 02483550b89d2a3070c2ed003357fd6e6a3059707b8ee3fbc0c67f83ca898437 # [osx] folder: zig-macos-x86_64-0.10.1 # [osx] build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('vcflib', max_pin="x") }} @@ -70,6 +73,8 @@ about: summary: Command-line tools for manipulating VCF files extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - jpuritz identifiers: From f71f1dffa06feec7953504d301dcedae95c7bc51 Mon Sep 17 00:00:00 2001 From: RolandFaure <64131971+RolandFaure@users.noreply.github.com> Date: Thu, 28 Mar 2024 23:28:29 +0100 Subject: [PATCH 1248/1813] Update HairSplitter version to remove bugs in the installation (#46762) * added hairsplitter * correct linting * corrected hairsplitter recipe * updated hairsplitter version to correct bugs in installation --- recipes/hairsplitter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hairsplitter/meta.yaml b/recipes/hairsplitter/meta.yaml index 9b7b60fea5adc..1f7c712cd742a 100644 --- a/recipes/hairsplitter/meta.yaml +++ b/recipes/hairsplitter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "HairSplitter" %} -{% set version = "1.7.13" %} -{% set sha256 = "4387ae2076fd4b8b5e5610ad3a8e678979522403a4735fa4a0522db2feb653f7" %} +{% set version = "1.7.14" %} +{% set sha256 = "4bfb058ad7d0b0ea760c1791bd8179a3a5b75b314f3034cb2979f1a26290a3d3" %} package: name: {{ name|lower }} From d98446e7b0d4f1f750be452116a16ac7409177fc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 21:26:51 -0400 Subject: [PATCH 1249/1813] Update skder to 1.0.9 (#46870) --- recipes/skder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skder/meta.yaml b/recipes/skder/meta.yaml index 4dd0dfc2b7538..4cdfb358228f0 100644 --- a/recipes/skder/meta.yaml +++ b/recipes/skder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skder" %} -{% set version = "1.0.8" %} +{% set version = "1.0.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/raufs/skDER/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5d48666d6c7db738777c3bbe2601b01707c2c961b987aecde0f4210154605254 + sha256: 0b72a416874235046eb5b4ad1edca98773013043319051b8cdea794c5ee39220 build: number: 0 From 8b694d3f10dab12dd75854cacc93dae75b7b9464 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 28 Mar 2024 20:56:02 -0500 Subject: [PATCH 1250/1813] Update pasa recipe (#46873) --- recipes/pasa/build.sh | 2 ++ recipes/pasa/meta.yaml | 8 ++++++-- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/pasa/build.sh b/recipes/pasa/build.sh index 726bc8573d514..788c19f7e9fdf 100644 --- a/recipes/pasa/build.sh +++ b/recipes/pasa/build.sh @@ -31,3 +31,5 @@ echo "export PASAHOME=${PASAHOME}" > ${PREFIX}/etc/conda/activate.d/${PKG_NAME}- mkdir -p ${PREFIX}/etc/conda/deactivate.d/ echo "unset PASAHOME" > ${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}-${PKG_VERSION}.sh + +make clean diff --git a/recipes/pasa/meta.yaml b/recipes/pasa/meta.yaml index 2de53fba67c7e..b86f75dd4dd78 100644 --- a/recipes/pasa/meta.yaml +++ b/recipes/pasa/meta.yaml @@ -7,7 +7,9 @@ package: version: {{ version }} build: - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('pasa', max_pin="x") }} source: url: https://github.com/PASApipeline/PASApipeline/releases/download/pasa-v{{ version }}/PASApipeline.v{{ version }}.FULL.tar.gz @@ -23,7 +25,7 @@ requirements: - cdbtools - slclust - transdecoder - - gmap >=2021.08.25 + - gmap >=2023.10.10 - lighttpd # [linux] - samtools - perl @@ -48,9 +50,11 @@ test: about: home: "https://github.com/PASApipeline/PASApipeline" license: BSD-3-Clause + license_family: BSD license_file: LICENSE summary: "PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments." doc_url: "https://github.com/PASApipeline/PASApipeline/wiki" + dev_url: "https://github.com/PASApipeline/PASApipeline" extra: identifiers: From eecd36827bfcfa727391a70e600d165442ec93ef Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 28 Mar 2024 21:04:44 -0500 Subject: [PATCH 1251/1813] Patch vcflib recipe (#46871) * Patch vcflib recipe * edit tests * edit tests * edit tests once again * edit tests once again --- recipes/vcflib/backport_pr_394.patch | 16 ++++++++++++---- recipes/vcflib/meta.yaml | 4 ++-- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/recipes/vcflib/backport_pr_394.patch b/recipes/vcflib/backport_pr_394.patch index fa6e5e24c0671..b2be5bdcc49da 100644 --- a/recipes/vcflib/backport_pr_394.patch +++ b/recipes/vcflib/backport_pr_394.patch @@ -2,11 +2,19 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt index 088605d..286c9fc 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -445,6 +445,8 @@ if (NOT BUILD_ONLY_LIB) +@@ -462,6 +462,15 @@ if (NOT BUILD_ONLY_LIB) + target_link_libraries(vcfallelicprimitives PUBLIC ${WFALIB}) + target_link_libraries(vcfcleancomplex PUBLIC ${WFALIB}) target_link_libraries(vcfparsealts PUBLIC ${WFALIB}) - target_link_libraries(vcfroc PUBLIC ${WFALIB}) - target_link_libraries(vcfstats PUBLIC ${WFALIB}) + target_link_libraries(vcfstreamsort PUBLIC ${WFALIB}) + target_link_libraries(vcfuniq PUBLIC ${WFALIB}) ++ target_link_libraries(vcfcreatemulti PUBLIC ${WFALIB}) ++ target_link_libraries(vcfld PUBLIC ${WFALIB}) ++ target_link_libraries(vcfecho PUBLIC ${WFALIB}) ++ target_link_libraries(vcfuniqalleles PUBLIC ${WFALIB}) ++ target_link_libraries(vcffilter PUBLIC ${WFALIB}) ++ target_link_libraries(permuteGPAT++ PUBLIC ${WFALIB}) ++ target_link_libraries(vcfintersect PUBLIC ${WFALIB}) + target_link_libraries(vcfroc PUBLIC ${WFALIB}) + target_link_libraries(vcfstats PUBLIC ${WFALIB}) target_link_libraries(vcfwave PUBLIC ${WFALIB}) - install(TARGETS ${BINS} RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) diff --git a/recipes/vcflib/meta.yaml b/recipes/vcflib/meta.yaml index 7b67cbff59f6c..03b091e5953c1 100644 --- a/recipes/vcflib/meta.yaml +++ b/recipes/vcflib/meta.yaml @@ -25,7 +25,7 @@ source: folder: zig-macos-x86_64-0.10.1 # [osx] build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('vcflib', max_pin="x") }} @@ -37,13 +37,13 @@ requirements: - pybind11-global # python really only used as a build tool; no ${PREFIX}/bin/python needed. - python >=3 + - pkg-config host: - libgomp # [linux] - llvm-openmp # [osx] - zlib - htslib - tabixpp - - pkg-config - wfa2-lib run: - python >=3 From b242d1047e3181360fb21c707e9360a5451a2bb9 Mon Sep 17 00:00:00 2001 From: schorlton-bugseq <165083261+schorlton-bugseq@users.noreply.github.com> Date: Thu, 28 Mar 2024 19:34:51 -0700 Subject: [PATCH 1252/1813] bump stecfinder 1.1.2 (#46869) Co-authored-by: Sam Chorlton <> --- recipes/stecfinder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/stecfinder/meta.yaml b/recipes/stecfinder/meta.yaml index 93560d5d7a168..4309d12496f0b 100644 --- a/recipes/stecfinder/meta.yaml +++ b/recipes/stecfinder/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} {% set name = "stecfinder" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/LanLab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 270a80b78f7ab9d69f35b67128da967e23a08538a608dc919865158236ca5de5 + sha256: 56143eca071f750d9aad69451c3028ecffb7c4f701386b7cf923a193ef916965 build: noarch: python From 5a2c3543e64c6be12935800ca49306ffb6ea079a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Mar 2024 22:42:19 -0400 Subject: [PATCH 1253/1813] Update dajin2 to 0.4.3 (#46875) --- recipes/dajin2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index 5ffd4d0f18afd..23fad00eb9725 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.4.2" %} +{% set version = "0.4.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: 34f25000f2f2d0c7ff40163cd68f2702549b7ae703cf9c665f3a208601f549fa + sha256: 1a5334a6639f8958e2a8b0254e73066991ff849f00a1194d236a324b3507fbb3 build: entry_points: From 2b37972ea63c9d3d80d7510ac1a405edcfa4dcbf Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 28 Mar 2024 23:06:35 -0500 Subject: [PATCH 1254/1813] Update trinity recipe (#46872) * Update trinity recipe * edit build.sh * src_dir * edit build.sh --- recipes/trinity/build.sh | 25 +++++++++++++------------ recipes/trinity/meta.yaml | 8 ++++---- 2 files changed, 17 insertions(+), 16 deletions(-) diff --git a/recipes/trinity/build.sh b/recipes/trinity/build.sh index 4d6f8b5e7ea0f..453ee990e1564 100644 --- a/recipes/trinity/build.sh +++ b/recipes/trinity/build.sh @@ -5,7 +5,7 @@ export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -fopenmp" -export CXXFLAGS="-O3 -I${PREFIX}/include ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}" export BINARY_HOME="${PREFIX}/bin" export TRINITY_HOME="${PREFIX}/opt/trinity-${PKG_VERSION}" @@ -32,18 +32,20 @@ cp -LR PyLib ${TRINITY_HOME}/ cp -LR trinity-plugins ${TRINITY_HOME}/ cp -LR util ${TRINITY_HOME}/ +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${TRINITY_HOME}/util/misc/fastq_stats.pl + # add link to Trinity from bin so in PATH cd ${BINARY_HOME} -ln -s ${TRINITY_HOME}/Trinity -ln -s ${TRINITY_HOME}/util/*.pl . -ln -s ${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -ln -s ${TRINITY_HOME}/Analysis/DifferentialExpression/run_DE_analysis.pl -ln -s ${TRINITY_HOME}/Analysis/DifferentialExpression/analyze_diff_expr.pl -ln -s ${TRINITY_HOME}/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl -ln -s ${TRINITY_HOME}/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py -ln -s ${TRINITY_HOME}/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py -ln -s ${TRINITY_HOME}/util/support_scripts/get_Trinity_gene_to_trans_map.pl -ln -s ${TRINITY_HOME}/util/misc/contig_ExN50_statistic.pl +ln -sf ${TRINITY_HOME}/Trinity +ln -sf ${TRINITY_HOME}/util/*.pl . +ln -sf ${TRINITY_HOME}/Analysis/DifferentialExpression/PtR +ln -sf ${TRINITY_HOME}/Analysis/DifferentialExpression/run_DE_analysis.pl +ln -sf ${TRINITY_HOME}/Analysis/DifferentialExpression/analyze_diff_expr.pl +ln -sf ${TRINITY_HOME}/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl +ln -sf ${TRINITY_HOME}/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py +ln -sf ${TRINITY_HOME}/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py +ln -sf ${TRINITY_HOME}/util/support_scripts/get_Trinity_gene_to_trans_map.pl +ln -sf ${TRINITY_HOME}/util/misc/contig_ExN50_statistic.pl cp ${TRINITY_HOME}/trinity-plugins/BIN/seqtk-trinity . # Find real path when executing from a symlink @@ -56,7 +58,6 @@ sed -i.bak "s/\$ROOTDIR\/trinity-plugins\/Trimmomatic/\/opt\/anaconda1anaconda2a sed -i.bak 's/my $TRIMMOMATIC = "\([^"]\+\)"/my $TRIMMOMATIC = '"'"'\1'"'"'/' ${TRINITY_HOME}/Trinity sed -i.bak 's/my $TRIMMOMATIC_DIR = "\([^"]\+\)"/my $TRIMMOMATIC_DIR = '"'"'\1'"'"'/' ${TRINITY_HOME}/Trinity - find ${TRINITY_HOME} -type f -name "*.bak" -print0 | xargs -0 rm -f # export TRINITY_HOME as ENV variable diff --git a/recipes/trinity/meta.yaml b/recipes/trinity/meta.yaml index c686e8c82f057..721036e21f6e1 100644 --- a/recipes/trinity/meta.yaml +++ b/recipes/trinity/meta.yaml @@ -13,7 +13,9 @@ source: - makefile.patch build: - number: 3 + number: 4 + run_exports: + - {{ pin_subpackage('trinity', max_pin="x") }} requirements: build: @@ -72,9 +74,7 @@ about: home: https://github.com/trinityrnaseq/trinityrnaseq/ license: BSD-3-Clause license_family: BSD - license_file: - - LICENSE - - LICENSE.txt + license_file: LICENSE summary: "Trinity assembles transcript sequences from Illumina RNA-Seq data." doc_url: https://github.com/trinityrnaseq/trinityrnaseq/wiki dev_url: https://github.com/trinityrnaseq/trinityrnaseq/ From 8c95e97111191339f719343d6c8eb6b3a30e8767 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 29 Mar 2024 00:21:48 -0500 Subject: [PATCH 1255/1813] Update freebayes recipe (#46882) * Update freebayes recipe * add zlib back to run * edit build.sh * add macos patch * add build selector --- recipes/freebayes/0003-meson-macos.patch | 13 +++++++++++++ recipes/freebayes/LICENSE | 19 ------------------- recipes/freebayes/build.sh | 8 ++++---- recipes/freebayes/meta.yaml | 7 ++++--- 4 files changed, 21 insertions(+), 26 deletions(-) create mode 100644 recipes/freebayes/0003-meson-macos.patch delete mode 100644 recipes/freebayes/LICENSE diff --git a/recipes/freebayes/0003-meson-macos.patch b/recipes/freebayes/0003-meson-macos.patch new file mode 100644 index 0000000000000..47e1176d8d7ad --- /dev/null +++ b/recipes/freebayes/0003-meson-macos.patch @@ -0,0 +1,13 @@ +diff --git a/meson.build b/meson.build +index 66b8016..bf0bf10 100644 +--- a/meson.build ++++ b/meson.build +@@ -16,7 +16,7 @@ + + project('freebayes', ['cpp', 'c'], + version : '1.3.7', +- default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3']) ++ default_options : ['warning_level=1', 'cpp_std=c++14', 'optimization=3']) + static_build = get_option('static') + + cc = meson.get_compiler('cpp') diff --git a/recipes/freebayes/LICENSE b/recipes/freebayes/LICENSE deleted file mode 100644 index 9e3322e991a3d..0000000000000 --- a/recipes/freebayes/LICENSE +++ /dev/null @@ -1,19 +0,0 @@ -Copyright (c) 2010 Erik Garrison, Gabor Marth - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE. diff --git a/recipes/freebayes/build.sh b/recipes/freebayes/build.sh index 660009d1b0fc8..a090a95414a3a 100644 --- a/recipes/freebayes/build.sh +++ b/recipes/freebayes/build.sh @@ -1,9 +1,10 @@ #!/bin/bash mkdir build -meson setup --buildtype debug --prefix "${PREFIX}" -Dprefer_system_deps=true build/ - +mkdir -p ${PREFIX}/bin +CXX="${CXX}" CC="${CC}" meson setup --buildtype release --prefix "${PREFIX}" \ + --strip --prefer-static -Dprefer_system_deps=true build/ cd build ninja -v @@ -13,7 +14,6 @@ ninja -v install ##Copy scripts over ## This will likely need to be removed with an updated build cp -n ../scripts/*.py $PREFIX/bin cp -n ../scripts/*.sh $PREFIX/bin -cp -n ../scripts/*.pl $PREFIX/bin -#cp -n ../scripts/*.R $PREFIX/bin +cp -n ../scripts/*.pl $PREFIX/bin cp -n ../scripts/freebayes-parallel $PREFIX/bin diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index e6a3953d98e42..f10c0fa32a4b2 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -1,7 +1,8 @@ +{% set name = "freebayes" %} {% set version = "1.3.7" %} package: - name: freebayes + name: {{ name }} version: {{ version }} source: @@ -10,10 +11,10 @@ source: patches: - 0001-make-meson-build-conda-friendly.patch - 0002-fix-intervaltree-include-path.patch + - 0003-meson-macos.patch # [osx] build: - number: 1 - skip: true # [osx] + number: 2 run_exports: - {{ pin_subpackage("freebayes", max_pin="x") }} From 402ebd7582ace5e7027c14777ef3ca5fd3a43dba Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 15:01:39 +0800 Subject: [PATCH 1256/1813] linux-aarch64 build for bcftools-gtc2vcf-plugin (#46877) Co-authored-by: HWsunqian0027 --- recipes/bcftools-gtc2vcf-plugin/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/bcftools-gtc2vcf-plugin/meta.yaml b/recipes/bcftools-gtc2vcf-plugin/meta.yaml index cc1e37047ad6f..414d0485f8c57 100644 --- a/recipes/bcftools-gtc2vcf-plugin/meta.yaml +++ b/recipes/bcftools-gtc2vcf-plugin/meta.yaml @@ -16,7 +16,7 @@ source: sha256: "782b5f1bc690415192231e82213b3493b047f45e630dc8ef6f154d6126ab3e68" build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage("bcftools-gtc2vcf-plugin", max_pin="x") }} @@ -45,3 +45,7 @@ about: home: https://github.com/freeseek/gtc2vcf license: MIT summary: Tools to convert Illumina and Affymetrix array intensity data files into VCF files. + +extra: + additional-platforms: + - linux-aarch64 From 13e3afb63e085787fe9ac7618027e1ec7c94c774 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 15:01:52 +0800 Subject: [PATCH 1257/1813] linux-aarch64 build for bcov (#46876) Co-authored-by: HWsunqian0027 --- recipes/bcov/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/bcov/meta.yaml b/recipes/bcov/meta.yaml index ed9b0afbe2fd2..a4d012b14a847 100644 --- a/recipes/bcov/meta.yaml +++ b/recipes/bcov/meta.yaml @@ -6,7 +6,9 @@ package: version: {{ version }} build: - number: 7 + number: 8 + run_exports: + - {{ pin_subpackage("bcov", max_pin="x.x.x") }} source: url: http://biocomp.unibo.it/savojard/bcov/bcov-1.0.tar.gz @@ -40,3 +42,5 @@ extra: identifiers: - biotools:bcov - doi:10.1093/bioinformatics/btt555 + additional-platforms: + - linux-aarch64 From 091b33f78773687aa21cf5cc1521f114794c5c5e Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Fri, 29 Mar 2024 16:19:06 +0800 Subject: [PATCH 1258/1813] linux-aarch64 build for ancestry_hmm-s (#46796) * linux-aarch64 build for ancestry_hmm-s * edit run_exports Co-authored-by: Martin Grigorov --------- Co-authored-by: yejianbang Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Martin Grigorov --- recipes/ancestry_hmm-s/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/ancestry_hmm-s/meta.yaml b/recipes/ancestry_hmm-s/meta.yaml index 1080842dc5b44..27e8fb91c3ef8 100644 --- a/recipes/ancestry_hmm-s/meta.yaml +++ b/recipes/ancestry_hmm-s/meta.yaml @@ -10,7 +10,9 @@ source: sha256: 3bbee77945f7c90b6aeddb27ca388411d91bc61c4b770dd1750492beeee9583f build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x.x") }} requirements: build: @@ -39,3 +41,5 @@ about: extra: identifiers: - doi:10.1101/2020.08.02.232934 # bioRxiv preprint + additional-platforms: + - linux-aarch64 From cd6a391608353563ee6d83a518e5bdaa409d2200 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Mar 2024 10:33:07 -0400 Subject: [PATCH 1259/1813] Update assembly_finder to 0.6.1 (#46886) --- recipes/assembly_finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index fc5c7bdc74dc3..b50bcabd479bb 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.6.0" %} +{% set version = "0.6.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: fe5dbe825730852005c382b88e3d89ac88f16e74cb0d6a5f26ad8c566df07119 + sha256: 4892df7c710fe13674047a0059be710eef3e7b93b893167e7930760a62ad6273 build: number: 0 From fdb47b2f88c8c27455f88d9b54b8b9cd8040a638 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Mar 2024 10:33:27 -0400 Subject: [PATCH 1260/1813] Update psm-utils to 0.8.1 (#46887) --- recipes/psm-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index 7620a67085e42..a74e7ad05c86c 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.8.0" %} -{% set sha256 = "735f44dce1f99ac7821d61fe87df955fa935cb06377cdfa7fd18ead464850c49" %} +{% set version = "0.8.1" %} +{% set sha256 = "ec800bd4931a934c09e2cc11e65bd22015fce1bb05898a5605bfb0d5c5502e20" %} package: name: {{ name|lower }} From 31a860b3f8ce43d4ed492a0a7dabe6fb5a3e4111 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 29 Mar 2024 17:24:25 +0100 Subject: [PATCH 1261/1813] remove unneded pin, fixed upstream (#46894) --- recipes/bcbio-gff/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/bcbio-gff/meta.yaml b/recipes/bcbio-gff/meta.yaml index 173e1c0c2cda6..cceb7684f852b 100644 --- a/recipes/bcbio-gff/meta.yaml +++ b/recipes/bcbio-gff/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d1dc3294147b95baced6033f6386a0fed45c43767ef02d1223df5ef497e9cca6 build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} @@ -23,8 +23,7 @@ requirements: run: - python - six - # see: https://github.com/chapmanb/bcbb/issues/138 - - biopython <=1.81 + - biopython - bx-python test: From 9ce1de5f9ede6b9c66abb6495be7dee8c3e4f914 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Sat, 30 Mar 2024 00:27:48 +0800 Subject: [PATCH 1262/1813] linux-aarch64 build for akt (#46847) * linux-aarch64 build for akt * fix akt * fix * fix --------- Co-authored-by: HWsunqian0027 --- recipes/akt/build.sh | 4 ++++ recipes/akt/meta.yaml | 6 +++++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/recipes/akt/build.sh b/recipes/akt/build.sh index 54a4de419bbc8..4eca9aec4baa4 100644 --- a/recipes/akt/build.sh +++ b/recipes/akt/build.sh @@ -1,4 +1,8 @@ #!/bin/bash +if [ `uname -m` == "aarch64" ]; then +sed -i 's/\-mpopcnt//g' Makefile +fi + make \ CC="${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" \ CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" diff --git a/recipes/akt/meta.yaml b/recipes/akt/meta.yaml index 166419b343c28..fe1cfb1e46ba5 100644 --- a/recipes/akt/meta.yaml +++ b/recipes/akt/meta.yaml @@ -10,7 +10,9 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("akt", max_pin="x.x.x") }} requirements: build: @@ -38,3 +40,5 @@ about: extra: identifiers: - doi:10.1093/bioinformatics/btw576 + additional-platforms: + - linux-aarch64 From e186ddd34161f998e5f13d901f8d87002b795d23 Mon Sep 17 00:00:00 2001 From: stuber Date: Fri, 29 Mar 2024 10:28:17 -0600 Subject: [PATCH 1263/1813] genoflu version 1.03 (#46893) --- recipes/genoflu/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genoflu/meta.yaml b/recipes/genoflu/meta.yaml index c7e66039d4536..4086881aa0d61 100644 --- a/recipes/genoflu/meta.yaml +++ b/recipes/genoflu/meta.yaml @@ -1,8 +1,8 @@ {% set user = "USDA-VS" %} {% set name = "GenoFLU" %} -{% set version = "1.02" %} -{% set sha256 = "8cae43be805ee1822d6acc3d1d51a7c4445c5252b5004ab700b7f807fc78070d" %} +{% set version = "1.03" %} +{% set sha256 = "fe814ff8e256b57e32a3398d4c16d449eb6222cbb02869bd876534484c5b070e" %} package: name: {{ name|lower }} From 87246ff02f0e5523e74ee7925014d63534f70508 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Mar 2024 12:28:25 -0400 Subject: [PATCH 1264/1813] Update nanomotif to 0.1.20 (#46891) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index 8620e63a0f280..f4e74096df9e9 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.19" %} +{% set version = "0.1.20" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: e62cc67dc23bc185aa9af77420e53be0d820fa70880d1b048c522d646def75ef + sha256: 2f8312b90d9bf845a91e9c1a8f86a72420e41fb4f9b04f7558b3e8e72f942d45 build: entry_points: From a7c7478a4f6b71213f4aec065dd5c6055f2b74dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Mar 2024 12:28:32 -0400 Subject: [PATCH 1265/1813] Update melon to 0.1.3 (#46890) --- recipes/melon/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/melon/meta.yaml b/recipes/melon/meta.yaml index 0474c549414fa..64f69442d1011 100644 --- a/recipes/melon/meta.yaml +++ b/recipes/melon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "melon" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/xinehc/melon/archive/refs/tags/v{{ version }}.tar.gz - sha256: a9c1f3bfb09c204c9be760cc156f8e604ac9138525b5b6c6e5ecc965a637016d + sha256: 099790947f54cca51ab0a47536cb846f884757db785822f04b540324a0bc6839 build: noarch: python From 10246eac28bad18c81a5d81be7f09319cf15527c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Mar 2024 12:28:39 -0400 Subject: [PATCH 1266/1813] Update pybiolib to 1.1.1923 (#46889) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index ea2d2a355045b..d0f690ceb4693 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1921" %} +{% set version = "1.1.1923" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 264482522ffa2b571c06421489c78b4bc9dddee95a402c6cc37e74f2cba66531 + sha256: e01e9acb1c1b1048157ee25abca234104f4d18e9d52fcd408f2f1efca7eed1ac build: noarch: python From 0c0fbacb11a310167ee5678c04eec7638a067309 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Sat, 30 Mar 2024 00:29:11 +0800 Subject: [PATCH 1267/1813] Update for arcas-hla (#46874) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * fix * linux-aarch64 for arcas-hls --------- Co-authored-by: yejianbang Co-authored-by: HWsunqian0027 --- recipes/arcas-hla/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/arcas-hla/meta.yaml b/recipes/arcas-hla/meta.yaml index 9121cf059a94f..c1508a625042b 100644 --- a/recipes/arcas-hla/meta.yaml +++ b/recipes/arcas-hla/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 75bef1a5596a9dfabccb901420f5d852d6d8a15d9c676e4c94787b8d25dd708b build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage("arcas-hla", max_pin="x.x") }} @@ -21,7 +21,7 @@ requirements: - coreutils - git - git-lfs - - kallisto ==0.44 + - kallisto ==0.50.1 - numpy - pandas - pigz From 74e3a992c1586fb1a7f01fdf341bb65ea66d4346 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Sat, 30 Mar 2024 00:29:23 +0800 Subject: [PATCH 1268/1813] linux-aarch64 build for adapterremoval (#46853) * linux-aarch64 build for adapterremoval * Update meta.yaml --------- Co-authored-by: HWsunqian0027 Co-authored-by: Robert A. Petit III --- recipes/adapterremoval/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/adapterremoval/meta.yaml b/recipes/adapterremoval/meta.yaml index b6c2fb86ec426..e916bf3a3bd45 100644 --- a/recipes/adapterremoval/meta.yaml +++ b/recipes/adapterremoval/meta.yaml @@ -10,7 +10,9 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage("adapterremoval", max_pin="x") }} requirements: build: @@ -34,3 +36,7 @@ about: license: GPL3 license_file: LICENSE summary: The AdapterRemoval v2 tool for merging and clipping reads. + +extra: + additional-platforms: + - linux-aarch64 From 30e380a951aa08ba20308e5691eaee23bac38af5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Mar 2024 13:03:37 -0400 Subject: [PATCH 1269/1813] Update skder to 1.0.10 (#46895) --- recipes/skder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skder/meta.yaml b/recipes/skder/meta.yaml index 4cdfb358228f0..f89f93f93ff8a 100644 --- a/recipes/skder/meta.yaml +++ b/recipes/skder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skder" %} -{% set version = "1.0.9" %} +{% set version = "1.0.10" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/raufs/skDER/archive/refs/tags/v{{ version }}.tar.gz - sha256: 0b72a416874235046eb5b4ad1edca98773013043319051b8cdea794c5ee39220 + sha256: af12a8a2709709036b84f79e39b7f13f728e45151d62251792991b23d002c54e build: number: 0 From 2b3e75ea0fa93cc2d542479cc38212b67bd9614c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Mar 2024 20:08:54 -0400 Subject: [PATCH 1270/1813] Update oarfish to 0.4.0 (#46898) --- recipes/oarfish/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oarfish/meta.yaml b/recipes/oarfish/meta.yaml index b712795b7de42..633bcc960583e 100644 --- a/recipes/oarfish/meta.yaml +++ b/recipes/oarfish/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.1" %} +{% set version = "0.4.0" %} package: name: oarfish @@ -11,7 +11,7 @@ build: source: url: https://github.com/COMBINE-lab/oarfish/archive/v{{ version }}.tar.gz - sha256: 242b524f2b1bd877df3c30b71283598f7386b1627b6a8534d943643089b63c16 + sha256: 97e5d42d7797977a12790d9986a7e28c2ec264ca7a9637916178594e868080c8 requirements: build: From 5a14a9c901ac0ca1910013b90af0ec4e4644028c Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Sat, 30 Mar 2024 12:40:41 -0700 Subject: [PATCH 1271/1813] hybran: update to version 1.8 (#46899) --- recipes/hybran/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/hybran/meta.yaml b/recipes/hybran/meta.yaml index 12695806c6bfb..4d343203276db 100644 --- a/recipes/hybran/meta.yaml +++ b/recipes/hybran/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.7.1" %} +{% set version = "1.8" %} package: name: hybran @@ -6,11 +6,11 @@ package: source: url: https://gitlab.com/LPCDRP/hybran/-/archive/{{ version }}/hybran-{{ version }}.tar.gz - sha256: 'c256e88009d0a2cc3fffcb021613392f6a71ee6905bfe1a1d806b962b5243017' + sha256: 'cd46ec155109e59ddadf6942a54edcd9c350c6571ae81524eab44d4b695cbbdb' build: noarch: python - number: 1 + number: 0 script: python -m pip install --no-deps --ignore-installed . run_exports: - {{ pin_subpackage('hybran', max_pin=None) }} @@ -20,7 +20,7 @@ requirements: - python >=3.9 - pip run: - - biopython >=1.80, <1.82 + - biopython >=1.80 - blast - cd-hit - diamond @@ -28,8 +28,10 @@ requirements: - eggnog-mapper - emboss - entrez-direct + - intervaltree - mcl - multiprocess + - networkx - prokka >=1.14 - python >=3.9 - ratt @@ -44,4 +46,4 @@ about: dev_url: https://gitlab.com/LPCDRP/hybran license: GPLv3 license_file: LICENSE - summary: Hybrid reference transfer and ab initio prokaryotic genome annotation + summary: Comparative prokaryotic genome annotation From a7a8243884b13a83efe69c226ca377ea2200cae1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 30 Mar 2024 17:40:04 -0400 Subject: [PATCH 1272/1813] Update pybiolib to 1.1.1930 (#46897) * Update pybiolib to 1.1.1928 * Update pybiolib to 1.1.1930 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index d0f690ceb4693..d01b39ef96adc 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1923" %} +{% set version = "1.1.1930" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: e01e9acb1c1b1048157ee25abca234104f4d18e9d52fcd408f2f1efca7eed1ac + sha256: cf59c083fa15c9c9316b5f95e70fd75560c17545d5bda91959b90fa973056652 build: noarch: python From a3d61c0cc599d4ba933e2e0935e4d862fe4fbd20 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 30 Mar 2024 21:38:10 -0400 Subject: [PATCH 1273/1813] Update pypgx to 0.24.0 (#46901) --- recipes/pypgx/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pypgx/meta.yaml b/recipes/pypgx/meta.yaml index 85fe340272681..97ff4a6509b4a 100644 --- a/recipes/pypgx/meta.yaml +++ b/recipes/pypgx/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypgx" %} -{% set version = "0.23.0" %} +{% set version = "0.24.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f38c23085b0102182cabc8cc0fc32eff05bc668bf68b6a751ad249c70b18242c + sha256: ba93afe9ec0d0dab31e25e7f21db5363c3cf46609403efdd0cc83c656d2744d8 build: number: 0 From 4c89db757ee5c63e9df23c9ca82c486f713dbb9a Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Sun, 31 Mar 2024 21:33:49 +0900 Subject: [PATCH 1274/1813] Update plass to 5.cf8933 (#46904) --- recipes/plass/build.sh | 16 ++++++++++++---- recipes/plass/meta.yaml | 23 +++++++++++++++-------- 2 files changed, 27 insertions(+), 12 deletions(-) diff --git a/recipes/plass/build.sh b/recipes/plass/build.sh index 78b3b14a704a3..b06956020200b 100644 --- a/recipes/plass/build.sh +++ b/recipes/plass/build.sh @@ -1,10 +1,18 @@ #!/bin/bash -git submodule init -git submodule update +ARCH_BUILD="" +case $(uname -m) in + x86_64) ARCH_BUILD="-DHAVE_SSE4_1=1" ;; + arm64|aarch64) ARCH_BUILD="-DHAVE_ARM8=1" ;; +esac + +if [ -z "${ARCH_BUILD}" ]; then + echo "Invalid architecture" + exit 1 +fi mkdir build cd build -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 -DHAVE_SSE4_1=1 -DVERSION_OVERRIDE="${PKG_VERSION}" .. -make -j 2 +cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 ${ARCH_BUILD} -DVERSION_OVERRIDE="${PKG_VERSION}" .. +make -j${CPU_COUNT} ${VERBOSE_CM} make install diff --git a/recipes/plass/meta.yaml b/recipes/plass/meta.yaml index 9625027645199..fe9f348a6774d 100644 --- a/recipes/plass/meta.yaml +++ b/recipes/plass/meta.yaml @@ -1,15 +1,18 @@ -{% set version = "4-687d7" %} +{% set version = "5-cf8933" %} +{% set sha256 = "04f8f695e925fd842667b1839c960afef93deb05131eba478426f622b97ab6a0" %} package: name: plass version: {{ version|replace("-", ".") }} build: - number: 5 + number: 0 + run_exports: + - {{ pin_subpackage('plass', max_pin=None) }} source: - git_url: https://github.com/soedinglab/plass.git - git_rev: {{ version }} + url: https://github.com/soedinglab/plass/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} requirements: build: @@ -32,16 +35,20 @@ requirements: test: commands: - plass > /dev/null + - penguin > /dev/null about: home: https://github.com/soedinglab/plass license: GPLv3 - summary: "Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level" + summary: "Plass (Protein-Level ASSembler) and PenguiN (Protein-guided Nucleotide assembler) are methods to assemble short read sequencing data on a protein level to proteins or DNA contigs" extra: - skip-lints: - - uses_vcs_url - - missing_hash identifiers: - doi:10.1038/s41592-019-0437-4 + - doi:10.1101/2024.03.29.587318 - biotools:plass + recipe-maintainers: + - milot-mirdita + - martin-steinegger + additional-platforms: + - linux-aarch64 From 3c2390e0376f79f9da3874075bcdc7f46ce5b0db Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 31 Mar 2024 11:08:29 -0400 Subject: [PATCH 1275/1813] Update swarm to 3.1.5 (#46905) * Update swarm to 3.1.5 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/swarm/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/swarm/meta.yaml b/recipes/swarm/meta.yaml index 1b196da3524e4..a7f72703f9624 100644 --- a/recipes/swarm/meta.yaml +++ b/recipes/swarm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "swarm" %} -{% set version = "3.1.4" %} +{% set version = "3.1.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/torognes/swarm/archive/v{{ version }}.tar.gz - sha256: 83353096d7df5de1a96b5f1c8987c2efec26635364521741e5691fd49b5a58e4 + sha256: 68ccd814adc06e5325b73e102d7c8a34ee1367d0bfca704d513e4f06bab860d0 requirements: build: @@ -30,6 +30,7 @@ test: about: home: https://github.com/torognes/swarm license: Affero GPL + license_file: LICENSE summary: A robust and fast clustering method for amplicon-based studies. extra: From afb9e79df15f75a2a99dd39f4e03cb1c6ce32ecc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 1 Apr 2024 00:58:16 -0400 Subject: [PATCH 1276/1813] Update sequali to 0.6.0 (#46888) * Update sequali to 0.6.0 * Update sequali dependencies --------- Co-authored-by: Ruben Vorderman Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/sequali/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index c59a316126691..288e8d1fc16d8 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.5.1" %} +{% set version = "0.6.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ac8cf49fa3c2dcfd3eb976c60a4c5e482db82d902c016570c6aebc6869d2f9ea + sha256: 29e0d802d2308e5e3d313c56a7ccb8cf2c1c0c86c901f35679566ad48e3d407e build: number: 0 @@ -28,10 +28,10 @@ requirements: host: - python run: - - pygal >=3.0.0 + - pygal >=3.0.4 - python - tqdm - - xopen >=1.8.0 + - xopen >=2.0.0 test: imports: From 070778949dcb6692dc93e7fa557df265f67ba06a Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Mon, 1 Apr 2024 12:58:39 +0800 Subject: [PATCH 1277/1813] update abawaca (#46883) * update abawaca * edit run_exports max_pin Co-authored-by: Martin Grigorov --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Martin Grigorov --- recipes/abawaca/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/abawaca/meta.yaml b/recipes/abawaca/meta.yaml index 8e93f86df7f49..22c0eb47290e3 100644 --- a/recipes/abawaca/meta.yaml +++ b/recipes/abawaca/meta.yaml @@ -11,7 +11,9 @@ source: - 0001-Use-CXX-and-flags.patch build: - number: 6 + number: 7 + run_exports: + - {{ pin_subpackage("abawaca", max_pin="x") }} requirements: build: @@ -34,3 +36,5 @@ extra: - keuv-grvl identifiers: - doi:10.1038/nature14486 + additional-platforms: + - linux-aarch64 \ No newline at end of file From 7d6f9efaa959666bef2359ebf957bdd86ff9e6f9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 1 Apr 2024 01:24:39 -0400 Subject: [PATCH 1278/1813] Update ddocent to 2.9.7 (#46892) * Update ddocent to 2.9.7 * add run_exports --------- Co-authored-by: mencian --- recipes/ddocent/meta.yaml | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/recipes/ddocent/meta.yaml b/recipes/ddocent/meta.yaml index 643ad6a48b5f6..ae926ea5ff7e8 100644 --- a/recipes/ddocent/meta.yaml +++ b/recipes/ddocent/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.9.4" %} -{% set sha256 = "4d44f72ad9c4bee3587f58ff7a18a972a5e31063396c3200705c72f02c4ee96b" %} +{% set version = "2.9.7" %} +{% set sha256 = "28ad3a597a2477cffc1b8a7dd4dcb204e0912f40664c128e8cfd783e56d46a04" %} package: name: ddocent @@ -8,14 +8,14 @@ package: source: url: https://github.com/jpuritz/dDocent/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} - + build: - number: 1 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('ddocent', max_pin="x") }} requirements: - build: - host: run: - fastp >=0.20.0 - seqtk >=1.3 @@ -42,10 +42,14 @@ test: commands: - "samtools --version" - "dDocent --help" + about: - home: "http://ddocent.com" - license: "The MIT License (MIT)" - summary: " dDocent is an interactive bash wrapper to QC, assemble, map, and call SNPs from all types of RAD data" + home: "https://ddocent.com" + license: MIT + license_family: MIT + summary: "dDocent is an interactive bash wrapper to QC, assemble, map, and call SNPs from all types of RAD data" + dev_url: https://github.com/jpuritz/dDocent + doc_url: https://www.ddocent.com/UserGuide/ extra: container: From f85806fdfba111f532e516383426213413205a3b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 1 Apr 2024 01:53:06 -0400 Subject: [PATCH 1279/1813] Update r-crbhits to 0.0.5 (#46868) * Update r-crbhits to 0.0.5 * add run_exports --------- Co-authored-by: mencian --- recipes/r-crbhits/meta.yaml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/recipes/r-crbhits/meta.yaml b/recipes/r-crbhits/meta.yaml index 4afc84a3c4e5e..290bc8fe95bf1 100644 --- a/recipes/r-crbhits/meta.yaml +++ b/recipes/r-crbhits/meta.yaml @@ -1,5 +1,5 @@ {% set name = "r-crbhits" %} -{% set version = "0.0.4" %} +{% set version = "0.0.5" %} package: name: "{{ name }}" @@ -7,22 +7,21 @@ package: source: url: https://github.com/kullrich/CRBHits/archive/refs/tags/v{{ version }}.tar.gz - sha256: a44ae1f6f16bf321adf9a0342e3f577ea8322e0f49e507908254f2229c55cc00 + sha256: 2b16cebb11acb1460c7c99c3455f7570cd2b1e485e986bb02a609a956849a43f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-crbhits', max_pin="x.x") }} requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - make - - last - - kakscalculator2 - - dagchainer host: - r-base - bioconductor-biostrings @@ -45,6 +44,9 @@ requirements: - r-stringi - r-testthat - r-tibble + - last + - kakscalculator2 + - dagchainer run: - r-base - bioconductor-biostrings @@ -52,7 +54,7 @@ requirements: - r-curl - r-doParallel - r-dplyr - - r-foreach + - r-foreach - r-ggplot2 - r-gridExtra - r-readr @@ -79,6 +81,7 @@ about: summary: "CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R." description: "CRBHits is a reimplementation of the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast in R. It covers all necessary steps from CRBHit pair calculation to Codon Alignments and Ka/Ks. (see [Ullrich (2020) ])" license_family: MIT + extra: identifiers: - doi:10.21105/joss.02424 From dda8d00e9e7be3745269a111133d61b22bcb7a87 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Myl=C3=A8ne=20Mariana=20Gonzales=20Andr=C3=A9?= <103585173+mari-ga@users.noreply.github.com> Date: Mon, 1 Apr 2024 08:49:26 +0200 Subject: [PATCH 1280/1813] Add gmm demux (#46440) * changes to cellhashr * yaml for gmm_demux * fix for lint * fix package lint * package name lowercase * fix lint * lint fix * corrections * lowercase changes * gmm-demux out * gmm demux back * out versions established by grayskull * changed versions python * version for packages * fix versions and lint * fixn versions * versions * fix version * problems with versions * fixed python version * summary update * try pinning python to <3.12 * edit dependencies * try unpinning python * python version lower * fix python version * added suggestions for versions * python version minor than 3.11 * only version minor than * added _python_rc * only python restriction * old recipe out * new generated recipe * added lint * error with lint * out unnecessary versions * clean up recipe * clean up recipe --------- Co-authored-by: mencian --- recipes/gmm-demux/meta.yaml | 50 +++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 recipes/gmm-demux/meta.yaml diff --git a/recipes/gmm-demux/meta.yaml b/recipes/gmm-demux/meta.yaml new file mode 100644 index 0000000000000..7836d387489f5 --- /dev/null +++ b/recipes/gmm-demux/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "GMM-Demux" %} +{% set version = "0.2.2.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/GMM_Demux-{{ version }}.tar.gz + sha256: 989092feea7a61e309f6a75ce77246f619c2eff997f1f7a1a7457dfaf5a10ecf + +build: + entry_points: + - GMM-demux = GMM_Demux.GMM_Demux:main + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('gmm-demux', max_pin="x.x") }} + +requirements: + host: + - python + - pip + run: + - python + - pandas >=1.4.3 + - numpy >=1.22.4 + - scipy >=1.12.0 + - tabulate + - bitvector + - scikit-learn + +test: + imports: + - GMM_Demux + commands: + - GMM-demux --help + +about: + home: https://github.com/CHPGenetics/GMM-demux + summary: GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq). + license: MIT + license_family: MIT + license_file: LICENSE + dev_url: https://github.com/CHPGenetics/GMM-demux + +extra: + identifiers: + - doi:10.1186/s13059-020-02084-2 From f642601bb8796ea8abcf0c0deaf8c24378cf9eb7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Myl=C3=A8ne=20Mariana=20Gonzales=20Andr=C3=A9?= <103585173+mari-ga@users.noreply.github.com> Date: Mon, 1 Apr 2024 09:05:51 +0200 Subject: [PATCH 1281/1813] Add cellhashr (#46367) * changes to cellhashr * cellhashr fixes * deleted word in bash * changes for linting * fixes cellhashr * minor fix * fixes run_exports and summary * sha code update * stable sha256 added * fix link to get right SHA * change sha * out incompatible packages * fixes to bash * test cellhashr * fix bash * out first line build sh * cellhashR change to bash file * fix bash file * fix build * changes * out compiler * missing dependencies * added missing packages * update packages * clean up recipe * rename folder to bioconductor-* * rename folder to bioconductor-* --------- Co-authored-by: mencian --- recipes/bioconductor-cellhashr/meta.yaml | 82 ++++++++++++++++++++++++ 1 file changed, 82 insertions(+) create mode 100644 recipes/bioconductor-cellhashr/meta.yaml diff --git a/recipes/bioconductor-cellhashr/meta.yaml b/recipes/bioconductor-cellhashr/meta.yaml new file mode 100644 index 0000000000000..86c58266837e7 --- /dev/null +++ b/recipes/bioconductor-cellhashr/meta.yaml @@ -0,0 +1,82 @@ +{% set version = "1.04" %} +{% set sha256 = "a017cf985e78c39c899c5e2d43a7a1ff940f61c79145b6c4b1112e9bf8433de1" %} + +package: + name: bioconductor-cellhashr + version: {{version}} + +source: + url: https://github.com/BimberLab/cellhashR/archive/refs/tags/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: generic + script: R CMD INSTALL --build . + run_exports: + - {{ pin_subpackage('bioconductor-cellhashr', max_pin="x") }} + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-essentials + - r-devtools + - r-rcpp + - r-rcpparmadillo + - r-rcppeigen + - r-rcppparallel + - r-rcppprogress + - bioconductor-preprocesscore + - r-pdftools + - bioconductor-demuxmix + - r-magick + - bioconductor-s4vectors + - bioconductor-dropletutils + - bioconductor-singlecellexperiment + - r-biocmanager + - r-seurat + - r-rmdformats + - r-ggforce + - r-reticulate + - r-ggextra + - r-ggthemes + - r-patchwork + - r-egg + - bioconductor-nempi + run: + - r-base + - r-essentials + - r-devtools + - r-rcpp + - r-rcpparmadillo + - r-rcppeigen + - r-rcppparallel + - r-rcppprogress + - bioconductor-preprocesscore + - bioconductor-dropletutils + - bioconductor-demuxmix + - r-seurat + - r-seuratobject + - r-rmdformats + - r-ggforce + - r-reticulate + - r-ggextra + - r-ggthemes + - r-patchwork + - r-egg + - bioconductor-nempi + +test: + commands: + - $R -e "library('cellhashR')" # [not win] + - "\"%R%\" -e \"library('cellhashR')\"" # [win] + +about: + home: https://github.com/BimberLab/cellhashR + license: MIT + license_family: MIT + summary: "An R package designed to demultiplex cell hashing data.\n More information in https://bimberlab.github.io/cellhashR/Lab B (2024). \n cellhashR: A Package for Demultiplexing Cell Hashing Data.\n" + dev_url: https://github.com/BimberLab/cellhashR From aa00b12e37ca26d251f481bba1f40b3ea2d174ac Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 1 Apr 2024 03:35:23 -0500 Subject: [PATCH 1282/1813] Update python-edlib recipe (#46906) * Update python-edlib recipe * add license_file * add doi --- recipes/python-edlib/LICENSE | 20 ++++++++++++++++++++ recipes/python-edlib/build.sh | 3 --- recipes/python-edlib/meta.yaml | 17 ++++++++++++----- 3 files changed, 32 insertions(+), 8 deletions(-) create mode 100644 recipes/python-edlib/LICENSE delete mode 100644 recipes/python-edlib/build.sh diff --git a/recipes/python-edlib/LICENSE b/recipes/python-edlib/LICENSE new file mode 100644 index 0000000000000..d8f3fefba092a --- /dev/null +++ b/recipes/python-edlib/LICENSE @@ -0,0 +1,20 @@ +The MIT License (MIT) + +Copyright (c) 2014 Martin Šošić + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of +the Software, and to permit persons to whom the Software is furnished to do so, +subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS +FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR +COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER +IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/recipes/python-edlib/build.sh b/recipes/python-edlib/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/python-edlib/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/python-edlib/meta.yaml b/recipes/python-edlib/meta.yaml index 902225772e83a..54fe7588ea123 100644 --- a/recipes/python-edlib/meta.yaml +++ b/recipes/python-edlib/meta.yaml @@ -9,16 +9,18 @@ source: sha256: 64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766 build: - number: 5 + number: 6 + script: "EDLIB_USE_CYTHON=1 {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" run_exports: - - {{ pin_subpackage("python-edlib", max_pin="x.x") }} + - {{ pin_subpackage("python-edlib", max_pin="x") }} requirements: build: - {{ compiler('cxx') }} host: - python - - setuptools + - pip + - cython run: - python @@ -28,10 +30,15 @@ test: about: home: https://github.com/Martinsos/edlib - license: MIT License + license: MIT summary: 'Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.' license_family: MIT + license_file: LICENSE + dev_url: https://github.com/Martinsos/edlib + doc_url: https://martinsos.github.io/edlib/ extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 + identifiers: + - doi:10.1093/bioinformatics/btw753 From 4ffc0acc8b689b69688676fd7c6e76fe7933099b Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 1 Apr 2024 06:22:19 -0500 Subject: [PATCH 1283/1813] flye: enable linux-aarch64 build (#46908) --- recipes/flye/0001-Makefile-aarch64.patch | 15 ++++++++++++ recipes/flye/build.sh | 8 +++---- recipes/flye/meta.yaml | 29 +++++++++++++++++------- 3 files changed, 40 insertions(+), 12 deletions(-) create mode 100644 recipes/flye/0001-Makefile-aarch64.patch diff --git a/recipes/flye/0001-Makefile-aarch64.patch b/recipes/flye/0001-Makefile-aarch64.patch new file mode 100644 index 0000000000000..c408cad27e3e3 --- /dev/null +++ b/recipes/flye/0001-Makefile-aarch64.patch @@ -0,0 +1,15 @@ +diff --git a/Makefile b/Makefile +index 75f62ae..91b9571 100644 +--- a/Makefile ++++ b/Makefile +@@ -16,6 +16,10 @@ ifeq ($(shell uname -m),arm64) + export aarch64=1 + endif + ++ifeq ($(shell uname -m),aarch64) ++ export aarch64=1 ++endif ++ + .PHONY: clean all profile debug minimap2 samtools + + .DEFAULT_GOAL := all diff --git a/recipes/flye/build.sh b/recipes/flye/build.sh index 371f8f3d1246c..56b1d69744ebc 100644 --- a/recipes/flye/build.sh +++ b/recipes/flye/build.sh @@ -7,16 +7,16 @@ export CFLAGS="-L$PREFIX/lib" export INCLUDES="-I$PREFIX/include" #zlib headers for flye binaries -export CXXFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" +export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" #install_name_tool error fix if [[ "$(uname)" == Darwin ]]; then export LDFLAGS="$LDFLAGS -headerpad_max_install_names" fi -#dynamic flag is needed for backtrace printing, +#dynamic flag is needed for backtrace printing, #but it seems it fails OSX build sed -i.bak 's/-rdynamic//' src/Makefile -$PYTHON setup.py install --single-version-externally-managed --record record.txt +$PYTHON -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv diff --git a/recipes/flye/meta.yaml b/recipes/flye/meta.yaml index 708a33bcce936..6820267409726 100644 --- a/recipes/flye/meta.yaml +++ b/recipes/flye/meta.yaml @@ -7,26 +7,25 @@ package: source: url: https://github.com/fenderglass/Flye/archive/{{ version }}.tar.gz sha256: 09580390ed0558c131ca0b836a2374d3cc7993cba2a6500024c2ee1d96666edc + patches: + - 0001-Makefile-aarch64.patch build: - number: 0 + number: 1 + entry_points: + - flye = flye.main:main run_exports: - - {{ pin_subpackage("flye", max_pin="x.x") }} + - {{ pin_subpackage("flye", max_pin="x") }} + requirements: build: - {{ compiler('cxx') }} - make host: - python - - setuptools - zlib run: - python - - setuptools - -extra: - skip-lints: - - uses_setuptools #uses pkg_resources test: commands: @@ -37,4 +36,18 @@ test: about: home: https://github.com/fenderglass/Flye/ license: BSD-3-Clause + license_family: BSD + license_file: LICENSE summary: Fast and accurate de novo assembler for single molecule sequencing reads + doc_url: https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md + dev_url: https://github.com/fenderglass/Flye/ + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:Flye + - doi:10.1038/s41592-020-00971-x + - doi:10.1038/s41587-019-0072-8 + - doi:10.1073/pnas.1604560113 + - usegalaxy-eu:flye From 0bcfc672fcb90442e08f624cfec68b2ebe1afb97 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 1 Apr 2024 12:35:20 -0400 Subject: [PATCH 1284/1813] Update gb-io to 0.3.2 (#46910) --- recipes/gb-io/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gb-io/meta.yaml b/recipes/gb-io/meta.yaml index c546baf02d07b..e346cc5b35e5a 100644 --- a/recipes/gb-io/meta.yaml +++ b/recipes/gb-io/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gb-io" %} -{% set version = "0.3.1" %} +{% set version = "0.3.2" %} package: name: "{{ name }}" @@ -12,7 +12,7 @@ build: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 4400d9b9864402b410ee1753e0cd8c405f692bfee4032fe8ab8ce4d50bef80ce + sha256: 5bf0a5b2755e5e4aa928184043a44c28e2658158965901abb003ede8c794ad6e requirements: build: From 0dea4fd1571e30d040eca7d81f679d00353f601f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 1 Apr 2024 13:07:32 -0400 Subject: [PATCH 1285/1813] Update lemur to 1.0.1 (#46909) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/lemur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/lemur/meta.yaml b/recipes/lemur/meta.yaml index 731b4749ab532..1e8ba3fb9aaa2 100644 --- a/recipes/lemur/meta.yaml +++ b/recipes/lemur/meta.yaml @@ -1,5 +1,5 @@ {% set name = "lemur" %} -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: 'https://github.com/treangenlab/lemur/archive/refs/tags/v{{version}}.tar.gz' - sha256: 591cc3d1d8a7ebb8b51486cb9c74b61dc39aeb8d8e3baf4d318e04278f9f6459 + sha256: 190b6302deabe5d09428bc541e5ab924ab6b727c30fc0c93554c2a131e7fd0d7 build: run_exports: From e3c77fa04ac3b647698da01adeb3b73d5c99eead Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 1 Apr 2024 14:45:49 -0400 Subject: [PATCH 1286/1813] Update bioconda-utils to 2.14.0 (#46914) --- recipes/bioconda-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 3ca830e56ace9..7181cbcc84667 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.13.2" %} -{% set sha256 = "da2b1d2a816c3b647c684fd389f941463e5c37bd502fc7cb650f8db8e2458232" %} +{% set version = "2.14.0" %} +{% set sha256 = "0ae05ba291a1ad7ae956a42bc7e3123a9789ffcd10bf23f2de4499091b8a9e36" %} package: name: bioconda-utils From 9dd6924dcc4beba2605910762a1ceec9556ff851 Mon Sep 17 00:00:00 2001 From: ylf9811 Date: Tue, 2 Apr 2024 04:53:15 +0800 Subject: [PATCH 1287/1813] Add rabbitqcplus (#46838) * add rabbitqcplus * add rabbitqcplus with run_exports * remove make -j8 * linux test only * add rabbitqcplus executable file * Cleanup and added license file --------- Co-authored-by: Christian Brueffer --- recipes/rabbitqcplus/build.sh | 10 ++++++++++ recipes/rabbitqcplus/meta.yaml | 35 ++++++++++++++++++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 recipes/rabbitqcplus/build.sh create mode 100644 recipes/rabbitqcplus/meta.yaml diff --git a/recipes/rabbitqcplus/build.sh b/recipes/rabbitqcplus/build.sh new file mode 100644 index 0000000000000..28712451f1912 --- /dev/null +++ b/recipes/rabbitqcplus/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +export CC=${CC:-gcc} +export CXX=${CXX:-g++} + +export LIBRARY_DIRS="$LIBRARY_DIRS $PREFIX/lib" + +make +make install + diff --git a/recipes/rabbitqcplus/meta.yaml b/recipes/rabbitqcplus/meta.yaml new file mode 100644 index 0000000000000..239c6a4fa0299 --- /dev/null +++ b/recipes/rabbitqcplus/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.2.7" %} + +package: + name: rabbitqcplus + version: {{ version }} + +source: + url: https://github.com/RabbitBio/RabbitQCPlus/archive/refs/tags/{{ version }}.tar.gz + sha256: adecd53feb56432b4515d70f7816bcfba582a1a02e8f8b0f6d4049bfbb69af8b + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage("rabbitqcplus", max_pin="x.x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - {{ compiler('c') }} + - make + host: + - zlib + run: + - zlib + +test: + commands: + - rabbitqcplus --help + +about: + home: https://github.com/RabbitBio/RabbitQCPlus + license: MIT + license_file: LICENSE + summary: RabbitQCPlus is an efficient quality control tool for sequencing data From 95273baa450da38a51a8ca6e307e21ffef403e2b Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Tue, 2 Apr 2024 21:24:26 +1100 Subject: [PATCH 1288/1813] Update dexseq to reinstate htseq-count dependency (#46916) * reinstate htseq-count * typo --- recipes/bioconductor-dexseq/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 29b4cbc81fbe4..c2dea7842a4e5 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8e5876f927b0b0cdfc4a402bfb4fb3d6 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -54,6 +54,7 @@ requirements: - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'htseq >=2.0.2,<2.1' - r-base - r-hwriter - r-rcolorbrewer @@ -62,6 +63,8 @@ requirements: test: commands: - '$R -e "library(''{{ name }}'')"' + - dexseq_prepare_annotation.py --help + - dexseq_count.py --help about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' From 6f666fd2c03adf396a0327a27b6ea14dacba0c55 Mon Sep 17 00:00:00 2001 From: Adam Cribbs Date: Tue, 2 Apr 2024 13:31:29 +0200 Subject: [PATCH 1289/1813] Update cgatcore 0.6.16 (#46922) --- recipes/cgatcore/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/cgatcore/meta.yaml b/recipes/cgatcore/meta.yaml index c654b1ae42507..2dfaeabb0c6ac 100644 --- a/recipes/cgatcore/meta.yaml +++ b/recipes/cgatcore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cgatcore" %} -{% set version = "0.6.15" %} +{% set version = "0.6.16" %} package: name: {{ name|lower }} @@ -7,11 +7,13 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: a8a4e5867ae327307cbd49118d52add5ec7429d9ac1ac70f5189eff997f40360 + sha256: ae32907ff806829fa2389c6e27e658097c0a8dab1e4bed4123d9f85f4ba04be0 build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('cgatcore', max_pin="x.x") }} script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" requirements: From d89178f046b5e7df0d54d6d6f1f26eccd4117829 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Apr 2024 11:04:46 -0400 Subject: [PATCH 1290/1813] Update rabbitqcplus to 2.2.8 (#46931) --- recipes/rabbitqcplus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rabbitqcplus/meta.yaml b/recipes/rabbitqcplus/meta.yaml index 239c6a4fa0299..3431c61fe6e4b 100644 --- a/recipes/rabbitqcplus/meta.yaml +++ b/recipes/rabbitqcplus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.2.7" %} +{% set version = "2.2.8" %} package: name: rabbitqcplus @@ -6,7 +6,7 @@ package: source: url: https://github.com/RabbitBio/RabbitQCPlus/archive/refs/tags/{{ version }}.tar.gz - sha256: adecd53feb56432b4515d70f7816bcfba582a1a02e8f8b0f6d4049bfbb69af8b + sha256: 2466f50d735e6445200698ea9ad8041ce93ec8335a94b6181648b44d6a0ee4af build: number: 0 From 5a5fbcd53fa9518f86fd415ea3ae591ad1f3918e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Apr 2024 15:29:45 -0400 Subject: [PATCH 1291/1813] Update hybracter to 0.7.2 (#46917) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index c3620151f7ed6..bc40e258f7861 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.7.1" %} +{% set version = "0.7.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 1edd91904d91d9fd17889f7e762acda33f92fe5f8553d2e055a2b6bff8778c45 + sha256: 404fa2144ef10c924256b07826726f1b1df8fadac0e5a4206b3d021bf61dc1a3 build: number: 0 From b5235526341633fd823b1f33840e849673cac396 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Apr 2024 19:11:31 -0400 Subject: [PATCH 1292/1813] Update harpy to 0.9.1 (#46935) * Update harpy to 0.9.0 * Update harpy to 0.9.1 --- recipes/harpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index 8c458665b2709..1075fe061f052 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.0" %} -{% set sha256 = "40314dba83fc20e7f57bcacc706eed3bd6c52391327c1b10b5ba41aa5ae0d4f0" %} +{% set version = "0.9.1" %} +{% set sha256 = "3d05a4995f6c6c9059b5fba269ff6dee7f8befd1bdc7cb622c7f753dea49af79" %} package: name: harpy From b7ab65d077b5a4e3372c1d4e7f6a24c2ff7bef05 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Apr 2024 19:11:49 -0400 Subject: [PATCH 1293/1813] Update hmftools-mark-dups to 1.1.4 (#46937) --- recipes/hmftools-mark-dups/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-mark-dups/meta.yaml b/recipes/hmftools-mark-dups/meta.yaml index 7ea235b90e2b7..0946d070a6942 100644 --- a/recipes/hmftools-mark-dups/meta.yaml +++ b/recipes/hmftools-mark-dups/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.3" %} -{% set sha256 = "46ee9419c5e0809feb54a1a7a0a4646aedd7c9fcada7dd346844d7c2b7c86561" %} +{% set version = "1.1.4" %} +{% set sha256 = "0cf4bf1113321fb821b041b8be77d6d4948fda13998ad3d4e72c36bea41379b1" %} package: name: hmftools-mark-dups From 81a6867440a1ff1a76e372a8652e9589bbeb3557 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Apr 2024 19:12:08 -0400 Subject: [PATCH 1294/1813] Update locityper to 0.14.4 (#46929) --- recipes/locityper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/locityper/meta.yaml b/recipes/locityper/meta.yaml index 556ab0c9d5398..b785fc0a3b164 100644 --- a/recipes/locityper/meta.yaml +++ b/recipes/locityper/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.13.4" %} +{% set version = "0.14.4" %} package: name: locityper @@ -11,7 +11,7 @@ build: source: url: https://github.com/tprodanov/locityper/archive/refs/tags/v{{ version }}.tar.gz - sha256: 2e7290d6a6a63f594906de02a30e3f1f1e495bbb5f99640ac66708ac37c1113e + sha256: 83381d3600d4ad5b08f03c579bdd1ac5dcb149edd966a39516fa6d12192cd16d requirements: build: From bf07327e429af0e46c95b0e9bfd852d25eb2c074 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Apr 2024 19:12:34 -0400 Subject: [PATCH 1295/1813] Update varvamp to 1.1.2 (#46932) --- recipes/varvamp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index 98241a40fce99..8926113ede596 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 3036bb0b0f9f1453e2978b95c75a5adf3c9f08cec9f3a4a2f38affa28b1fd04b + sha256: 391281c3f00436f88a63b659afbac5e32a215964e4ee9c0f82cbd0dcc4dcefec build: entry_points: From ada1d71690665119b4fc6294402acf57648ca573 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Apr 2024 19:13:38 -0400 Subject: [PATCH 1296/1813] Update ebi-eva-common-pyutils to 0.6.5 (#46925) --- recipes/ebi-eva-common-pyutils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ebi-eva-common-pyutils/meta.yaml b/recipes/ebi-eva-common-pyutils/meta.yaml index 8769334eca87a..be5d7171e3bb3 100644 --- a/recipes/ebi-eva-common-pyutils/meta.yaml +++ b/recipes/ebi-eva-common-pyutils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ebi-eva-common-pyutils" %} -{% set version = "0.6.4" %} +{% set version = "0.6.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ebi_eva_common_pyutils-{{ version }}.tar.gz - sha256: 71dc20212bc7899c65cdabda042cd3aca78b51e7acc0d60b506a478454e9852e + sha256: 4ef517d1dc594510b46b7cc6e039f1c9ee67af6d6810bcad866265e05df89b13 build: script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation From 4aed8c2ddf520fe2a05dace9c798f59011e94d17 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Apr 2024 22:12:13 -0400 Subject: [PATCH 1297/1813] Update treeswift to 1.1.42 (#46934) * Update treeswift to 1.1.41 * Update treeswift to 1.1.42 --- recipes/treeswift/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/treeswift/meta.yaml b/recipes/treeswift/meta.yaml index 96939ec1e97d6..4f6f75311c9c6 100644 --- a/recipes/treeswift/meta.yaml +++ b/recipes/treeswift/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.40" %} +{% set version = "1.1.42" %} package: name: "treeswift" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/t/treeswift/treeswift-{{ version }}.tar.gz - sha256: 51c1bf1f0455866f10980d042831d4c1c244d4861808eb53d7730db99279ec14 + sha256: 3dbd1ba139ad28ca71154a61e362cefeee8a18bf3436123404f6269f0f38a44d build: noarch: python From 3496b458e269bf9121f7adf823f2317813db2450 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Apr 2024 22:12:58 -0400 Subject: [PATCH 1298/1813] Update wgd to 2.0.30 (#46926) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index ccd95f04a20aa..c274a221059fe 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.29" %} +{% set version = "2.0.30" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: e1d3e08540c9ba88f10f0cefc636225ac31ea9300c318757eb860df954dc153a + sha256: 97abc0f32c05eba6dc98bd50df801164a046c1a423a0fb1be078f381cb2a658b build: number: 0 From b74cdcc39a0bfc485569f3e7b4143f25470bdaf7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 2 Apr 2024 22:13:13 -0400 Subject: [PATCH 1299/1813] Update seqnado to 0.5.0 (#46912) --- recipes/seqnado/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqnado/meta.yaml b/recipes/seqnado/meta.yaml index 8442d89bc166a..762463faf64bf 100644 --- a/recipes/seqnado/meta.yaml +++ b/recipes/seqnado/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqnado" %} -{% set version = "0.4.3" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqnado-{{ version }}.tar.gz - sha256: 21a943093411bc81e82a23ab64a59945d9c5c142159abd5ddbcd75a0ca63fb85 + sha256: e5f226b590006b043c37cb1e4308950032cbd192b69d530f49682425e0efd677 build: From 0cc14016a6fdad4b77b0eed8b41d8c18f2ad74b1 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 3 Apr 2024 07:34:44 +0300 Subject: [PATCH 1300/1813] prank: add linux-aarch64 build (#46485) * prank: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Fix issues with GPL 3 licence Remove `v.` from the version (lint error) Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/prank/LICENSE.md | 619 +++++++++++++++++++++++++++++++++++++++ recipes/prank/meta.yaml | 13 +- 2 files changed, 628 insertions(+), 4 deletions(-) create mode 100644 recipes/prank/LICENSE.md diff --git a/recipes/prank/LICENSE.md b/recipes/prank/LICENSE.md new file mode 100644 index 0000000000000..51bbbe9e109b1 --- /dev/null +++ b/recipes/prank/LICENSE.md @@ -0,0 +1,619 @@ +### GNU GENERAL PUBLIC LICENSE + +Version 3, 29 June 2007 + +Copyright (C) 2007 Free Software Foundation, Inc. + + +Everyone is permitted to copy and distribute verbatim copies of this +license document, but changing it is not allowed. + +### Preamble + +The GNU General Public License is a free, copyleft license for +software and other kinds of works. + +The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom +to share and change all versions of a program--to make sure it remains +free software for all its users. We, the Free Software Foundation, use +the GNU General Public License for most of our software; it applies +also to any other work released this way by its authors. You can apply +it to your programs, too. + +When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + +To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you +have certain responsibilities if you distribute copies of the +software, or if you modify it: responsibilities to respect the freedom +of others. + +For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + +Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + +For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + +Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the +manufacturer can do so. This is fundamentally incompatible with the +aim of protecting users' freedom to change the software. The +systematic pattern of such abuse occurs in the area of products for +individuals to use, which is precisely where it is most unacceptable. +Therefore, we have designed this version of the GPL to prohibit the +practice for those products. If such problems arise substantially in +other domains, we stand ready to extend this provision to those +domains in future versions of the GPL, as needed to protect the +freedom of users. + +Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish +to avoid the special danger that patents applied to a free program +could make it effectively proprietary. To prevent this, the GPL +assures that patents cannot be used to render the program non-free. + +The precise terms and conditions for copying, distribution and +modification follow. + +### TERMS AND CONDITIONS + +#### 0. Definitions. + +"This License" refers to version 3 of the GNU General Public License. + +"Copyright" also means copyright-like laws that apply to other kinds +of works, such as semiconductor masks. + +"The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + +To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of +an exact copy. The resulting work is called a "modified version" of +the earlier work or a work "based on" the earlier work. + +A "covered work" means either the unmodified Program or a work based +on the Program. + +To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + +To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user +through a computer network, with no transfer of a copy, is not +conveying. + +An interactive user interface displays "Appropriate Legal Notices" to +the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + +#### 1. Source Code. + +The "source code" for a work means the preferred form of the work for +making modifications to it. "Object code" means any non-source form of +a work. + +A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + +The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + +The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + +The Corresponding Source need not include anything that users can +regenerate automatically from other parts of the Corresponding Source. + +The Corresponding Source for a work in source code form is that same +work. + +#### 2. Basic Permissions. + +All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + +You may make, run and propagate covered works that you do not convey, +without conditions so long as your license otherwise remains in force. +You may convey covered works to others for the sole purpose of having +them make modifications exclusively for you, or provide you with +facilities for running those works, provided that you comply with the +terms of this License in conveying all material for which you do not +control copyright. Those thus making or running the covered works for +you must do so exclusively on your behalf, under your direction and +control, on terms that prohibit them from making any copies of your +copyrighted material outside their relationship with you. + +Conveying under any other circumstances is permitted solely under the +conditions stated below. Sublicensing is not allowed; section 10 makes +it unnecessary. + +#### 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + +No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + +When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such +circumvention is effected by exercising rights under this License with +respect to the covered work, and you disclaim any intention to limit +operation or modification of the work as a means of enforcing, against +the work's users, your or third parties' legal rights to forbid +circumvention of technological measures. + +#### 4. Conveying Verbatim Copies. + +You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + +You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + +#### 5. Conveying Modified Source Versions. + +You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these +conditions: + +- a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. +- b) The work must carry prominent notices stating that it is + released under this License and any conditions added under + section 7. This requirement modifies the requirement in section 4 + to "keep intact all notices". +- c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. +- d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + +A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + +#### 6. Conveying Non-Source Forms. + +You may convey a covered work in object code form under the terms of +sections 4 and 5, provided that you also convey the machine-readable +Corresponding Source under the terms of this License, in one of these +ways: + +- a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. +- b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the Corresponding + Source from a network server at no charge. +- c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. +- d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. +- e) Convey the object code using peer-to-peer transmission, + provided you inform other peers where the object code and + Corresponding Source of the work are being offered to the general + public at no charge under subsection 6d. + +A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + +A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, +family, or household purposes, or (2) anything designed or sold for +incorporation into a dwelling. In determining whether a product is a +consumer product, doubtful cases shall be resolved in favor of +coverage. For a particular product received by a particular user, +"normally used" refers to a typical or common use of that class of +product, regardless of the status of the particular user or of the way +in which the particular user actually uses, or expects or is expected +to use, the product. A product is a consumer product regardless of +whether the product has substantial commercial, industrial or +non-consumer uses, unless such uses represent the only significant +mode of use of the product. + +"Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to +install and execute modified versions of a covered work in that User +Product from a modified version of its Corresponding Source. The +information must suffice to ensure that the continued functioning of +the modified object code is in no case prevented or interfered with +solely because modification has been made. + +If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + +The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or +updates for a work that has been modified or installed by the +recipient, or for the User Product in which it has been modified or +installed. Access to a network may be denied when the modification +itself materially and adversely affects the operation of the network +or violates the rules and protocols for communication across the +network. + +Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + +#### 7. Additional Terms. + +"Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + +Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders +of that material) supplement the terms of this License with terms: + +- a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or +- b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or +- c) Prohibiting misrepresentation of the origin of that material, + or requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or +- d) Limiting the use for publicity purposes of names of licensors + or authors of the material; or +- e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or +- f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions + of it) with contractual assumptions of liability to the recipient, + for any liability that these contractual assumptions directly + impose on those licensors and authors. + +All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + +If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; the +above requirements apply either way. + +#### 8. Termination. + +You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + +However, if you cease all violation of this License, then your license +from a particular copyright holder is reinstated (a) provisionally, +unless and until the copyright holder explicitly and finally +terminates your license, and (b) permanently, if the copyright holder +fails to notify you of the violation by some reasonable means prior to +60 days after the cessation. + +Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + +Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + +#### 9. Acceptance Not Required for Having Copies. + +You are not required to accept this License in order to receive or run +a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + +#### 10. Automatic Licensing of Downstream Recipients. + +Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + +An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + +You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + +#### 11. Patents. + +A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + +A contributor's "essential patent claims" are all patent claims owned +or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + +Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + +In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + +If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + +A patent license is "discriminatory" if it does not include within the +scope of its coverage, prohibits the exercise of, or is conditioned on +the non-exercise of one or more of the rights that are specifically +granted under this License. You may not convey a covered work if you +are a party to an arrangement with a third party that is in the +business of distributing software, under which you make payment to the +third party based on the extent of your activity of conveying the +work, and under which the third party grants, to any of the parties +who would receive the covered work from you, a discriminatory patent +license (a) in connection with copies of the covered work conveyed by +you (or copies made from those copies), or (b) primarily for and in +connection with specific products or compilations that contain the +covered work, unless you entered into that arrangement, or that patent +license was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + +#### 12. No Surrender of Others' Freedom. + +If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under +this License and any other pertinent obligations, then as a +consequence you may not convey it at all. For example, if you agree to +terms that obligate you to collect a royalty for further conveying +from those to whom you convey the Program, the only way you could +satisfy both those terms and this License would be to refrain entirely +from conveying the Program. + +#### 13. Use with the GNU Affero General Public License. + +Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + +#### 14. Revised Versions of this License. + +The Free Software Foundation may publish revised and/or new versions +of the GNU General Public License from time to time. Such new versions +will be similar in spirit to the present version, but may differ in +detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies that a certain numbered version of the GNU General Public +License "or any later version" applies to it, you have the option of +following the terms and conditions either of that numbered version or +of any later version published by the Free Software Foundation. If the +Program does not specify a version number of the GNU General Public +License, you may choose any version ever published by the Free +Software Foundation. + +If the Program specifies that a proxy can decide which future versions +of the GNU General Public License can be used, that proxy's public +statement of acceptance of a version permanently authorizes you to +choose that version for the Program. + +Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + +#### 15. Disclaimer of Warranty. + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT +WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND +PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR +CORRECTION. + +#### 16. Limitation of Liability. + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR +CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES +ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT +NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR +LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM +TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER +PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +#### 17. Interpretation of Sections 15 and 16. + +If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + +END OF TERMS AND CONDITIONS diff --git a/recipes/prank/meta.yaml b/recipes/prank/meta.yaml index 5960392c08e83..9e752eaedf3f2 100644 --- a/recipes/prank/meta.yaml +++ b/recipes/prank/meta.yaml @@ -1,19 +1,20 @@ package: name: prank - version: "v.170427" + version: "170427" source: url: http://wasabiapp.org/download/prank/prank.source.170427.tgz sha256: 623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859 build: - number: 7 + number: 0 + run_exports: + - {{ pin_subpackage('prank', max_pin="x.x") }} requirements: build: - make - {{ compiler('cxx') }} - run: test: commands: @@ -21,10 +22,14 @@ test: about: home: http://wasabiapp.org/software/prank/ - license: GPL-3 + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE.md summary: PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:prank - doi:10.1007/978-1-62703-646-7_10 From d8252da6c04f1529e99906d7e91f1514bcec7e36 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 3 Apr 2024 12:45:08 +0800 Subject: [PATCH 1301/1813] linux-aarch64 build for gatk (#46854) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * linux-aarch64 build for adapterremoval * fix * linux-aarch64 build for gatk * linux-aarch64 build for gatk * fix * fix --------- Co-authored-by: yejianbang Co-authored-by: HWsunqian0027 --- recipes/gatk/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/gatk/meta.yaml b/recipes/gatk/meta.yaml index 77decd93b1470..cc2a442f6d1b3 100644 --- a/recipes/gatk/meta.yaml +++ b/recipes/gatk/meta.yaml @@ -11,7 +11,9 @@ package: build: noarch: generic - number: 11 + number: 12 + run_exports: + - {{ pin_subpackage("gatk", max_pin="x") }} source: url: https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2 From 7c68032775dbdbc2d4dd9c99ad8f772a6eddd16c Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 3 Apr 2024 12:46:21 +0800 Subject: [PATCH 1302/1813] Update for Annotsv (#46789) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * fix * linux-aarch64 build for annotsv --------- Co-authored-by: yejianbang Co-authored-by: HWsunqian0027 --- recipes/annotsv/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/annotsv/meta.yaml b/recipes/annotsv/meta.yaml index 8b2d6880cc386..573fe8dc6f9be 100644 --- a/recipes/annotsv/meta.yaml +++ b/recipes/annotsv/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('annotsv', max_pin="x") }} From 092cf3e6a60756fbbae89bf480a3969a8d3e7bf1 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 3 Apr 2024 13:12:59 +0800 Subject: [PATCH 1303/1813] update for abcas (#46881) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * fix * linux-aarch64 build for abacas * edit run_exports max_pin --------- Co-authored-by: yejianbang Co-authored-by: HWsunqian0027 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/abacas/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/abacas/meta.yaml b/recipes/abacas/meta.yaml index 9ce4d033664dd..2373004ce8222 100644 --- a/recipes/abacas/meta.yaml +++ b/recipes/abacas/meta.yaml @@ -13,7 +13,9 @@ source: - patches/path.patch build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage("abacas", max_pin="x") }} noarch: generic requirements: From 9b32d8dc11bb0305fc9c726d5d3e1e2c9b156cfe Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 3 Apr 2024 13:13:34 +0800 Subject: [PATCH 1304/1813] update for Annotwg (#46793) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * fix * linux-aarch64 build for annotwg * edit run_exports max_pin --------- Co-authored-by: yejianbang Co-authored-by: HWsunqian0027 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/annotwg/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/annotwg/meta.yaml b/recipes/annotwg/meta.yaml index fd06dc96d44b1..d2e294561f1b9 100644 --- a/recipes/annotwg/meta.yaml +++ b/recipes/annotwg/meta.yaml @@ -7,7 +7,9 @@ package: version: {{ version }} build: - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage("annotwg", max_pin="x") }} noarch: generic source: From 668fb5b5cf2c11f4ddfa17f1226262a5f59a8859 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 3 Apr 2024 13:13:43 +0800 Subject: [PATCH 1305/1813] Update for amplicon_coverage_plot (#46671) * linux-aarch64 build for amplicon_coverage_plot * Update meta.yaml * edit run_exports max_pin --------- Co-authored-by: yejianbang Co-authored-by: yejianbang <145335562+yejianbang@users.noreply.github.com> Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/amplicon_coverage_plot/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/amplicon_coverage_plot/meta.yaml b/recipes/amplicon_coverage_plot/meta.yaml index a0868b494288c..e870eaaf49531 100644 --- a/recipes/amplicon_coverage_plot/meta.yaml +++ b/recipes/amplicon_coverage_plot/meta.yaml @@ -11,8 +11,10 @@ source: build: noarch: python - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps -vv" + run_exports: + - {{ pin_subpackage("amplicon_coverage_plot", max_pin="x.x") }} requirements: host: From 46c2553ed3ac6e8eb11d15e5edf28089f0241bc6 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 3 Apr 2024 13:14:17 +0800 Subject: [PATCH 1306/1813] linux-aarch64 build for angsd (#46629) * linux-aarch64 build for angsd * edit run_exports max_pin --------- Co-authored-by: HWsunqian0027 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/angsd/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/angsd/meta.yaml b/recipes/angsd/meta.yaml index 4b2e5be264ddf..ada38cb647493 100644 --- a/recipes/angsd/meta.yaml +++ b/recipes/angsd/meta.yaml @@ -12,7 +12,9 @@ source: build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage("angsd", max_pin="x.x") }} skip: True # [osx] requirements: @@ -45,3 +47,5 @@ extra: identifiers: - biotools:angsd - doi:10.1186/s12859-014-0356-4 + additional-platforms: + - linux-aarch64 From 36acf874be0951676c3648913ab7c85bb68bacdb Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 3 Apr 2024 13:17:57 +0800 Subject: [PATCH 1307/1813] Update for amdirt (#46634) * linux-aarch64 build for amdirt * linux-aarch64 build for amdirt * fix --------- Co-authored-by: HWsunqian0027 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/amdirt/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/amdirt/meta.yaml b/recipes/amdirt/meta.yaml index 32fcaf104f35f..e0b4ff0da53a8 100644 --- a/recipes/amdirt/meta.yaml +++ b/recipes/amdirt/meta.yaml @@ -14,7 +14,7 @@ build: - AMDirT = AMDirT.cli:cli noarch: python script: {{ PYTHON }} -m pip install . -vv - number: 0 + number: 1 run_exports: - {{ pin_subpackage("amdirt", max_pin="x.x") }} @@ -26,6 +26,7 @@ requirements: - click - colorlog - jsonschema + - defusedxml - numpy - pandas - python >=3.9 From 23c2dbf6269807e6f0dd5c99eaa8d31b5d8a12a4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 05:56:05 -0400 Subject: [PATCH 1308/1813] Update pyega3 to 5.2.0 (#46946) --- recipes/pyega3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyega3/meta.yaml b/recipes/pyega3/meta.yaml index b2560c1d2c903..5e8ff430248aa 100644 --- a/recipes/pyega3/meta.yaml +++ b/recipes/pyega3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyega3" %} -{% set version = "5.1.0" %} +{% set version = "5.2.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: f8ffa8558da52ad17b83bda2c94a289cd51f24e86e3230b8eff3aaba3f7db3ce + sha256: 95539b8e153f2311d89a6905723598013fd12a9d0784a911ed1b550a4094bad1 build: number: 0 From e9b59e5c80db76a16b4e970249807aad1f58f94e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 07:04:35 -0400 Subject: [PATCH 1309/1813] Update panaroo to 1.5.0 (#46944) --- recipes/panaroo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/panaroo/meta.yaml b/recipes/panaroo/meta.yaml index 5fbf153632352..1a459568ac0be 100644 --- a/recipes/panaroo/meta.yaml +++ b/recipes/panaroo/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.2" %} +{% set version = "1.5.0" %} {% set name = "panaroo" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/gtonkinhill/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 7f3e06d19dfc8b65e761ea0199e0a1363ee8b708bab327679000e770de9f3af3 + sha256: 0a80f87cde8ee3d59cd62cdae434341979a03dfdeb07142c2f9ff3b54dc0477a build: number: 0 From 7a724b84074e8adfba6a2ac067e23fa0fa0a0819 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 3 Apr 2024 16:30:57 +0300 Subject: [PATCH 1310/1813] ci: [CircleCI] Use tr to drop {{ and }} (#46952) Using sed does not work with inputs like: ``` - {{ name | lower }} --version | grep {{ version }} ``` i.e. with several placeholders on the same line. I was not able to tell sed to use non-gready match. Found the issue while debugging https://github.com/bioconda/bioconda-recipes/pull/46880 Signed-off-by: Martin Tzvetanov Grigorov --- .circleci/check-for-additional-platforms.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/check-for-additional-platforms.sh b/.circleci/check-for-additional-platforms.sh index a05da11215509..5e3cdec3f013a 100755 --- a/.circleci/check-for-additional-platforms.sh +++ b/.circleci/check-for-additional-platforms.sh @@ -24,7 +24,7 @@ for file in $files; do # variable setting with {% %} and remove variable use with {{ }}. additional_platforms=$(cat $file \ | sed -E 's/(.*)\{%(.*)%\}(.*)/# \1\2\3/g' \ - | sed -E 's/(.*)\{\{(.*)\}\}(.*)/\1\2\3/g' \ + | tr -d '{{' | tr -d '}}' \ | yq '.extra.additional-platforms[]') # Check if any additional platforms match this job for additional_platform in $additional_platforms; do From 6726392e398505a6ea8b897f6275476bd2d9ec6b Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 3 Apr 2024 16:51:35 +0300 Subject: [PATCH 1311/1813] Save `yq` to ~/bin/ (#46950) Saving to `/usr/local/bin` fails with `Permission denied` error. For example https://app.circleci.com/pipelines/github/bioconda/bioconda-recipes/112535/workflows/40d63e46-327b-4fcd-8386-b4384a686ce7/jobs/183359?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-checks-link&utm_content=summary is a successful job that fails with `Permission denied`. It seems (an older version of) `yq` is still available in the PATH that is used later. Signed-off-by: Martin Tzvetanov Grigorov --- .circleci/check-for-additional-platforms.sh | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.circleci/check-for-additional-platforms.sh b/.circleci/check-for-additional-platforms.sh index 5e3cdec3f013a..9a0fcd6a304e6 100755 --- a/.circleci/check-for-additional-platforms.sh +++ b/.circleci/check-for-additional-platforms.sh @@ -12,7 +12,9 @@ job_name=$2 yq_platform=$(uname) yq_arch=$(uname -m) [[ $yq_arch = "aarch64" ]] && yq_arch="arm64" -wget https://github.com/mikefarah/yq/releases/latest/download/yq_${yq_platform}_${yq_arch} -O /usr/local/bin/yq +mkdir -p ${HOME}/bin +wget https://github.com/mikefarah/yq/releases/latest/download/yq_${yq_platform}_${yq_arch} -O ${HOME}/bin/yq +chmod +x ${HOME}/bin/yq # Find recipes changed from this merge files=`git diff --name-only --diff-filter AMR ${git_range} | grep -E 'meta.yaml$' ` @@ -25,7 +27,7 @@ for file in $files; do additional_platforms=$(cat $file \ | sed -E 's/(.*)\{%(.*)%\}(.*)/# \1\2\3/g' \ | tr -d '{{' | tr -d '}}' \ - | yq '.extra.additional-platforms[]') + | ${HOME}/bin/yq '.extra.additional-platforms[]') # Check if any additional platforms match this job for additional_platform in $additional_platforms; do if [ "${CIRCLE_JOB}" = "${job_name}-${additional_platform}" ] From 640884e6139bf79a23c5467b9b301853eb763146 Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Wed, 3 Apr 2024 22:10:03 +0800 Subject: [PATCH 1312/1813] Update anansescanpy (#46841) * linux-aarch64 build for anansescanpy * edit run_exports max_pin --------- Co-authored-by: yejianbang Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/anansescanpy/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/anansescanpy/meta.yaml b/recipes/anansescanpy/meta.yaml index e53033971199d..7939a37e114b6 100644 --- a/recipes/anansescanpy/meta.yaml +++ b/recipes/anansescanpy/meta.yaml @@ -11,7 +11,9 @@ source: sha256: 9efd6ca2c1e5a9fc1ab70030f74f4a063f7e7ac065e6c7942d8b8cd08626accf build: - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage("anansescanpy", max_pin="x.") }} noarch: python script: {{ PYTHON }} -m pip install . -vv From 0ac5250891cf6a4eef1ca37dde8cf80ed4833c65 Mon Sep 17 00:00:00 2001 From: Henning Timm Date: Wed, 3 Apr 2024 17:25:23 +0200 Subject: [PATCH 1313/1813] Update dinopy (#46953) Updated dinopy to version 3.0.0 --- recipes/dinopy/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/dinopy/meta.yaml b/recipes/dinopy/meta.yaml index e3ff0b18c9196..53f879bd28e6b 100644 --- a/recipes/dinopy/meta.yaml +++ b/recipes/dinopy/meta.yaml @@ -1,14 +1,17 @@ +{% set version = "3.0.0" %} + package: name: dinopy - version: "2.2.1" + version: {{ version }} source: - url: https://files.pythonhosted.org/packages/2f/6c/eb26221f3b28e05ceede15e02a31c6fb3762940d46ac5cd3b1f56951b59a/dinopy-2.2.1.tar.gz - sha256: 092323edddf48c9d3082dfaf934f5c3e4011c7e1248503cd352105e6e50bfcf5 + url: https://files.pythonhosted.org/packages/e3/fd/06182a3e21bd400c172ef973512a070968c039a0f18f41c54c933fcafef9/dinopy-{{ version }}.tar.gz + sha256: 9b2238c20c946a7ea34b979fec4dd182f3474958e9a03075dfbbb464e9d84028 build: - skip: True # [py27 or py36] - number: 5 + number: 0 + run_exports: + - {{ pin_subpackage("dinopy", max_pin="x") }} requirements: build: @@ -16,7 +19,7 @@ requirements: host: - python - setuptools - - cython >=0.22 + - cython >=3.0.0 - numpy =1.21 run: - python From f7ba1e4a10f0c02e7b508d65d9bd5a063292b259 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 11:50:16 -0400 Subject: [PATCH 1314/1813] Update galaxy-files to 24.0.0 (#46941) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/galaxy-files/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml index e62f7e1bcf271..574bbf277470b 100644 --- a/recipes/galaxy-files/meta.yaml +++ b/recipes/galaxy-files/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.2.1" %} -{% set sha256 = "aa658c52eac6e7a7aa9eca7b132714d0887bf2649d5de472f90776d1c2ca7838" %} +{% set version = "24.0.0" %} +{% set sha256 = "d00dab002d94a6463bb93d6c7fab4d5dce921e7ab54de5ca59c615faa1a14038" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From 577e4148d7174e4325438cbf4c4e44248342a3e2 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 3 Apr 2024 19:00:48 +0300 Subject: [PATCH 1315/1813] paml: add linux-aarch64 build (#46954) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/paml/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/paml/meta.yaml b/recipes/paml/meta.yaml index 1509d22de4f07..e2eeb810e8291 100644 --- a/recipes/paml/meta.yaml +++ b/recipes/paml/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('paml', max_pin="x.x") }} @@ -37,6 +37,8 @@ about: license_file: LICENSE extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:paml - doi:10.1093/bioinformatics/13.5.555 From 8c0bb5e2ffd235d5c253191a131f97af8ae21753 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 12:18:23 -0400 Subject: [PATCH 1316/1813] Update galaxy-objectstore to 24.0.0 (#46942) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/galaxy-objectstore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml index d2ec30dbfa0d2..d8ec586420831 100644 --- a/recipes/galaxy-objectstore/meta.yaml +++ b/recipes/galaxy-objectstore/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.2.1" %} -{% set sha256 = "31deb13282286c4f8baae364049726686559ab2575a8b2360fda12af26146f47" %} +{% set version = "24.0.0" %} +{% set sha256 = "0cd30eff8285b83320b3eb5677bb93e3d368a8e771747c906861f88ca5036cd6" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From 600342f41e3cc3a5ee8c3ad277100151daa14a5b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 12:28:01 -0400 Subject: [PATCH 1317/1813] Update ezomero to 3.0.0 (#46959) --- recipes/ezomero/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ezomero/meta.yaml b/recipes/ezomero/meta.yaml index c7c97d63bc839..a5586bc74da1a 100644 --- a/recipes/ezomero/meta.yaml +++ b/recipes/ezomero/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.1.0" %} +{% set version = "3.0.0" %} {% set name = "ezomero" %} package: @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 729db284c27067b8accb127c6501b2205f63e639045339e6939f7c991f0759c7 + sha256: dab92f66453f223a949256833dbad8e60281f29535308f378a213bd93a9c78c6 build: noarch: python From 0af5491c819ac39cc9272a833cce90f3b9542591 Mon Sep 17 00:00:00 2001 From: Florian Zwagemaker <49153065+florianzwagemaker@users.noreply.github.com> Date: Wed, 3 Apr 2024 18:36:05 +0200 Subject: [PATCH 1318/1813] Update recipe for AmpliGone 1.3.1 (#46949) * Update ampligone to v1.3.1 add run_exports section to recipe * change pin_subpackage to semantic versioning --- recipes/ampligone/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/ampligone/meta.yaml b/recipes/ampligone/meta.yaml index 7abf6fa3729ca..9189a1164ae51 100644 --- a/recipes/ampligone/meta.yaml +++ b/recipes/ampligone/meta.yaml @@ -1,5 +1,5 @@ {% set name = "AmpliGone" %} -{% set version = "1.3.0" %} +{% set version = "1.3.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,13 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d2fb6b0b526e784a6ddaac19e92ab074266a25905de539f227a5131297c41aa0 + sha256: f53520874f5f3301b6099142e1d79264a96820add09affb0130744eb39ae4139 build: noarch: python number: 0 + run_exports: + - {{ pin_subpackage("ampligone", max_pin="x") }} entry_points: - ampligone = AmpliGone.AmpliGone:main - AmpliGone = AmpliGone.AmpliGone:main @@ -51,4 +53,4 @@ extra: recipe-maintainers: - florianzwagemaker - KHajji - - ids-bioinformatics + - ids-bioinformatics \ No newline at end of file From 8478f03433851dc80c674d84827170adbdbbd310 Mon Sep 17 00:00:00 2001 From: Matthew Berkeley <42berkeley@cua.edu> Date: Wed, 3 Apr 2024 17:49:21 +0100 Subject: [PATCH 1319/1813] Update to 5.7.1 (#46948) * Update to 5.7.1 * reset build number --- recipes/busco/0001-Set-conda-distribution.patch | 14 +------------- recipes/busco/meta.yaml | 6 +++--- 2 files changed, 4 insertions(+), 16 deletions(-) diff --git a/recipes/busco/0001-Set-conda-distribution.patch b/recipes/busco/0001-Set-conda-distribution.patch index b8a0ac5f2531e..68091d67a5b1f 100644 --- a/recipes/busco/0001-Set-conda-distribution.patch +++ b/recipes/busco/0001-Set-conda-distribution.patch @@ -1,18 +1,6 @@ --- a/src/busco/run_BUSCO.py +++ b/src/busco/run_BUSCO.py -@@ -121,18 +121,12 @@ class BuscoMaster: - logger.debug("File upload failed. Status code: {}".format(response.status)) - - def get_dist_info(self): -- if ( # todo: fix -- "conda" in __file__ -- and os.environ("CONDA_DEFAULT_ENV") -- and os.environ("CONDA_PREFIX") -- ): -- self.run_data["distribution"] = "conda" -- elif os.path.exists("/.dockerenv"): -+ if os.path.exists("/.dockerenv"): - self.run_data["distribution"] = "docker" +@@ -126,7 +126,7 @@ class BuscoMaster: elif os.path.exists("/.singularity.d"): self.run_data["distribution"] = "singularity" else: diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml index f1a9e3e254dcf..528eb257d49c9 100644 --- a/recipes/busco/meta.yaml +++ b/recipes/busco/meta.yaml @@ -1,13 +1,13 @@ {% set name = "busco" %} -{% set version = "5.7.0" %} -{% set sha256 = "dbd9e07a5fb42583bd6ddbbfe06c420d5317a6f3698e6f4be0f53baa6c3ccc5e" %} +{% set version = "5.7.1" %} +{% set sha256 = "d57066b68d533f0b86518653430ba47b748ef14db56d2a992601d3e26096cad6" %} package: name: busco version: {{ version }} build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} From a5f265fc9e61ffb3b2e8143f9ead5dd5f632d7fd Mon Sep 17 00:00:00 2001 From: sunqian2116 <163837843+sunqian2116@users.noreply.github.com> Date: Thu, 4 Apr 2024 01:05:34 +0800 Subject: [PATCH 1320/1813] linux-aarch64 build for abpoa (#46880) * add linux-aarch64-aligncov * add linux-aarch64-aligncov * fix * linux-aarch64 build for abpoa * change variables to name for consistency * edit license to MIT --------- Co-authored-by: yejianbang Co-authored-by: HWsunqian0027 Co-authored-by: Robert A. Petit III Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/abpoa/meta.yaml | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/recipes/abpoa/meta.yaml b/recipes/abpoa/meta.yaml index a4fdf9234fc98..e0cbaba96a5cd 100644 --- a/recipes/abpoa/meta.yaml +++ b/recipes/abpoa/meta.yaml @@ -1,19 +1,18 @@ {% set version = "1.5.1" %} -{% set program = "abpoa" %} -{% set PROGRAM = "abPOA" %} +{% set name = "abPOA" %} package: - name: abpoa + name: {{ name | lower }} version: {{ version }} source: - url: https://github.com/yangao07/{{ PROGRAM }}/releases/download/v{{ version }}/{{ PROGRAM }}-v{{ version }}.tar.gz + url: https://github.com/yangao07/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz sha256: f0e1b41b1c9e18ecd2096df9b60ad053260ec773d70eecb307b02cca0efab89d build: - number: 0 + number: 1 run_exports: - - {{ pin_subpackage(program, max_pin="x.x") }} + - {{ pin_subpackage(name | lower, max_pin="x") }} requirements: build: @@ -24,10 +23,15 @@ requirements: test: commands: - - {{ program }} --version | grep {{ version }} + - {{ name | lower }} --version | grep {{ version }} about: - home: https://github.com/yangao07/{{ PROGRAM }} - license: GPL + home: https://github.com/yangao07/{{ name }} + license: MIT + license_family: MIT license_file: LICENSE summary: 'abPOA: fast SIMD-based partial order alignment using adaptive band' + +extra: + additional-platforms: + - linux-aarch64 From a75ca6551832c169fb410740c6c3d55441141f4f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 15:10:58 -0400 Subject: [PATCH 1321/1813] Update apscale to 1.7.1 (#46930) * Update apscale to 1.7.1 * add run_exports --------- Co-authored-by: mencian --- recipes/apscale/meta.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/apscale/meta.yaml b/recipes/apscale/meta.yaml index 495fa59ecdf6a..35804d0fc32bf 100644 --- a/recipes/apscale/meta.yaml +++ b/recipes/apscale/meta.yaml @@ -1,5 +1,5 @@ {% set name = "apscale" %} -{% set version = "1.6.3" %} +{% set version = "1.7.1" %} package: name: {{ name|lower }} @@ -7,14 +7,16 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/apscale-{{ version }}.tar.gz - sha256: cb9c08810cb2c55377ea4dde936f4321fd0a753ef853bb0fad621d4bb39d28da + sha256: 99ea723823313e33ee69373fbb9b12d7a62765fe6d74c9f69d61a2d4dc2ea69f build: entry_points: - apscale = apscale.__main__:main noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv number: 0 + run_exports: + - {{ pin_subpackage('apscale', max_pin="x") }} requirements: host: @@ -38,16 +40,15 @@ test: imports: - apscale commands: - - pip check - apscale --help - requires: - - pip about: home: https://github.com/DominikBuchner/apscale summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data license: MIT + license_family: MIT license_file: LICENSE + dev_url: https://github.com/DominikBuchner/apscale extra: recipe-maintainers: From 05565ed57fdd4dbcffbd36d01f35702da92159f5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 15:22:06 -0400 Subject: [PATCH 1322/1813] Update goldrush to 1.1.1 (#46963) --- recipes/goldrush/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/goldrush/meta.yaml b/recipes/goldrush/meta.yaml index c4f4260040bd1..14d75ccce8eec 100644 --- a/recipes/goldrush/meta.yaml +++ b/recipes/goldrush/meta.yaml @@ -1,5 +1,5 @@ {% set name = "goldrush" %} -{% set version = "1.1.0" %} +{% set version = "1.1.1" %} package: name: {{ name|lower }} @@ -7,11 +7,11 @@ package: source: url: https://github.com/bcgsc/goldrush/releases/download/{{ version }}/{{ name|lower }}-{{ version }}.tar.xz - sha256: b1687aab7e9b44074fe1e2aa1f49d4e851677622c7869f24c011ba73bb3cbdcf + sha256: f9847c3bed5bb16494789661d4e12137537b1987c6bb19a0932ae0dd90b6e3ed build: skip: true # [py < 38 or win or py > 39] - number: 1 + number: 0 run_exports: {{ pin_subpackage("goldrush", max_pin="x") }} requirements: From b0e26b45fb0d9e08c15180b89255cc09d845e74f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 15:22:16 -0400 Subject: [PATCH 1323/1813] Update rabbitqcplus to 2.2.9 (#46962) --- recipes/rabbitqcplus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rabbitqcplus/meta.yaml b/recipes/rabbitqcplus/meta.yaml index 3431c61fe6e4b..63767734b6e46 100644 --- a/recipes/rabbitqcplus/meta.yaml +++ b/recipes/rabbitqcplus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.2.8" %} +{% set version = "2.2.9" %} package: name: rabbitqcplus @@ -6,7 +6,7 @@ package: source: url: https://github.com/RabbitBio/RabbitQCPlus/archive/refs/tags/{{ version }}.tar.gz - sha256: 2466f50d735e6445200698ea9ad8041ce93ec8335a94b6181648b44d6a0ee4af + sha256: 076cb1e11046d5a41464f74d7df363e2ea337e2cf3ad8e8b0712c5c7df746466 build: number: 0 From 9d611ed45b360a9426638388e8185cd786ead041 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 16:37:49 -0400 Subject: [PATCH 1324/1813] Update viroconstrictor to 1.4.2 (#46965) --- recipes/viroconstrictor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viroconstrictor/meta.yaml b/recipes/viroconstrictor/meta.yaml index 9f8aefdc77b11..d34ea1322c12f 100644 --- a/recipes/viroconstrictor/meta.yaml +++ b/recipes/viroconstrictor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ViroConstrictor" %} -{% set version = "1.4.1" %} +{% set version = "1.4.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/RIVM-bioinformatics/ViroConstrictor/archive/v{{ version }}.tar.gz - sha256: fb2c80018762b5809d3b6a404c27f60b7534d4a0dc00543365a21fd1efc0dd7a + sha256: 7b7f8c0f129b9fa1ccc8c374c7436b6065f7dea87ee6e0423d75fd7f04d81d29 build: noarch: python From de86ed9260f8eca89ef78e683d2fa0f62b3a0099 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 23:01:44 -0400 Subject: [PATCH 1325/1813] Update btllib to 1.7.1 (#46967) --- recipes/btllib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/btllib/meta.yaml b/recipes/btllib/meta.yaml index 6a7e631686d5b..a01f150fcc8b3 100644 --- a/recipes/btllib/meta.yaml +++ b/recipes/btllib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "btllib" %} -{% set version = "1.7.0" %} +{% set version = "1.7.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bcgsc/btllib/releases/download/v{{ version }}/{{ name|lower }}-{{ version }}.tar.gz - sha256: a9a2b7d5c65865b20ee6467657c08ac05c9ea1f7c993bf44c3ffcf044b200def + sha256: 7fa600b34a1d46fa4a4dcd214a76c1c5e08c6f7e99a60a61f8bfc477e3fdfdfe build: skip: true # [py < 38 or win] From bcefd37a46259e8be5a54c03e44284181c868983 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Apr 2024 23:01:57 -0400 Subject: [PATCH 1326/1813] Update igv to 2.17.4 (#46969) --- recipes/igv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/igv/meta.yaml b/recipes/igv/meta.yaml index f6b4328bcb2b3..de70d2e597401 100644 --- a/recipes/igv/meta.yaml +++ b/recipes/igv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "IGV" %} -{% set version = "2.17.3" %} -{% set sha256 = "81ab0164014612ff37eea6c7673072fb38ba65b527c05c1197f605c3e9cf3c39" %} +{% set version = "2.17.4" %} +{% set sha256 = "1c42fcca6fcb17d6ca6eced4bc27075f45aed62d2f9cc0d6a149e69cc56113c0" %} package: name: {{ name|lower }} From 08247f99cd8bd1b3e86a015422ef60c03cbd1aec Mon Sep 17 00:00:00 2001 From: ylf9811 Date: Thu, 4 Apr 2024 12:03:30 +0800 Subject: [PATCH 1327/1813] update rabbitqcplus 2.2.9, fix illegal instruction (#46971) * update rabbitqcplus to 2.2.8 * update rabbitqcplus 2.2.9, fix illegal instruction * update rabbitqcplus 2.2.9 (build number 1), fix illegal instruction --- recipes/rabbitqcplus/build.sh | 2 +- recipes/rabbitqcplus/meta.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rabbitqcplus/build.sh b/recipes/rabbitqcplus/build.sh index 28712451f1912..008b8deee4fb0 100644 --- a/recipes/rabbitqcplus/build.sh +++ b/recipes/rabbitqcplus/build.sh @@ -5,6 +5,6 @@ export CXX=${CXX:-g++} export LIBRARY_DIRS="$LIBRARY_DIRS $PREFIX/lib" -make +make BIOCONDA=1 make install diff --git a/recipes/rabbitqcplus/meta.yaml b/recipes/rabbitqcplus/meta.yaml index 63767734b6e46..d85b61e5b355c 100644 --- a/recipes/rabbitqcplus/meta.yaml +++ b/recipes/rabbitqcplus/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 076cb1e11046d5a41464f74d7df363e2ea337e2cf3ad8e8b0712c5c7df746466 build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("rabbitqcplus", max_pin="x.x") }} From 712e1cfc41a1f2142c0a394080c9fa541c9a22a0 Mon Sep 17 00:00:00 2001 From: Chenkai Li Date: Wed, 3 Apr 2024 21:04:02 -0700 Subject: [PATCH 1328/1813] Update AMPlify build (#46972) * Update amplify to 2.0.0 * Specify package version * Add run_exports * Specify version information for all packages * Add more detailed version information * Change everything back * Add run_exports * Update version * update tensorflow version * change order * try host * change back * try channels * change back * try * change back * try * try * change back * try * change back * try * change back * try * try * try * switch source * try * try * try * try * try * try * try * try * try * try * try * try * update version * remove pip * update absl-py version information --------- Co-authored-by: mark0428 --- recipes/amplify/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/amplify/meta.yaml b/recipes/amplify/meta.yaml index ec02b944b75d4..6df2912c42852 100644 --- a/recipes/amplify/meta.yaml +++ b/recipes/amplify/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 94418a9e2f09b1cfc63eff047fab6d15cce5a7afae5283e50ab809dac2de8752 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} @@ -27,6 +27,7 @@ requirements: - pandas - scikit-learn - h5py <3 + - absl-py <2 test: commands: From 94e00944980cdc20d9da463166c08daa23ec0098 Mon Sep 17 00:00:00 2001 From: Adam Cribbs Date: Thu, 4 Apr 2024 06:04:39 +0200 Subject: [PATCH 1329/1813] Update cgat-apps 0.7.0 (#46964) * Update cgat-apps to 0.7.0 * fixed lints * removed from blacklist * looks like bedtobigbed isnt used in any of the scripts so have removed --- build-fail-blacklist | 1 - recipes/cgat-apps/meta.yaml | 23 ++++++++++++----------- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 94d6a11bd8263..ff3fedc6f0e8c 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -24,7 +24,6 @@ recipes/lordec recipes/octopus recipes/bttcmp recipes/bttoxin_scanner -recipes/cgat-apps recipes/hail recipes/monocle3-cli recipes/phenix diff --git a/recipes/cgat-apps/meta.yaml b/recipes/cgat-apps/meta.yaml index a31ea03d5e61f..8a9d7865d52bd 100644 --- a/recipes/cgat-apps/meta.yaml +++ b/recipes/cgat-apps/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "0.6.5" %} +{% set name = "cgat-apps" %} +{% set version = "0.7.0" %} package: - name: cgat-apps + name: {{ name|lower }} version: {{ version }} source: url: https://pypi.io/packages/source/c/cgat/cgat-{{ version }}.tar.gz - sha256: c2350e2e1e6897839537b0ed17b4a03140141d0f0c15cb804e6e7aa12e2d2b70 + sha256: 42d23ffed9dcea37f816912a2b8679c353299f55c285cb4d20250622ee39cd5c build: - skip: True # [py2k or py == 39 or py == 36] - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage('cgat-apps', max_pin="x.x") }} entry_points: - cgat = cgat.cgat:main @@ -20,16 +22,16 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} host: - - python + - python >=3.8 - cython - numpy - - pysam>=0.17.0 + - pysam >=0.17.0 - htslib - setuptools - ucsc-wigtobigwig run: - - python - - cgatcore>=0.6.5 + - python >=3.8 + - cgatcore >=0.6.5 - alignlib-lite - biopython - future @@ -38,7 +40,7 @@ requirements: - pandas - pybedtools - pybigwig - - pysam>=0.17.0 + - pysam >=0.17.0 - htslib - pyyaml - quicksect @@ -50,7 +52,6 @@ requirements: # Misc dependencies - bedtools - ucsc-bedgraphtobigwig - - ucsc-bedtobigbed - ucsc-wigtobigwig - coreutils - grep From de42f35e88bb278e6331663f53a8c4ce112d0037 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 01:33:28 -0400 Subject: [PATCH 1330/1813] Update r-signac to 1.13.0 (#46974) --- recipes/r-signac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-signac/meta.yaml b/recipes/r-signac/meta.yaml index a3a41ca45a8f0..ed619910d09f3 100644 --- a/recipes/r-signac/meta.yaml +++ b/recipes/r-signac/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.12.0' %} +{% set version = '1.13.0' %} package: name: r-signac @@ -8,7 +8,7 @@ source: url: - {{ cran_mirror }}/src/contrib/Signac_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/Signac/Signac_{{ version }}.tar.gz - sha256: 0a4f1e53bcb6c3ba1e3a8e0800d6c4e65983560ff1147a643b7109452374c937 + sha256: d9b4103c6437391834b2d9e2aab8829f186b6e09d070dfe2a66cc12583241b2a build: number: 0 From 9dd78a978203c6a958c80b713cc8589048da0a53 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 01:33:42 -0400 Subject: [PATCH 1331/1813] Update clipkit to 2.2.5 (#46973) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index bbde91a49bb3d..893833b69c120 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.2.4" %} +{% set version = "2.2.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 86f33e78f2aa18be093056c92cf69b9853e65022593280876900f1eaaf70daa2 + sha256: c3b530dcd712c26fff626d9ba55a0a8b1517f9f1fbc46e13888cecf7512cd1fb build: number: 0 From 03bae9cfb2f1c4babec468934449d5f8824be8dc Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 4 Apr 2024 07:36:52 +0100 Subject: [PATCH 1332/1813] Fix tw organizations sub command (#46933) * Fix tw organizations sub command * Remove tower ARM build --- recipes/tower-cli/meta.yaml | 3 ++- recipes/tower-cli/tw.sh | 8 +------- 2 files changed, 3 insertions(+), 8 deletions(-) diff --git a/recipes/tower-cli/meta.yaml b/recipes/tower-cli/meta.yaml index bad22f588a3a3..4df0c97fac1f8 100644 --- a/recipes/tower-cli/meta.yaml +++ b/recipes/tower-cli/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage("tower-cli", max_pin="x.x") }} @@ -23,6 +23,7 @@ requirements: test: commands: - tw --help + - tw organizations --help about: home: "https://github.com/seqeralabs/tower-cli" diff --git a/recipes/tower-cli/tw.sh b/recipes/tower-cli/tw.sh index e1175961f7b93..09af6ae2257ff 100644 --- a/recipes/tower-cli/tw.sh +++ b/recipes/tower-cli/tw.sh @@ -61,10 +61,4 @@ if [ "$jvm_mem_opts" == "" ]; then fi pass_arr=($pass_args) -if [[ ${pass_arr[0]:=} == org* ]] -then - eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/$jar_file" $pass_args -else - eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/$jar_file" $pass_args -fi -exit +eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/$jar_file" $pass_args \ No newline at end of file From 9e3666069e724d5edd1ac86a5e667b06a7b4a029 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=A3o=20Cavalcante?= Date: Thu, 4 Apr 2024 03:37:49 -0300 Subject: [PATCH 1333/1813] Update PhiSpy with fixed biopython version (#46939) * fix: Change biopython version in PhiSpy * fix: Add run_exports Signed-off-by: jvfe * fix: Remove space Signed-off-by: jvfe --------- Signed-off-by: jvfe --- recipes/phispy/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/phispy/meta.yaml b/recipes/phispy/meta.yaml index 1c96458f5a46e..0102087cd18f1 100644 --- a/recipes/phispy/meta.yaml +++ b/recipes/phispy/meta.yaml @@ -11,9 +11,11 @@ source: sha256: "1dc3ec45c15328577557908517254d8e4ba152416f0e6bbad39e965b86730e28" build: - number: 2 + number: 3 skip: True # [py27 or py < 37] script: "{{ PYTHON }} -m pip install . --no-deps -vv " + run_exports: + - {{ pin_subpackage('phispy', max_pin="x") }} requirements: build: @@ -22,7 +24,7 @@ requirements: - pip - python run: - - biopython + - biopython <=1.81 - numpy - python - hmmer From 821045b1935250304db21cec5d2b05376c8054f2 Mon Sep 17 00:00:00 2001 From: Reid Wagner <74672860+reid-wagner@users.noreply.github.com> Date: Thu, 4 Apr 2024 01:37:55 -0500 Subject: [PATCH 1334/1813] Downgrade philosopher version to 5.0.0 for compatibility with FragPipe 20.0. (#46940) --- recipes/fragpipe/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/fragpipe/meta.yaml b/recipes/fragpipe/meta.yaml index 26d268719fd09..873f31d126e29 100644 --- a/recipes/fragpipe/meta.yaml +++ b/recipes/fragpipe/meta.yaml @@ -1,6 +1,6 @@ {% set name = "FragPipe" %} {% set version = "20.0" %} -{% set philosopher_version = "5.1.0" %} +{% set philosopher_version = "5.0.0" %} # These keys were generated ONLY for the testing of this bioconda package. # Users must generate their own key by agreeing to the terms at https://msfragger-upgrader.nesvilab.org/upgrader/ and https://msfragger.arsci.com/ionquant/. @@ -12,7 +12,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage('fragpipe', max_pin="x.x") }} @@ -22,7 +22,7 @@ source: sha256: 0d77db85ae26c190a915823e1c68238f3a19533810734b008564b2a8d85d1bd6 folder: fragpipe_source - url: https://github.com/Nesvilab/philosopher/releases/download/v{{ philosopher_version }}/philosopher_v{{ philosopher_version }}_linux_amd64.zip - sha256: cf15a2d6321ecb530170b2410f5873f89e283b52d5f1ab0f27eebc124f4f4a1a + sha256: b0f6a6d22ca72efd54d1143142648e110b211eccaba20fe169ee65509da02fad folder: philosopher_source requirements: From fd92eedac2c289abfb56bb0f946dc16088340da1 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Thu, 4 Apr 2024 17:39:25 +1100 Subject: [PATCH 1335/1813] Update captus recipe so BLAT can find libbz2 (#46943) * add bzip to captus * bump build * bzip * add bzip2 to host * zlib * add symlink to libbz2 * restore dependencies * Update build.sh * Update build.sh * Update meta.yaml --- recipes/captus/build.sh | 8 ++++++++ recipes/captus/meta.yaml | 4 +--- 2 files changed, 9 insertions(+), 3 deletions(-) create mode 100644 recipes/captus/build.sh diff --git a/recipes/captus/build.sh b/recipes/captus/build.sh new file mode 100644 index 0000000000000..374c3b8aca8dd --- /dev/null +++ b/recipes/captus/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +if [ `uname -s` == "Linux" ]; +then + ln -s "${PREFIX}/lib/libbz2.so.1.0" "${PREFIX}/lib/libbz2.so.1" +fi + +$PYTHON -m pip install . --ignore-installed -vv diff --git a/recipes/captus/meta.yaml b/recipes/captus/meta.yaml index dfabb039bb92b..8a22b833b4489 100644 --- a/recipes/captus/meta.yaml +++ b/recipes/captus/meta.yaml @@ -10,9 +10,8 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 noarch: python - script: "{{ PYTHON }} -m pip install . --ignore-installed -vv" run_exports: - {{ pin_subpackage("captus", max_pin="x.x") }} @@ -22,7 +21,6 @@ requirements: - python >=3.6 - pip - setuptools - run: - python >=3.6 - pip From b8a79fe3d87920e31a92aaa641c89595f2ade4ed Mon Sep 17 00:00:00 2001 From: Mathieu Fourment Date: Thu, 4 Apr 2024 17:40:46 +1100 Subject: [PATCH 1336/1813] Add physher recipe (#46844) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Initialize physher recipe * Add make in requirements * Update recipes/physher/meta.yaml Co-authored-by: Björn Grüning --------- Co-authored-by: Björn Grüning --- recipes/physher/build.sh | 5 +++++ recipes/physher/meta.yaml | 43 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 recipes/physher/build.sh create mode 100644 recipes/physher/meta.yaml diff --git a/recipes/physher/build.sh b/recipes/physher/build.sh new file mode 100644 index 0000000000000..9e841b22143c6 --- /dev/null +++ b/recipes/physher/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +cmake -S . -B build -DBUILD_CPP_WRAPPER=on -DCMAKE_INSTALL_PREFIX=$PREFIX + +cmake --build build/ --target install \ No newline at end of file diff --git a/recipes/physher/meta.yaml b/recipes/physher/meta.yaml new file mode 100644 index 0000000000000..7c864f1e5360d --- /dev/null +++ b/recipes/physher/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "physher" %} +{% set version = "2.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +build: + number: 0 + run_exports: + - {{ pin_subpackage('physher', max_pin="x") }} + +source: + url: https://github.com/4ment/physher/archive/refs/tags/v{{ version }}.tar.gz + sha256: 89de0789af1136ca9a08f009b1db45d441bcb1d4ea7519103a998916b37c618f + + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - cmake + - make + host: + - gsl + +test: + commands: + - physher + +about: + home: https://github.com/4ment/physher + license: GPL-2.0-or-later + license_family: GPL2 + license_file: LICENSE + summary: A multi-algorithmic framework for phylogenetic inference + +extra: + maintainers: + - 4ment + identifiers: + - doi:10.1186/s12862-014-0163-6 + - biotools:physher From 808344f0e88f7fe7d7037296aeff2fd87262f85b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 02:44:24 -0400 Subject: [PATCH 1337/1813] Update pybiolib to 1.1.1934 (#46975) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index d01b39ef96adc..56c7ba88dd7ee 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1930" %} +{% set version = "1.1.1934" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: cf59c083fa15c9c9316b5f95e70fd75560c17545d5bda91959b90fa973056652 + sha256: 4e1867fba20ffe4845ccad9d947afaa284f4c1f54fef89dfcc076c501b4fa8e8 build: noarch: python From 07d832c9d73f1503197447eea2718b234228c9a3 Mon Sep 17 00:00:00 2001 From: Patrick T West Date: Thu, 4 Apr 2024 00:22:56 -0700 Subject: [PATCH 1338/1813] Add phava recipe (#46919) --- recipes/mappy/build_failure.osx-64.yaml | 104 ------------------------ recipes/phava/build.sh | 6 ++ recipes/phava/meta.yaml | 42 ++++++++++ 3 files changed, 48 insertions(+), 104 deletions(-) delete mode 100644 recipes/mappy/build_failure.osx-64.yaml create mode 100644 recipes/phava/build.sh create mode 100644 recipes/phava/meta.yaml diff --git a/recipes/mappy/build_failure.osx-64.yaml b/recipes/mappy/build_failure.osx-64.yaml deleted file mode 100644 index 8c01d13a166b7..0000000000000 --- a/recipes/mappy/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 624d20276cc122996176684e48e0e6d529dbccfcf7a07d55454e754e178d9d32 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - map.c:367:70: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'const int64_t' (aka 'const long long') [-Wsign-compare] - if (kmst.largest > 1U<<28 || (opt->cap_kalloc > 0 && kmst.capacity > opt->cap_kalloc)) { - ~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~ - 1 warning generated. - x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mappy-2.26 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I. -I$PREFIX/include/python3.10 -c misc.c -o build/temp.macosx-10.9-x86_64-cpython-310/misc.o -DHAVE_KALLOC -msse4.1 - x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mappy-2.26 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I. -I$PREFIX/include/python3.10 -c options.c -o build/temp.macosx-10.9-x86_64-cpython-310/options.o -DHAVE_KALLOC -msse4.1 - x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mappy-2.26 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I. -I$PREFIX/include/python3.10 -c pe.c -o build/temp.macosx-10.9-x86_64-cpython-310/pe.o -DHAVE_KALLOC -msse4.1 - x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mappy-2.26 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I. -I$PREFIX/include/python3.10 -c python/mappy.c -o build/temp.macosx-10.9-x86_64-cpython-310/python/mappy.o -DHAVE_KALLOC -msse4.1 - python/mappy.c:10830:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] - CYTHON_FALLTHROUGH; - ^ - python/mappy.c:345:34: note: expanded from macro 'CYTHON_FALLTHROUGH' - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - ^ - python/mappy.c:10841:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] - CYTHON_FALLTHROUGH; - ^ - python/mappy.c:345:34: note: expanded from macro 'CYTHON_FALLTHROUGH' - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - ^ - python/mappy.c:10941:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] - CYTHON_FALLTHROUGH; - ^ - python/mappy.c:345:34: note: expanded from macro 'CYTHON_FALLTHROUGH' - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - ^ - python/mappy.c:10952:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] - CYTHON_FALLTHROUGH; - ^ - python/mappy.c:345:34: note: expanded from macro 'CYTHON_FALLTHROUGH' - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - ^ - python/mappy.c:11089:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] - CYTHON_FALLTHROUGH; - ^ - python/mappy.c:345:34: note: expanded from macro 'CYTHON_FALLTHROUGH' - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - ^ - python/mappy.c:11100:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] - CYTHON_FALLTHROUGH; - ^ - python/mappy.c:345:34: note: expanded from macro 'CYTHON_FALLTHROUGH' - #define CYTHON_FALLTHROUGH __attribute__((fallthrough)) - ^ - 6 warnings generated. - x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mappy-2.26 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I. -I$PREFIX/include/python3.10 -c sdust.c -o build/temp.macosx-10.9-x86_64-cpython-310/sdust.o -DHAVE_KALLOC -msse4.1 - x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mappy-2.26 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I. -I$PREFIX/include/python3.10 -c seed.c -o build/temp.macosx-10.9-x86_64-cpython-310/seed.o -DHAVE_KALLOC -msse4.1 - seed.c:9:12: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare] - if (mv->n <= q_occ_max || q_occ_frac <= 0.0f || q_occ_max <= 0) return; - ~~~~~ ^ ~~~~~~~~~ - seed.c:65:14: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare] - if (a[i].n > max_occ) m; - ~~~~~~ ^ ~~~~~~~ - seed.c:68:24: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare] - if (i == n || a[i].n <= max_occ) { - ~~~~~~ ^ ~~~~~~~ - seed.c:81:18: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int32_t' (aka 'int') [-Wsign-compare] - if (a[j].n < (int32_t)(b[0]>>32)) { // then update the heap - ~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~ - seed.c:90:17: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare] - if (a[j].n > max_max_occ) - ~~~~~~ ^ ~~~~~~~~~~~ - seed.c:109:17: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] - for (i = 0; i < n_m0; i) - ~ ^ ~~~~ - seed.c:110:15: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare] - if (m[i].n > max_occ) - ~~~~~~ ^ ~~~~~~~ - seed.c:113:49: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] - for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; i) { - ~ ^ ~~~~ - 8 warnings generated. - x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mappy-2.26 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I. -I$PREFIX/include/python3.10 -c sketch.c -o build/temp.macosx-10.9-x86_64-cpython-310/sketch.o -DHAVE_KALLOC -msse4.1 - x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mappy-2.26 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I. -I$PREFIX/include/python3.10 -c splitidx.c -o build/temp.macosx-10.9-x86_64-cpython-310/splitidx.o -DHAVE_KALLOC -msse4.1 - creating build/lib.macosx-10.9-x86_64-cpython-310 - x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mappy-2.26 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 build/temp.macosx-10.9-x86_64-cpython-310/align.o build/temp.macosx-10.9-x86_64-cpython-310/bseq.o build/temp.macosx-10.9-x86_64-cpython-310/esterr.o build/temp.macosx-10.9-x86_64-cpython-310/format.o build/temp.macosx-10.9-x86_64-cpython-310/hit.o build/temp.macosx-10.9-x86_64-cpython-310/index.o build/temp.macosx-10.9-x86_64-cpython-310/kalloc.o build/temp.macosx-10.9-x86_64-cpython-310/ksw2_extd2_sse.o build/temp.macosx-10.9-x86_64-cpython-310/ksw2_exts2_sse.o build/temp.macosx-10.9-x86_64-cpython-310/ksw2_extz2_sse.o build/temp.macosx-10.9-x86_64-cpython-310/ksw2_ll_sse.o build/temp.macosx-10.9-x86_64-cpython-310/kthread.o build/temp.macosx-10.9-x86_64-cpython-310/lchain.o build/temp.macosx-10.9-x86_64-cpython-310/map.o build/temp.macosx-10.9-x86_64-cpython-310/misc.o build/temp.macosx-10.9-x86_64-cpython-310/options.o build/temp.macosx-10.9-x86_64-cpython-310/pe.o build/temp.macosx-10.9-x86_64-cpython-310/python/mappy.o build/temp.macosx-10.9-x86_64-cpython-310/sdust.o build/temp.macosx-10.9-x86_64-cpython-310/seed.o build/temp.macosx-10.9-x86_64-cpython-310/sketch.o build/temp.macosx-10.9-x86_64-cpython-310/splitidx.o -lz -lm -lpthread -o build/lib.macosx-10.9-x86_64-cpython-310/mappy.cpython-310-darwin.so - dyld[21993]: Library not loaded: '@rpath/libtapi.dylib' - Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h8ce0179_13/bin/x86_64-apple-darwin13.4.0-ld' - Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h8ce0179_13/bin/../lib/libtapi.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h8ce0179_13/bin/../lib/libtapi.dylib' (no such file), '/usr/local/lib/libtapi.dylib' (no such file), '/usr/lib/libtapi.dylib' (no such file) - clang-15: error: unable to execute command: Abort trap: 6 - clang-15: error: linker command failed due to signal (use -v to see invocation) - error: command '/opt/mambaforge/envs/bioconda/conda-bld/mappy_1686046171677/_build_env/bin/x86_64-apple-darwin13.4.0-clang' failed with exit code 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/mappy_1686046171677/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/phava/build.sh b/recipes/phava/build.sh new file mode 100644 index 0000000000000..2364fa6aad2be --- /dev/null +++ b/recipes/phava/build.sh @@ -0,0 +1,6 @@ +#!/usr/bin/env bash + +mkdir -p $PREFIX/bin +cp bin/phava $PREFIX/bin +cp -r PhaVa $PREFIX +cp -r tests $PREFIX diff --git a/recipes/phava/meta.yaml b/recipes/phava/meta.yaml new file mode 100644 index 0000000000000..03c499baa7dc2 --- /dev/null +++ b/recipes/phava/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "0.2.3" %} + +package: + name: phava + version: {{ version }} + +source: + url: https://github.com/patrickwest/PhaVa/archive/refs/tags/v{{version}}.tar.gz + sha256: 1860afecf8d2867f105a7fa00540b7d88c6c6ca21e1bbcba89faeda60d0acbcc + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('phava', max_pin="x.x") }} + +requirements: + host: + - python >=3.9 + run: + - python >=3.9 + - emboss >=6.5.7 + - minimap2 >=2.17 + - pysam >=0.17.0 + - biopython >=1.81 + - mmseqs2 + - samtools + +test: + commands: + - phava test + +about: + home: https://github.com/patrickwest/PhaVa + dev_url: https://github.com/patrickwest/PhaVa + license: MIT + license_family: MIT + summary: Detection of invertons from long-read sequencing datasets + +extra: + recipe-maintainers: + - patrickwest From 710012d1ed82f9a19022f0e9f481ab3e7abcfde9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 10:24:11 -0400 Subject: [PATCH 1339/1813] Update planemo to 0.75.22 (#46978) --- recipes/planemo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 6ac4349111683..4d0b0f2dcb6c6 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.21" %} -{% set sha256 = "c8b238d258ee85244a2a7d067452ef14f191c78e1e0923945bdd5e759682716e" %} +{% set version = "0.75.22" %} +{% set sha256 = "ad6b7b0eeb8d180004963b72bad5ec630d396a3ac0c36f9d1403927413158b8b" %} package: name: {{ name|lower }} From 840cb4b1fea2d7b390db6dc593f9816ae0f9ee31 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 4 Apr 2024 17:47:23 +0300 Subject: [PATCH 1340/1813] megahit: add linux-aarch64 build (#46803) * megahit: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Apply https://github.com/voutcn/megahit/pull/368 as a patch to fix the build on Linux ARM64 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- .../linux-aarch64-support-pr-368.patch | 74 +++++++++++++++++++ recipes/megahit/meta.yaml | 8 +- 2 files changed, 81 insertions(+), 1 deletion(-) create mode 100644 recipes/megahit/linux-aarch64-support-pr-368.patch diff --git a/recipes/megahit/linux-aarch64-support-pr-368.patch b/recipes/megahit/linux-aarch64-support-pr-368.patch new file mode 100644 index 0000000000000..01b9f2d556f98 --- /dev/null +++ b/recipes/megahit/linux-aarch64-support-pr-368.patch @@ -0,0 +1,74 @@ +From 296ad6b5359ac5072a97fe0b7f72cad08031542f Mon Sep 17 00:00:00 2001 +From: Martin Tzvetanov Grigorov +Date: Wed, 27 Mar 2024 15:07:02 +0200 +Subject: [PATCH 1/5] Add support for non-x86_64 architectures (e.g. Linux + ARM64) + +Fixes https://github.com/voutcn/megahit/issues/320 +Based on: https://github.com/voutcn/megahit/pull/329 + +Preserves the x86_64 specifics when building on x86_64 machine + +Signed-off-by: Martin Tzvetanov Grigorov +--- + CMakeLists.txt | 8 ++++++-- + src/kmlib/kmrns.h | 2 ++ + src/utils/cpu_dispatch.h | 6 ++++++ + 3 files changed, 14 insertions(+), 2 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 172a03d..d21b2d3 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -73,8 +73,12 @@ add_executable(megahit_core_popcnt ${OTHER_SOURCE} ${ASMBL_SOURCE} ${IDBA_SOURCE + ${CX1_SOURCE} ${TOOLKIT_SOURCE}) + add_executable(megahit_core_no_hw_accel ${OTHER_SOURCE} ${ASMBL_SOURCE} ${IDBA_SOURCE} ${SDBG_SOURCE} ${LCASM_SOURCE} + ${SEQ_SOURCE} ${CX1_SOURCE} ${TOOLKIT_SOURCE}) +-set_target_properties(megahit_core PROPERTIES COMPILE_FLAGS "-mbmi2 -DUSE_BMI2 -mpopcnt") +-set_target_properties(megahit_core_popcnt PROPERTIES COMPILE_FLAGS "-mpopcnt") ++ ++if (CMAKE_SYSTEM_PROCESSOR MATCHES "(x86_64)|(amd64)|(AMD64)") ++ set_target_properties(megahit_core PROPERTIES COMPILE_FLAGS "-mbmi2 -DUSE_BMI2 -mpopcnt") ++ set_target_properties(megahit_core_popcnt PROPERTIES COMPILE_FLAGS "-mpopcnt") ++endif () ++ + + if (STATIC_BUILD) + # TODO dirty +diff --git a/src/kmlib/kmrns.h b/src/kmlib/kmrns.h +index 9f2e9dd..0352858 100644 +--- a/src/kmlib/kmrns.h ++++ b/src/kmlib/kmrns.h +@@ -8,7 +8,9 @@ + #include + #include + #include ++#if defined(__x86_64__) + #include ++#endif + #include + + namespace kmlib { +diff --git a/src/utils/cpu_dispatch.h b/src/utils/cpu_dispatch.h +index ec01bb6..44ba1e2 100644 +--- a/src/utils/cpu_dispatch.h ++++ b/src/utils/cpu_dispatch.h +@@ -5,6 +5,7 @@ + #ifndef MEGAHIT_CPU_DISPATCH_H + #define MEGAHIT_CPU_DISPATCH_H + ++#if defined(__x86_64__) + inline bool HasPopcnt() { + unsigned eax, ebx, ecx, edx; + #ifdef _MSC_VER +@@ -32,5 +33,10 @@ inline bool HasBmi2() { + #endif + return ebx >> 8U & 1U; + } ++#else ++inline bool HasPopcnt() { return false; } ++inline bool HasBmi2() { return false; } ++#endif ++ + + #endif // MEGAHIT_CPU_DISPATCH_H \ No newline at end of file diff --git a/recipes/megahit/meta.yaml b/recipes/megahit/meta.yaml index cdc6d877dde6a..35673ec2df9ee 100644 --- a/recipes/megahit/meta.yaml +++ b/recipes/megahit/meta.yaml @@ -8,12 +8,16 @@ package: source: sha256: '{{sha256}}' url: https://github.com/voutcn/megahit/archive/v{{version}}.tar.gz + patches: + - linux-aarch64-support-pr-368.patch build: - number: 4 + number: 5 # TODO test fails on osx without visible error. # Feel free to fix and enable again. skip: true # [osx] + run_exports: + - {{ pin_subpackage('megahit', max_pin='x') }} requirements: build: @@ -45,6 +49,8 @@ about: metagenomics assembly via succinct de Bruijn graph extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:megahit - doi:10.1093/bioinformatics/btv033 From a8f069d0ead02f3a0e16a90de4e018422a899154 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 12:47:26 -0400 Subject: [PATCH 1341/1813] Update pangu to 0.2.7 (#46982) --- recipes/pangu/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangu/meta.yaml b/recipes/pangu/meta.yaml index 17fe86f5d9ce6..bacfeee43db68 100644 --- a/recipes/pangu/meta.yaml +++ b/recipes/pangu/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.6" %} -{% set sha256 = "0484e73185bbed3d54e7a000cf2f0749871589d694dfe7b7d276aaad2892f9a3" %} +{% set version = "0.2.7" %} +{% set sha256 = "5b0cf818d9bc7a60a6da752ac8bd7ca028aaa382bcf6d622b1d3856da53928a1" %} package: name: pangu From 4f315c82aa76aac062bccd9995d2495e60e95587 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 14:58:18 -0400 Subject: [PATCH 1342/1813] Update locidex to 0.1.2 (#46987) --- recipes/locidex/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/locidex/meta.yaml b/recipes/locidex/meta.yaml index 19946a13bd778..213ecab088d71 100644 --- a/recipes/locidex/meta.yaml +++ b/recipes/locidex/meta.yaml @@ -1,6 +1,6 @@ {% set name = "locidex" %} -{% set version = "0.1.1" %} -{% set sha256 = "39b4d4f55cc6d13bae23fce36a46f818a2d43fd7b87bbd24408633d973e62458" %} +{% set version = "0.1.2" %} +{% set sha256 = "00134512c81ce4d752ca568e2fc5c3497004be4b8a4458fa38e4195e5cfb72d0" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ source: build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} From 9d9976a3452c6d171581a651c0c31e42324ee86f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 16:43:29 -0400 Subject: [PATCH 1343/1813] Update snakemake to 8.10.5 (#46989) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 0f6be51be0208..50bb9242bf59b 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.10.4" %} +{% set version = "8.10.5" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 8228185f85a1e861c3e8a828f405d575a37dcdcf80b82fc681958a0e85a9ebe6 + sha256: 3d516fe88e4c0cfebe08c8b5b2a761f7f83226498b8fa5c4d4ad10112f2de80f build: number: 0 From 9138d610d24f9eae47791eb081dc9a0db598adf3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 17:15:26 -0400 Subject: [PATCH 1344/1813] Update graphembed to 0.1.1 (#46990) --- recipes/graphembed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/graphembed/meta.yaml b/recipes/graphembed/meta.yaml index 99a1ca4a5f0bc..cbf25240a9302 100644 --- a/recipes/graphembed/meta.yaml +++ b/recipes/graphembed/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: graphembed @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/graphembed/archive/v{{ version }}.tar.gz - sha256: 5c38244781574c2dd1aa1c20e1b2b5ea181f3ffab42ea47a014be0de28810210 + sha256: 894ffd1e2042ef93501317059c018bef817225dcb994a932ceb7593a134e7d8e requirements: build: From 1c54087802b95ec7b509d599338d7ad96c8c221e Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Thu, 4 Apr 2024 17:19:26 -0400 Subject: [PATCH 1345/1813] arborator v1.0.0 build #1 -> added missing scipy dependency (#46979) * arborator added missing scipy dependency * arborator added missing scipy dependency --- recipes/arborator/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/arborator/meta.yaml b/recipes/arborator/meta.yaml index 59b2d10137088..23fe634945fa5 100644 --- a/recipes/arborator/meta.yaml +++ b/recipes/arborator/meta.yaml @@ -12,7 +12,7 @@ source: build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -29,6 +29,7 @@ requirements: - {{ pin_compatible('numpy', max_pin="x") }} - pyarrow ==12.0.0 - pandas ==2.0.2 + - scipy >=1.0.0 - numba ==0.57.1 - pytables - psutil From b74b79d2527aaf870590f49859498f56ddc953bb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 17:52:09 -0400 Subject: [PATCH 1346/1813] Update pbstarphase to 0.9.0 (#46995) --- recipes/pbstarphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml index 9df0b989ccb6b..2767f8e755965 100644 --- a/recipes/pbstarphase/meta.yaml +++ b/recipes/pbstarphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbstarphase" %} -{% set version = "0.8.2" %} -{% set sha256 = "a5db035cc26dc097f20ef1943caf99ae9387475e9ac23d50441aab2b81765992" %} +{% set version = "0.9.0" %} +{% set sha256 = "0a875b66503b234b63c4af33d2537454db78385beddd77147383a6f63d6e0ad9" %} package: name: {{ name }} From 47da9c5a154708171d9074c31e96faf7c26f5363 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 18:49:48 -0400 Subject: [PATCH 1347/1813] Update scib to 1.1.5 (#46911) * Update scib to 1.1.5 * bump python requirement * scanpy <1.10 --------- Co-authored-by: mencian Co-authored-by: Thanh Lee --- recipes/scib/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/scib/meta.yaml b/recipes/scib/meta.yaml index f33f37de8a644..ceedea58c4998 100644 --- a/recipes/scib/meta.yaml +++ b/recipes/scib/meta.yaml @@ -1,20 +1,20 @@ {% set name = "scib" %} -{% set version = "1.1.4" %} +{% set version = "1.1.5" %} package: name: "{{ name|lower }}" version: "{{ version }}" build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" - skip: True # [ py < 37 or py > 311] + skip: True # [ py < 38 or py > 311] run_exports: - {{ pin_subpackage(name, max_pin='x') }} source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/scib-{{ version }}.tar.gz - sha256: b7800f308cd6acc36db6e159a53b0432adb2f48e9b7b434240bc5d696df10bfb + sha256: 7ab3183065f2d861b64f88823a55cec767327a37ad6d0eaccce7b43c996293ad patches: - setup_compiler.patch @@ -36,7 +36,7 @@ requirements: - pandas <2 - pydot - python - - scanpy >=1.5 + - scanpy >=1.5, <1.10 - scikit-learn - scikit-misc - scipy From 565ee9c8869dcc3fbb84366cc49e00f9cb6a453d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 18:50:09 -0400 Subject: [PATCH 1348/1813] Update snakemake to 8.10.6 (#46996) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 50bb9242bf59b..9d19370e920a6 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.10.5" %} +{% set version = "8.10.6" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 3d516fe88e4c0cfebe08c8b5b2a761f7f83226498b8fa5c4d4ad10112f2de80f + sha256: 2b624f033bb020a4763c4274f11eb0b34b51fb3b73cc64598005eaa897f11dd6 build: number: 0 From 466ea0b2cf53fbdd012810b4f59ebd30a9a84f15 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Apr 2024 18:51:10 -0400 Subject: [PATCH 1349/1813] Update hybracter to 0.7.3 (#46998) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index bc40e258f7861..15305a69002fc 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.7.2" %} +{% set version = "0.7.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 404fa2144ef10c924256b07826726f1b1df8fadac0e5a4206b3d021bf61dc1a3 + sha256: 01ee53bb84c37ba2a4c37431dd34ada4383cf29aab4127acb3131ab1be58adac build: number: 0 From bb04591cf1e0d0ec3b78dc1b3f7a0e154e9394e9 Mon Sep 17 00:00:00 2001 From: Henning Timm Date: Fri, 5 Apr 2024 09:04:23 +0200 Subject: [PATCH 1350/1813] Update ddRAGE to 1.8.1 (#46997) --- recipes/ddrage/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/ddrage/meta.yaml b/recipes/ddrage/meta.yaml index 87d3345a7373c..a4046dab43b7f 100644 --- a/recipes/ddrage/meta.yaml +++ b/recipes/ddrage/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "1.7.1" %} +{% set version = "1.8.1" %} package: name: ddrage version: {{ version }} source: - url: https://bitbucket.org/genomeinformatics/rage/get/{{ version }}.tar.gz - sha256: 4ae5a34428658087ca70ad29ae8d3c7a3b55170bfa419d3adcf727fe807d93f3 + url: https://files.pythonhosted.org/packages/f8/bf/a3156beda9476a3ed69d1fd049465f70cad5f3df1de0a0efeb55c401f0e3/ddrage-{{ version }}.tar.gz + sha256: a08962227144a8de0d47b8dbfb51aaf692660d5a7c519a11561b91c6217186ac build: noarch: python number: 0 + run_exports: + - {{ pin_subpackage("ddrage", max_pin="x") }} script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - rage = ddrage.__main__:main From dee34fc1e9f03769b769ecddd015b64430d66a3b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 03:14:09 -0400 Subject: [PATCH 1351/1813] Update micom to 0.34.1 (#46994) --- recipes/micom/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/micom/meta.yaml b/recipes/micom/meta.yaml index 103288784536f..89346affc6dcd 100644 --- a/recipes/micom/meta.yaml +++ b/recipes/micom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "micom" %} -{% set version = "0.33.2" %} +{% set version = "0.34.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 0fd335b178badcd9a1d96d1b6f2568b15da922be2fa57e8a6004971510f3708b + sha256: 9575949a6c93a32cead889b10f8c0f5ff5ffbee1acbe3ef0b3a521fd76fcb791 build: number: 0 From c0d4bd028fe280a9a4299133d90cc89fd3b48e2b Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Fri, 5 Apr 2024 00:14:37 -0700 Subject: [PATCH 1352/1813] Add mtgrasp (#46986) --- recipes/mtgrasp/build.sh | 7 +++++++ recipes/mtgrasp/meta.yaml | 44 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 recipes/mtgrasp/build.sh create mode 100644 recipes/mtgrasp/meta.yaml diff --git a/recipes/mtgrasp/build.sh b/recipes/mtgrasp/build.sh new file mode 100644 index 0000000000000..41100de173091 --- /dev/null +++ b/recipes/mtgrasp/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash +set -eu -o pipefail + +mkdir -p ${PREFIX}/bin/ +cp *mtgrasp* ${PREFIX}/bin/ +cp -r data ${PREFIX}/bin/ +cp -r test ${PREFIX}/bin/ diff --git a/recipes/mtgrasp/meta.yaml b/recipes/mtgrasp/meta.yaml new file mode 100644 index 0000000000000..629a1559ffd0b --- /dev/null +++ b/recipes/mtgrasp/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.1.3" %} +{% set name = "mtGrasp" %} + +package: + name: {{ name | lower }} + version: {{ version }} + +source: + url: https://github.com/bcgsc/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz + sha256: b9a8a250938fee584f73469fc33d04e1100d9af0475fac5f702ae373842b9e86 + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('mtgrasp', max_pin="x") }} + +requirements: + host: + - python + run: + - python + - snakemake + - blast >=2.9.0 + - biopython + - seqtk + - abyss + - ntjoin + - bwa + - samtools + - pilon + - ntcard + - mitos >=2.1.7 + + +test: + commands: + - mtgrasp.py -h + +about: + home: https://github.com/bcgsc/mtGrasp + license: GPL-3.0 + license_file: LICENSE + summary: 'reference-grade de novo animal mitochondrial genome assembly and standardization' From 8bb72f60e2d6f00b9c5a4fec86a0cb7f3e4b9580 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 03:28:25 -0400 Subject: [PATCH 1353/1813] Update perl-uri-db to 0.22 (#47000) --- recipes/perl-uri-db/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-uri-db/meta.yaml b/recipes/perl-uri-db/meta.yaml index 08e0ce5867582..db450ccaf3c63 100644 --- a/recipes/perl-uri-db/meta.yaml +++ b/recipes/perl-uri-db/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-uri-db" %} -{% set version = "0.21" %} -{% set sha256 = "a6433dc1517a907e189912a4c76b5dfc76332e3fd7fc8b38a137e4019c780b34" %} +{% set version = "0.22" %} +{% set sha256 = "1ff437591022b440716676526cca0a729b465f606bdd9e1d0a60561d6fdd458f" %} package: name: {{ name }} From 155f145306e7d7b311038732e17221ba13d3332d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 03:33:04 -0400 Subject: [PATCH 1354/1813] Update r-liger to 2.0.1 (#46999) --- recipes/r-liger/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/r-liger/meta.yaml b/recipes/r-liger/meta.yaml index 4d150e4e9dfbd..bef57845d132b 100644 --- a/recipes/r-liger/meta.yaml +++ b/recipes/r-liger/meta.yaml @@ -1,5 +1,5 @@ {% set name = "liger" %} -{% set version = '2.0.0' %} +{% set version = '2.0.1' %} package: name: r-{{ name }} @@ -9,10 +9,10 @@ source: url: - {{ cran_mirror }}/src/contrib/rliger_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/rliger/rliger_{{ version }}.tar.gz - sha256: a189285513e5a11d658056de55670fe877bcf2f52ce65837f9b8a4b3ff7bab2f + sha256: e1163722608ba2c2424e87f44b4d62c36dacca429dfb4fee41eb9a0da99703a4 build: - number: 1 + number: 0 script: R CMD INSTALL --build . rpaths: - lib/R/lib/ From 5afbb601c12e3cbdde06e4c75044c29e32cfac1f Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Fri, 5 Apr 2024 03:33:43 -0400 Subject: [PATCH 1355/1813] Update graphembed v0.1.1 (#46993) * Update graphembed v0.1.1 * Update graphembed v0.1.1 * Update graphembed v0.1.1 --- recipes/graphembed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/graphembed/meta.yaml b/recipes/graphembed/meta.yaml index cbf25240a9302..08b5d38bbf652 100644 --- a/recipes/graphembed/meta.yaml +++ b/recipes/graphembed/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('graphembed', max_pin="x.x") }} skip: True # [osx] @@ -28,7 +28,7 @@ test: about: home: https://github.com/jean-pierreBoth/graphembed license: MIT - summary: Efficient Graph Embedding via Recursive Sketching or High-order Transitivity Preserving + summary: Efficient Graph Embedding via Recursive Sketching or High-order Transitivity Preserving with Benchmarking extra: maintainers: - Jean Pierre-Both From 0968cf233f2e7108485f3ca78034ae99da5eca8e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 04:21:20 -0400 Subject: [PATCH 1356/1813] Update seqsero2 to 1.3.1 (#47001) * Update seqsero2 to 1.3.1 * add run_exports --------- Co-authored-by: mencian --- recipes/seqsero2/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/seqsero2/meta.yaml b/recipes/seqsero2/meta.yaml index 2ee2a03b296e5..a904b60557fc3 100644 --- a/recipes/seqsero2/meta.yaml +++ b/recipes/seqsero2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SeqSero2" %} -{% set version = "1.2.1" %} -{% set sha256 = "911b3f31ed35b7ac421001ab739782895c479f1e3a733ad17210069c8b7011ff" %} +{% set version = "1.3.1" %} +{% set sha256 = "5fa2a0957d053f36061fa76f5a4de6ea3d33b5307f4c122dc4cdf807d1c3514d" %} package: name: '{{ name | lower }}' @@ -13,7 +13,9 @@ source: build: number: 0 noarch: python - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('seqsero2', max_pin="x") }} requirements: host: @@ -38,7 +40,7 @@ test: about: home: https://github.com/denglab/{{ name }} - license: GPLv2 + license: GPL-2.0-or-later license_family: GPL license_file: 'LICENSE' summary: Salmonella serotype prediction from genome sequencing data From ae7fab5966f5aa7191c6deaacc875c0751ed5ebf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 08:39:17 -0400 Subject: [PATCH 1357/1813] Update cgat-apps to 0.7.2 (#47002) * Update cgat-apps to 0.7.1 * updated cgat-apps to new release as old setup.py would not build for conda. Also updated some deps --------- Co-authored-by: Acribbs --- recipes/cgat-apps/meta.yaml | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/recipes/cgat-apps/meta.yaml b/recipes/cgat-apps/meta.yaml index 8a9d7865d52bd..86e794512e9ef 100644 --- a/recipes/cgat-apps/meta.yaml +++ b/recipes/cgat-apps/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cgat-apps" %} -{% set version = "0.7.0" %} +{% set version = "0.7.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/c/cgat/cgat-{{ version }}.tar.gz - sha256: 42d23ffed9dcea37f816912a2b8679c353299f55c285cb4d20250622ee39cd5c + sha256: 746701d1a6677e8200092894c35c942383123fd8e22ab172f3ef6b2222b8eaef build: @@ -22,19 +22,18 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} host: - - python >=3.8 + - python - cython - numpy - - pysam >=0.17.0 + - pysam - htslib - setuptools - ucsc-wigtobigwig run: - - python >=3.8 - - cgatcore >=0.6.5 + - python + - cgatcore - alignlib-lite - biopython - - future - matplotlib-base - numpy - pandas @@ -45,8 +44,6 @@ requirements: - pyyaml - quicksect - scipy - - six - - jinja2 - scikit-learn - sortedcontainers # Misc dependencies From bb594068db4a3674990d3cd7dcbdc9eca653fc9b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 09:32:12 -0400 Subject: [PATCH 1358/1813] Update psm-utils to 0.8.2 (#47008) --- recipes/psm-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index a74e7ad05c86c..4448df6ee1330 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.8.1" %} -{% set sha256 = "ec800bd4931a934c09e2cc11e65bd22015fce1bb05898a5605bfb0d5c5502e20" %} +{% set version = "0.8.2" %} +{% set sha256 = "b225f70caacccd6cec3838083fd6c3ff77052c4589e455bd789d900ec2f80baa" %} package: name: {{ name|lower }} From c2c3bfae1cc0338fc3aa6c4ca8b48d7051a4bab2 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Fri, 5 Apr 2024 10:14:23 -0400 Subject: [PATCH 1359/1813] ci: exclude bioconda-repodata-patches that's already built (#46960) --- azure-pipeline-nightly.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/azure-pipeline-nightly.yml b/azure-pipeline-nightly.yml index fd7f1f5e7da97..439dcdad88a82 100644 --- a/azure-pipeline-nightly.yml +++ b/azure-pipeline-nightly.yml @@ -76,7 +76,7 @@ jobs: # build and push all leftover packages bioconda-utils build recipes config.yml \ --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ - --prelint + --prelint --exclude bioconda-repodata-patches docker rmi quay.io/dpryan79/mulled_container:latest env: QUAY_OAUTH_TOKEN: $(QUAY_OAUTH_TOKEN) From e0d9ff5a0a06d3941fd7a11d0bf95f75859ff1dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 11:16:10 -0400 Subject: [PATCH 1360/1813] Update agat to 1.4.0 (#47015) --- recipes/agat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/agat/meta.yaml b/recipes/agat/meta.yaml index a1bae16c77a83..a91fde31f4758 100755 --- a/recipes/agat/meta.yaml +++ b/recipes/agat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "AGAT" %} -{% set version = "1.3.3" %} -{% set sha256 = "08fa159f7badb418a681a514d471d7233bb1cc09a5e41d875118eaec4c2ec813" %} +{% set version = "1.4.0" %} +{% set sha256 = "d5e30db44b5d05ed51c606a823894c01c85c1ed85580148ad5473cb2f2b2ac77" %} package: name: "{{ name|lower }}" From f0400f1cce2665261c400a9fc0ed13809a49db20 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 13:13:16 -0400 Subject: [PATCH 1361/1813] Update r-acidgenerics to 0.7.8 (#47014) --- recipes/r-acidgenerics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenerics/meta.yaml b/recipes/r-acidgenerics/meta.yaml index 92f114f611075..e3a427c3792d3 100644 --- a/recipes/r-acidgenerics/meta.yaml +++ b/recipes/r-acidgenerics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.7" %} +{% set version = "0.7.8" %} {% set github = "https://github.com/acidgenomics/r-acidgenerics" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 67fc00a1bab3b65dcce30264439f065edb01c7a258cbb5adec8544914ff86948 + sha256: baa0346b8cd0ebcdbef2d15028eb2d0c425731acfea718f057c6faef1606ff3b build: number: 0 From 8d264758d3bfb4fd960e95a0669f67718f02c9d3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 14:50:38 -0400 Subject: [PATCH 1362/1813] Update pybiolib to 1.1.1942 (#47013) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 56c7ba88dd7ee..882a362262ffb 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1934" %} +{% set version = "1.1.1942" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 4e1867fba20ffe4845ccad9d947afaa284f4c1f54fef89dfcc076c501b4fa8e8 + sha256: 814a66825ed4c47857f9891dff7fff75d7f6c39de94f72cbb87e09791af60a70 build: noarch: python From d7160864a4949c69a8c3e2b3226271cd71a34f53 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 14:51:09 -0400 Subject: [PATCH 1363/1813] Update assembly_finder to 0.6.2 (#47016) --- recipes/assembly_finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index b50bcabd479bb..32b3dd32db53e 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.6.1" %} +{% set version = "0.6.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 4892df7c710fe13674047a0059be710eef3e7b93b893167e7930760a62ad6273 + sha256: f3e47042ff6be9fc22cb8a2b695692bd33cefe07b768f17c1b942940f20faa3a build: number: 0 From 0d22a2a8f557208e348f544b88c0b56c51c7aad2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 18:11:57 -0400 Subject: [PATCH 1364/1813] Update hifihla to 0.3.1 (#47017) --- recipes/hifihla/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hifihla/meta.yaml b/recipes/hifihla/meta.yaml index fdf95a9243a04..76ca74fd77e83 100644 --- a/recipes/hifihla/meta.yaml +++ b/recipes/hifihla/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hifihla" %} -{% set version = "0.3.0" %} -{% set hifihla_sha256 = "6d03ff73bce0c2c2805b2b3d51ec181e6aeae36a11a4cb99440914ffcecd2bb6" %} +{% set version = "0.3.1" %} +{% set hifihla_sha256 = "edeeb0208a545a0993df78989367da417b918621a8c76c69c16e86505c643dce" %} package: name: {{ name }} From b84ace6880e6abc8422888bf4ef133e8b0f65058 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Apr 2024 18:12:44 -0400 Subject: [PATCH 1365/1813] Update genoboo to 0.4.15 (#47007) * Update genoboo to 0.4.14 * Update genoboo to 0.4.15 --- recipes/genoboo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genoboo/meta.yaml b/recipes/genoboo/meta.yaml index 5a1a8efef34fd..b7eabb53df9ac 100644 --- a/recipes/genoboo/meta.yaml +++ b/recipes/genoboo/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'genoboo' %} -{% set version = '0.4.13' %} -{% set sha256 = '7a300f2cc9d885e2c5bf51ddcbdd9c952ef3f74d5801918e0f9114cdc3991b41' %} +{% set version = '0.4.15' %} +{% set sha256 = 'af315b785b5bf849b1ab859fb56a0fc91dd8dadae130636e8ecc5c99be33c792' %} package: name: {{ name|lower }} From 776492e7296e1ed05f0bfe7d89c9bae80cd813f8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 6 Apr 2024 14:36:41 -0400 Subject: [PATCH 1366/1813] Update sdrf-pipelines to 0.0.26 (#47021) --- recipes/sdrf-pipelines/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sdrf-pipelines/meta.yaml b/recipes/sdrf-pipelines/meta.yaml index 1fd34b609a64e..3727971a305b5 100644 --- a/recipes/sdrf-pipelines/meta.yaml +++ b/recipes/sdrf-pipelines/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sdrf-pipelines" %} -{% set version = "0.0.25" %} +{% set version = "0.0.26" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a390a61a5fc696a60f7e27c221e078b2e8d1f7e81625cec05e5486c5554d9ebc + sha256: eba64fddad8ecc05ac3efecc43e19a7ba556ede7cd5b57475277a3ec20195216 build: number: 0 From 11a552a74abe9b1fd9f8fb927930541f01fe080a Mon Sep 17 00:00:00 2001 From: Vedanth Ramji <86137377+Vedanth-Ramji@users.noreply.github.com> Date: Sun, 7 Apr 2024 07:02:29 +1000 Subject: [PATCH 1367/1813] Add argNorm recipe (#46784) * add argnorm recipe * BUG fixed noarch and run exports errors * Add license_File Co-authored-by: Thanh Lee --------- Co-authored-by: Thanh Lee --- recipes/argnorm/meta.yaml | 52 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/argnorm/meta.yaml diff --git a/recipes/argnorm/meta.yaml b/recipes/argnorm/meta.yaml new file mode 100644 index 0000000000000..9cad1351c36e4 --- /dev/null +++ b/recipes/argnorm/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "argnorm" %} +{% set version = "0.2.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 8210aaa121272f2bd815498332bd076b9a5322b064c851dfb32d01486921a88c + +build: + noarch: python + number: 0 + entry_points: + - argnorm=argnorm.cli:main + script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + run_exports: + - {{ pin_subpackage('argnorm', max_pin='x') }} +requirements: + host: + - pandas + - pip + - pronto + - pytest + - python + - setuptools + run: + - pandas + - pronto + - pytest + - python + - setuptools + +test: + imports: + - argnorm + - argnorm.data + commands: + - argnorm --help + +about: + home: "https://github.com/BigDataBiology/argNorm" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Normalize antibiotic resistance genes (ARGs) abundance tables (e.g., from metagenomics) by using the ARO ontology (developed by CARD)." + doc_url: https://argnorm.readthedocs.io/en/latest/ + +extra: + recipe-maintainers: + - Vedanth-Ramji \ No newline at end of file From 0d9f1870fd8ae3ca020a08e4cbaba3af02216a4e Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Sun, 7 Apr 2024 14:25:58 +0100 Subject: [PATCH 1368/1813] Update SeqKit to v2.8.1 (#47030) --- recipes/seqkit/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index 9c3439e60dc09..da25cd788f00c 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.8.0" %} +{% set version = "2.8.1" %} package: name: seqkit @@ -6,16 +6,16 @@ package: source: url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx] - md5: f8310b1ff14e49c7506080e75d97e5dc # [osx] + md5: f68fcff143f20385110498803aabe9ac # [osx] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux] - md5: d53457672a8f7873bc17698bad9e8514 # [linux] + md5: bf0800bdfbdae8434a2c696e585740fc # [linux] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_arm64.tar.gz # [aarch64] - md5: d055c755dcf44cf9f4f59be69a3c884f # [aarch64] + md5: b84657ab1186f4ac07f92bb5f98e10d2 # [aarch64] build: - number: 1 + number: 0 skip: False run_exports: - {{ pin_subpackage("seqkit", max_pin="x.x") }} From 0b44bb88c3ecefaac7a96d05cc3a8fb4ff5bd3fb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Apr 2024 09:26:45 -0400 Subject: [PATCH 1369/1813] Update centrifuger to 1.0.2 (#47026) --- recipes/centrifuger/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/centrifuger/meta.yaml b/recipes/centrifuger/meta.yaml index dbb8ff62c7d69..c43cddff49074 100644 --- a/recipes/centrifuger/meta.yaml +++ b/recipes/centrifuger/meta.yaml @@ -1,5 +1,5 @@ {% set name = "centrifuger" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ build: source: url: https://github.com/mourisl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 4ce9a20d786a39ef26b1ef31851c180e0b1baae1efc2d9ad8442bec6203d04bb + sha256: b26e47c862fd5f2ac3a4e2cad13dcae0de5470c4875e16a2dc6f0948b53c9a9c requirements: build: From 8a03239014ba90a00ea48c46b05af4b593f44a60 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Apr 2024 17:55:20 -0400 Subject: [PATCH 1370/1813] Update seqwish to 0.7.10 (#47037) * Update seqwish to 0.7.10 * add `run_exports` --------- Co-authored-by: AndreaGuarracino --- recipes/seqwish/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/seqwish/meta.yaml b/recipes/seqwish/meta.yaml index 14eeca808d85c..61ad99d0a7389 100644 --- a/recipes/seqwish/meta.yaml +++ b/recipes/seqwish/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqwish" %} -{% set version = "0.7.9" %} +{% set version = "0.7.10" %} package: name: "{{ name }}" @@ -7,11 +7,13 @@ package: source: url: https://github.com/ekg/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 1ca7ebf02a35ad147c8a2b81f087aaba2deb878fec7acb4deb9f14e932e89d36 + sha256: 133b32c9c99caf44eba955b74bae338681da78300e4b21269e07475f88c88b29 build: skip: True # [osx] - number: 2 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + number: 0 requirements: build: From 9014dce7cce0b44ec3597db9508ba7dea5bbc348 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Apr 2024 18:32:51 -0400 Subject: [PATCH 1371/1813] Update smoothxg to 0.7.3 (#47038) --- recipes/smoothxg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/smoothxg/meta.yaml b/recipes/smoothxg/meta.yaml index da6405499ebc3..fcc72903be7dd 100644 --- a/recipes/smoothxg/meta.yaml +++ b/recipes/smoothxg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "smoothxg" %} -{% set version = "0.7.2" %} +{% set version = "0.7.3" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 68784e7f32accfadfbcbebaeb36099fc48296655adc67e62417f08a55459a8df + sha256: 49adee34e56184f4d61b6511e74c3515671c1f7472aeeeb4d2d6b2b78ac9a2ea patches: - CMakeLists.patch From 33563f841e6f08079f5c994a0a9ef097ed07fe2c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Apr 2024 19:20:55 -0400 Subject: [PATCH 1372/1813] Update odgi to 0.8.5 (#47039) --- recipes/odgi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/odgi/meta.yaml b/recipes/odgi/meta.yaml index 44d9dfd0ea1b0..ae6f2dd740fc5 100644 --- a/recipes/odgi/meta.yaml +++ b/recipes/odgi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "odgi" %} -{% set version = "0.8.4" %} +{% set version = "0.8.5" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: bc656e541a42c890f71e748e4420215e1efba5b7b890d8c009bfef114c811f47 + sha256: 5cf4850cdee78342af2f98c7fb95a75b0b170c7a2596b9dc4b3093520375358c build: skip: True # [osx or py27] From 0da5e14f8362a53a6c31b1721dc51cc4db8400a7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Apr 2024 21:14:13 -0400 Subject: [PATCH 1373/1813] Update smoothxg to 0.7.4 (#47042) --- recipes/smoothxg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/smoothxg/meta.yaml b/recipes/smoothxg/meta.yaml index fcc72903be7dd..b0382f7fd18a9 100644 --- a/recipes/smoothxg/meta.yaml +++ b/recipes/smoothxg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "smoothxg" %} -{% set version = "0.7.3" %} +{% set version = "0.7.4" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 49adee34e56184f4d61b6511e74c3515671c1f7472aeeeb4d2d6b2b78ac9a2ea + sha256: 6c15c1156ac3e1a29cdb4db20f46e1b22382b22640beaa7ec8e0d76564dc53ca patches: - CMakeLists.patch From bb64943cd5beabc26704577ecba36afb43af6569 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Apr 2024 21:28:48 -0400 Subject: [PATCH 1374/1813] Update odgi to 0.8.6 (#47041) --- recipes/odgi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/odgi/meta.yaml b/recipes/odgi/meta.yaml index ae6f2dd740fc5..155ecb1d55d78 100644 --- a/recipes/odgi/meta.yaml +++ b/recipes/odgi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "odgi" %} -{% set version = "0.8.5" %} +{% set version = "0.8.6" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 5cf4850cdee78342af2f98c7fb95a75b0b170c7a2596b9dc4b3093520375358c + sha256: a6db190b782608082b14b42c660389aa18010791de1e2d07e29f7f61d8787754 build: skip: True # [osx or py27] From 1d7b488c5fc2a9d7fb6cfe49fa5614a2761cb13b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 01:51:22 -0400 Subject: [PATCH 1375/1813] Update ccmetagen to 1.5.0 (#47048) --- recipes/ccmetagen/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ccmetagen/meta.yaml b/recipes/ccmetagen/meta.yaml index 9adb565f54b77..2041475df1daa 100644 --- a/recipes/ccmetagen/meta.yaml +++ b/recipes/ccmetagen/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ccmetagen" %} -{% set version = "1.4.2" %} +{% set version = "1.5.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: url: "https://github.com/vrmarcelino/CCMetagen/archive/v{{ version }}.tar.gz" - sha256: "9e01a3e123e6fb2d30ac0f17f452bc5262c938821def867cfaea705e4f327940" + sha256: "44a0591e6a5d0a5317cf2307c8da6851dde039679b32bd0cc743b210b4add81d" build: noarch: python - number: 1 + number: 0 script: "python -m pip install --no-deps --ignore-installed . " run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} From d8518de5bd793434c591b2b6e58222320ef23d74 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 8 Apr 2024 12:04:27 +0300 Subject: [PATCH 1376/1813] gofasta: add linux-aarch64 build (#47012) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/gofasta/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/gofasta/meta.yaml b/recipes/gofasta/meta.yaml index 243c4d0ec9f15..64a8626a53d44 100644 --- a/recipes/gofasta/meta.yaml +++ b/recipes/gofasta/meta.yaml @@ -13,7 +13,9 @@ requirements: - {{ compiler('go-nocgo') }} build: - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('gofasta', max_pin="x") }} script: - mkdir -p $PREFIX/bin - go build -o $PREFIX/bin/gofasta @@ -27,3 +29,7 @@ about: license: MIT license_file: LICENSE summary: Genomic epidemiology utilities for short genome alignments + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From dacc705530661eebb920781daafa513936f95191 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 8 Apr 2024 15:27:36 +0300 Subject: [PATCH 1377/1813] kma: add linux-aarch64 build (#47055) --- recipes/kma/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/kma/meta.yaml b/recipes/kma/meta.yaml index 9805f97f9b6e5..0ba3d848b9a81 100644 --- a/recipes/kma/meta.yaml +++ b/recipes/kma/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('kma', max_pin="x") }} @@ -38,5 +38,7 @@ about: license_family: APACHE extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1186/s12859-018-2336-6 From 2f28b2081a30607924fbc91df3fe3f0305e86f42 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 10:05:51 -0400 Subject: [PATCH 1378/1813] Update mehari to 0.25.5 (#47051) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 1ba7525a1d0fa..4dce1d8acc046 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.25.4" %} -{% set sha256 = "bd33b8942d51352151785a49ebcfb2f9ea076747ed110cc966d1f8778ad029cb" %} +{% set version = "0.25.5" %} +{% set sha256 = "4986b6249fdc4e726e9494c55340234f50307fc4442e4683ecf18c1bd6ace8fd" %} package: name: mehari From 2f4e4524a203a9c35d1782309b31b84a650ffd97 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 14:07:07 -0400 Subject: [PATCH 1379/1813] Update bindash to 2.2 (#47069) --- recipes/bindash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bindash/meta.yaml b/recipes/bindash/meta.yaml index 47ba2fb182600..8944473900559 100644 --- a/recipes/bindash/meta.yaml +++ b/recipes/bindash/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.1" %} +{% set version = "2.2" %} package: name: bindash @@ -6,7 +6,7 @@ package: source: url: https://github.com/jianshu93/bindash/archive/v{{ version }}.tar.gz - sha256: 185903149a2a14a4506f0a60d0f9fc0c03bace6705fb5eca8df4048d1b03592b + sha256: 0d7cec8c93cd435896ebaee41cee87f5baa8c0feddf8396dba00c1593de3757e build: skip: True # [osx] From f1b27e8b36db3966517ac491faa43bd5174e30b4 Mon Sep 17 00:00:00 2001 From: Adam Cribbs Date: Mon, 8 Apr 2024 20:17:34 +0200 Subject: [PATCH 1380/1813] Update cgat-apps v0.7.2 (#47020) * Update cgat-apps v0.7.2 to remove dependancies * forgot to bump build number * added back in matplotlib-base --- recipes/cgat-apps/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/cgat-apps/meta.yaml b/recipes/cgat-apps/meta.yaml index 86e794512e9ef..fa2fc24eb1ff5 100644 --- a/recipes/cgat-apps/meta.yaml +++ b/recipes/cgat-apps/meta.yaml @@ -11,7 +11,7 @@ source: build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('cgat-apps', max_pin="x.x") }} entry_points: @@ -28,7 +28,6 @@ requirements: - pysam - htslib - setuptools - - ucsc-wigtobigwig run: - python - cgatcore @@ -39,7 +38,7 @@ requirements: - pandas - pybedtools - pybigwig - - pysam >=0.17.0 + - pysam - htslib - pyyaml - quicksect From da0912f8c3a6e6f0c16db7872944555a8538257d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 15:46:53 -0400 Subject: [PATCH 1381/1813] Update crisprme to 2.1.3 (#46984) * Update crisprme to 2.1.3 * edit run_exports * Update crisprme to 2.1.3 --------- Co-authored-by: mencian --- recipes/crisprme/build.sh | 4 ++-- recipes/crisprme/meta.yaml | 18 ++++++++++++------ 2 files changed, 14 insertions(+), 8 deletions(-) diff --git a/recipes/crisprme/build.sh b/recipes/crisprme/build.sh index cd80a4ea7cf0d..48c4a11527c52 100644 --- a/recipes/crisprme/build.sh +++ b/recipes/crisprme/build.sh @@ -5,6 +5,6 @@ mkdir -p "${PREFIX}/opt/crisprme" chmod -R 700 . unzip PostProcess/pickle_data.zip mv CRISTA_predictors.pkl PostProcess/ -cp crisprme.py "${PREFIX}/bin/" +cp crisprme.py "${PREFIX}/bin/" && chmod +rx "${PREFIX}/bin/crisprme.py" cp crisprme_test_complete_package.sh "${PREFIX}/bin/" -cp -R * "${PREFIX}/opt/crisprme/" \ No newline at end of file +cp -R * "${PREFIX}/opt/crisprme/" diff --git a/recipes/crisprme/meta.yaml b/recipes/crisprme/meta.yaml index 8645e64e2d3dd..2bb063589ecf3 100644 --- a/recipes/crisprme/meta.yaml +++ b/recipes/crisprme/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.1.2" %} +{% set version = "2.1.3" %} package: name: crisprme @@ -6,14 +6,14 @@ package: source: url: https://github.com/pinellolab/CRISPRme/archive/refs/tags/v{{ version }}.tar.gz - sha256: 4f04cc791d2c562dffe6f88345a41795e5a0109490a9f33d91376677e41becc5 - + sha256: f4542accbbf26d4568212e88f7469fec06a8a8c6b52f884160e741d4e9d8bab0 + build: run_exports: - - {{ pin_subpackage('crisprme', max_pin="x.x.x") }} + - {{ pin_subpackage('crisprme', max_pin="x") }} number: 0 noarch: generic - + requirements: host: - unzip @@ -48,6 +48,12 @@ test: about: home: https://github.com/pinellolab/CRISPRme - license: AGPL-3.0 + license: AGPL-3.0-or-later + license_family: AGPL license_file: LICENSE summary: CRISPRme, tool package for CRISPR experiments assessment and analysis. + dev_url: https://github.com/pinellolab/CRISPRme + +extra: + identifiers: + - doi:10.1038/s41588-022-01257-y From ffd94baf0d3c3823b591391f502304cbf90aa2a6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 15:49:27 -0400 Subject: [PATCH 1382/1813] Update sylph to 0.6.0 (#47027) --- recipes/sylph/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml index c83ec07b1e0fd..b15925877f40c 100644 --- a/recipes/sylph/meta.yaml +++ b/recipes/sylph/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.1" %} +{% set version = "0.6.0" %} package: name: sylph @@ -11,7 +11,7 @@ build: source: url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz - sha256: 300b0f4ae77e25c28a05fd2f5323c112003a13111130f136d7d4bf4ded90e10c + sha256: 751a6ab193d8f35c8ff65d3da6fd9ab29c9132e004b32b3159d2bedf371a05eb requirements: build: From 6e105d13a5f7525b0322cd960daffd11df1d0159 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 15:50:32 -0400 Subject: [PATCH 1383/1813] Update attotree to 0.1.3 (#47073) --- recipes/attotree/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/attotree/meta.yaml b/recipes/attotree/meta.yaml index 577c993650692..c470d548d0d3a 100644 --- a/recipes/attotree/meta.yaml +++ b/recipes/attotree/meta.yaml @@ -1,5 +1,5 @@ {% set name = "attotree" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8ae3799fd513595a0d05625e420b17b7745a0fa067e2e100302a2ddefe438ebf + sha256: 67abe9965a89993481c22af63c6b49e384f0927b373c2c81cb954ed4f249a66a build: number: 0 From a9c054167fcac6f2dfb8b683c2792952aee8df37 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 15:51:52 -0400 Subject: [PATCH 1384/1813] Update trgt to 0.9.0 (#47072) --- recipes/trgt/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/trgt/meta.yaml b/recipes/trgt/meta.yaml index 686a008743d0f..030c04cde40a0 100644 --- a/recipes/trgt/meta.yaml +++ b/recipes/trgt/meta.yaml @@ -1,7 +1,7 @@ {% set name = "trgt" %} -{% set version = "0.8.0" %} -{% set trgt_sha256 = "1e927aa3befb6e4973798c742747a88e804ff39f34c6d1c9184b2fecf0f23757" %} -{% set trvz_sha256 = "fce346185d15809a5d1b72ca0c01521d5cdefd3fc924ad4682d0398129eb99e1" %} +{% set version = "0.9.0" %} +{% set trgt_sha256 = "fba2edb311c2ea4f15ae1e0f1b464ae470a73f803d12630b8ea6dbeeff3cc3f9" %} +{% set trvz_sha256 = "08dcb1e5ca9d317140f26d635b323d12a8384b1263fda542e293effb2ca81280" %} package: name: {{ name }} From ce184d660e53de21816b7a1e6a3df170a09e8b31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 16:36:33 -0400 Subject: [PATCH 1385/1813] Update pggb to 0.6.0 (#47045) * Update pggb to 0.6.0 * add `run_exports` and update tool versions * fix typos * remove a dep and decrease multiqc version * decrease multiqc version * fix versioning hack --------- Co-authored-by: AndreaGuarracino --- recipes/pggb/build.sh | 4 ++-- recipes/pggb/meta.yaml | 19 ++++++++++--------- 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/recipes/pggb/build.sh b/recipes/pggb/build.sh index e4dcc8ffa6c9f..9fd032f7e0aa0 100644 --- a/recipes/pggb/build.sh +++ b/recipes/pggb/build.sh @@ -1,9 +1,9 @@ #!/bin/bash # Write version in the script -n=$(grep '$show_version == true' ./pggb -n | cut -f 1 -d :) +n=$(grep '"$show_version" == true' ./pggb -n | cut -f 1 -d :) n=$((n-1)) -sed -i ${n}'a\if [ $show_version == true ]; then echo "pggb '$PKG_VERSION'"; exit; fi' pggb +sed -i ${n}'a\if [ "$show_version" == true ]; then echo "pggb '$PKG_VERSION'"; exit; fi' ./pggb mkdir -p $PREFIX/bin diff --git a/recipes/pggb/meta.yaml b/recipes/pggb/meta.yaml index 620a05e34db1f..23c511a7bad59 100644 --- a/recipes/pggb/meta.yaml +++ b/recipes/pggb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pggb" %} -{% set version = "0.5.4" %} +{% set version = "0.6.0" %} package: name: "{{ name }}" @@ -7,28 +7,29 @@ package: source: url: https://github.com/pangenome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 0f45e710e3a59225ae806db3686ecc32c59859671a8f1b7052259525dc6707f3 + sha256: e201410e5b7ca7c598267797a7fa30b065a1b2b76ee5c309341a93fc489704f3 build: noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} number: 0 requirements: run: - bc - tabix - - gfaffix ==0.1.4 + - gfaffix ==0.1.5b - gsl 2.7.0 - - idna <3,>=2.5 - - multiqc ==1.14 - - odgi ==0.8.3 + - multiqc ==1.19 + - odgi ==0.8.6 - pigz - bcftools - - seqwish ==0.7.9 - - smoothxg ==0.7.0 + - seqwish ==0.7.10 + - smoothxg ==0.7.4 - time - vg 1.40.0 - - wfmash ==0.10.3 + - wfmash ==0.13.0 - python-igraph ==0.10.4 test: From 46afe1243e4af12d69f5cce1ffff2fdfafd39452 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 01:53:01 +0300 Subject: [PATCH 1386/1813] racon: add linux-aarch64 build (#47009) * racon: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Set SPOA options specific for the CPU architecture See https://github.com/rvaser/spoa?tab=readme-ov-file#options Signed-off-by: Martin Tzvetanov Grigorov * Disable testing for Linux ARM64. There is a problem with the googletest dependency Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/racon/build.sh | 13 ++++++++++++- recipes/racon/meta.yaml | 8 +++++++- 2 files changed, 19 insertions(+), 2 deletions(-) diff --git a/recipes/racon/build.sh b/recipes/racon/build.sh index 468703346513e..5bca68065ae90 100644 --- a/recipes/racon/build.sh +++ b/recipes/racon/build.sh @@ -1,9 +1,20 @@ #!/bin/bash +case $(uname -m) in + x86_64) + SPOA_OPTS="-Dspoa_optimize_for_portability=ON" + ;; + aarch64) + SPOA_OPTS="-Dspoa_use_simde=ON -Dspoa_use_simde_nonvec=ON -Dspoa_use_simde_openmp=ON -DBUILD_TESTING=OFF" + ;; + *) + ;; +esac + mkdir -p $PREFIX/bin mkdir build cd build -cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${PREFIX} -Dracon_build_wrapper=ON -Dspoa_optimize_for_portability=ON .. +cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${PREFIX} -Dracon_build_wrapper=ON ${SPOA_OPTS} .. make chmod +w bin/racon_wrapper make install diff --git a/recipes/racon/meta.yaml b/recipes/racon/meta.yaml index 3a6b3fb266c94..f2f1e5d7e4e16 100644 --- a/recipes/racon/meta.yaml +++ b/recipes/racon/meta.yaml @@ -6,7 +6,9 @@ package: version: {{ version }} build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} source: url: https://github.com/lbcb-sci/racon/archive/refs/tags/{{ version }}.tar.gz @@ -37,3 +39,7 @@ about: license: MIT license_file: LICENSE summary: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 01684a14ba057a1ebf5dba9c00caefa9f7a493c0 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 01:53:21 +0300 Subject: [PATCH 1387/1813] htseq: add linux-aarch64 build (#47011) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/htseq/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/htseq/meta.yaml b/recipes/htseq/meta.yaml index 2d524cc2a529a..712c394b285fb 100644 --- a/recipes/htseq/meta.yaml +++ b/recipes/htseq/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation run_exports: - {{ pin_subpackage('htseq', max_pin="x") }} @@ -57,6 +57,8 @@ about: summary: 'HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:htseq - usegalaxy-eu:htseq_count From e7bff7e0f3d2cc2ecce56632914a2922381c6205 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 01:53:46 +0300 Subject: [PATCH 1388/1813] tidyp: add linux-aarch64 build (#47060) * tidyp: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Link $CC to ~/bin/gcc The Makefile uses hardcoded `gcc` and there is no way to overwrite it via env vars. Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/tidyp/build.sh | 11 +++++++++-- recipes/tidyp/meta.yaml | 6 +++++- 2 files changed, 14 insertions(+), 3 deletions(-) diff --git a/recipes/tidyp/build.sh b/recipes/tidyp/build.sh index 6e31603e6254a..591e6774ea67f 100644 --- a/recipes/tidyp/build.sh +++ b/recipes/tidyp/build.sh @@ -1,7 +1,14 @@ #!/bin/bash +set -xe +mkdir -p ${HOME}/bin +export PATH="${HOME}/bin:$PATH" +ln -s ${CC} ${HOME}/bin/gcc -./configure --prefix="$PREFIX" +pushd build/gmake make -make install +popd + +mkdir -p ${PREFIX}/bin +cp ./bin/tidyp ${PREFIX}/bin diff --git a/recipes/tidyp/meta.yaml b/recipes/tidyp/meta.yaml index e95b0d8d7be46..0ff496e43703c 100644 --- a/recipes/tidyp/meta.yaml +++ b/recipes/tidyp/meta.yaml @@ -7,7 +7,9 @@ source: sha256: 5f0965041119bed0ed70a7f0be39e8f0162141eea14d77f472b49f8b3303ab0b build: - number: 5 + number: 6 + run_exports: + - {{ pin_subpackage('tidyp', max_pin="x") }} requirements: build: @@ -20,5 +22,7 @@ about: summary: "Program for cleaning up and validating HTML" extra: + additional-platforms: + - linux-aarch64 skip-lints: - missing_tests From 950649051c412663aa7bb0390f42c030883d8f91 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 01:54:10 +0300 Subject: [PATCH 1389/1813] ucsc-fatotwobit: add linux-aarch64 build (#47053) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-fatotwobit/build.sh | 2 +- recipes/ucsc-fatotwobit/htmshell.patch | 11 +++++++++++ recipes/ucsc-fatotwobit/meta.yaml | 7 ++++++- 3 files changed, 18 insertions(+), 2 deletions(-) create mode 100644 recipes/ucsc-fatotwobit/htmshell.patch diff --git a/recipes/ucsc-fatotwobit/build.sh b/recipes/ucsc-fatotwobit/build.sh index 3af116406aaff..cd1c569ec1e88 100644 --- a/recipes/ucsc-fatotwobit/build.sh +++ b/recipes/ucsc-fatotwobit/build.sh @@ -1,6 +1,6 @@ #!/bin/bash mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export L="${LDFLAGS}" mkdir -p "$BINDIR" diff --git a/recipes/ucsc-fatotwobit/htmshell.patch b/recipes/ucsc-fatotwobit/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-fatotwobit/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-fatotwobit/meta.yaml b/recipes/ucsc-fatotwobit/meta.yaml index 9809766e8251f..2b337b0122fe1 100644 --- a/recipes/ucsc-fatotwobit/meta.yaml +++ b/recipes/ucsc-fatotwobit/meta.yaml @@ -12,10 +12,11 @@ source: sha256: "{{ sha256 }}" patches: - "include.patch" + - htmshell.patch build: skip: True # [osx] - number: 0 + number: 1 ignore_run_exports: - libpng - libuuid @@ -50,3 +51,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "Convert DNA from fasta to 2bit format" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From a0c852245fb232c781ff5a46e4c12ed83907a771 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 19:36:44 -0400 Subject: [PATCH 1390/1813] Update ipyrad to 0.9.95 (#47080) --- recipes/ipyrad/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ipyrad/meta.yaml b/recipes/ipyrad/meta.yaml index f1cf832e4036c..dc31ad13e636f 100644 --- a/recipes/ipyrad/meta.yaml +++ b/recipes/ipyrad/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ipyrad" %} -{% set version = "0.9.94" %} -{% set sha256 = "7a9ed2982cdec30afe480d38ae3208458c513f6302ca2a6c947935e5c03736cf" %} +{% set version = "0.9.95" %} +{% set sha256 = "c0a25f057cf5a6e812c4ff180291212b33bc50cd76f014b4d37337fd7ac0c335" %} package: name: {{ name }} From 0f421495aa32770f969321eb21b39774232c8d60 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 19:36:54 -0400 Subject: [PATCH 1391/1813] Update vg to 1.56.0 (#47079) --- recipes/vg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml index 7fa4d9974f826..bb45cdbd63658 100644 --- a/recipes/vg/meta.yaml +++ b/recipes/vg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vg" %} -{% set version = "1.55.0" %} +{% set version = "1.56.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg - sha256: 2c602084b4eab7b50147fba31f51e126135d7ceaaf405632445bff96d68ba6c7 + sha256: 8b82e300a386d6bf34d0d1025a7dc806b2b95bb57bd063226fc3984e920710e4 build: number: 0 From 250ee0cf8b22bd1b7d581461548430f320adfb71 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 19:37:09 -0400 Subject: [PATCH 1392/1813] Update amdirt to 1.6.0 (#47061) --- recipes/amdirt/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/amdirt/meta.yaml b/recipes/amdirt/meta.yaml index e0b4ff0da53a8..a28aeb665778a 100644 --- a/recipes/amdirt/meta.yaml +++ b/recipes/amdirt/meta.yaml @@ -1,5 +1,5 @@ {% set name = "amdirt" %} -{% set version = "1.5.0" %} +{% set version = "1.6.0" %} package: name: {{ name|lower }} @@ -7,14 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/AMDirT-{{ version }}.tar.gz - sha256: f52028b539767e7d8ae357aa0716716b7b18ee0231612ffc9c4d4a2eb1e74f24 + sha256: 15feb7872d98e73225886a81a6b7b1af0e6a962e9a398d6e0343c31adeb9640c build: entry_points: - AMDirT = AMDirT.cli:cli noarch: python script: {{ PYTHON }} -m pip install . -vv - number: 1 + number: 0 run_exports: - {{ pin_subpackage("amdirt", max_pin="x.x") }} From eebcb8383c8fedbf961528b55eac49601042a77c Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 02:37:24 +0300 Subject: [PATCH 1393/1813] gseapy: add linux-aarch64 build (#47059) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/gseapy/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 00d552a8a7b8f..c2470c14e2619 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -12,7 +12,7 @@ build: run_exports: - {{ pin_subpackage("gseapy", max_pin="x") }} skip: True # [py2k or py == 36 ] - number: 0 + number: 1 requirements: build: @@ -45,6 +45,8 @@ about: license_family: MIT extra: + additional-platforms: + - linux-aarch64 container: # matplotlib needs opengl support extended-base: true From c9bbc763754cb41eabff5e881aa538f3234d2379 Mon Sep 17 00:00:00 2001 From: Andre Faure <39261277+andrefaure@users.noreply.github.com> Date: Tue, 9 Apr 2024 01:38:21 +0200 Subject: [PATCH 1394/1813] Update r-dimsum to v1.3.1 (#47076) * Update to v1.3.1, add run_exports statement and requirements for r-base and fastqc * corrected sha256 and set build number to 0 --- recipes/r-dimsum/meta.yaml | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/recipes/r-dimsum/meta.yaml b/recipes/r-dimsum/meta.yaml index 561f9c65df523..e31cf6dc73e8e 100644 --- a/recipes/r-dimsum/meta.yaml +++ b/recipes/r-dimsum/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.3' %} +{% set version = '1.3.1' %} {% set github = "https://github.com/lehner-lab/DiMSum" %} package: @@ -7,22 +7,24 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 5f4181a8f4790f7a995db3f1d19408ebeb0fe00ed0cf520d28b1e37dc53a01ea + sha256: 068b490a8a38601298ea98f32b1e81ba98ecfaa8102e312d8c419d8ef7d3c9de build: - number: 2 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-dimsum', max_pin="x") }} requirements: build: - r-base host: - - r-base + - r-base =4.0 - pandoc >=1.17.2 - - fastqc >=0.11.3 + - fastqc =0.11 - cutadapt =2.4 - vsearch >=2.17 - starcode >=1.3 @@ -43,9 +45,9 @@ requirements: - r-seqinr - r-stringr run: - - r-base + - r-base =4.0 - pandoc >=1.17.2 - - fastqc >=0.11.3 + - fastqc =0.11 - cutadapt =2.4 - vsearch >=2.17 - starcode >=1.3 From 33f95a484a481a8dc5c953ce86fc540e174bc84c Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 02:39:08 +0300 Subject: [PATCH 1395/1813] ncls: add linux-aarch64 build (#47058) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ncls/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/ncls/meta.yaml b/recipes/ncls/meta.yaml index f593d34f8522e..44dbe4ad16faa 100644 --- a/recipes/ncls/meta.yaml +++ b/recipes/ncls/meta.yaml @@ -10,9 +10,11 @@ source: sha256: 81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93 build: - number: 1 + number: 2 skip: true # [py2k or osx] script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage(name, max_pin="x.x.x") }} requirements: build: @@ -37,6 +39,8 @@ about: summary: Fast overlap datastructure. extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - endrebak skip-lints: From a594d251ee66d8c978423e9385346c9adc9a50fc Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 02:39:21 +0300 Subject: [PATCH 1396/1813] ncbi-ngs-sdk: add linux-aarch64 build (#47057) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ncbi-ngs-sdk/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/ncbi-ngs-sdk/meta.yaml b/recipes/ncbi-ngs-sdk/meta.yaml index 549f2efd81420..09d85595c29bf 100644 --- a/recipes/ncbi-ngs-sdk/meta.yaml +++ b/recipes/ncbi-ngs-sdk/meta.yaml @@ -6,7 +6,9 @@ package: version: {{ version }} build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage('ncbi-ngs-sdk', max_pin="x") }} source: url: https://github.com/ncbi/ngs/archive/{{ version }}.tar.gz @@ -33,3 +35,7 @@ about: home: https://github.com/ncbi/ngs license: Public Domain summary: NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 1a2827ef0a2625e0faee9eb60cd37702fe9d2014 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 19:39:29 -0400 Subject: [PATCH 1397/1813] Update binchicken to 0.10.4 (#47049) --- recipes/binchicken/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/binchicken/meta.yaml b/recipes/binchicken/meta.yaml index ec1cc96708dbd..08e18db208ba6 100644 --- a/recipes/binchicken/meta.yaml +++ b/recipes/binchicken/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.10.3" %} +{% set version = "0.10.4" %} {% set name = "binchicken" %} -{% set sha256 = "da3a5a7e88c29e5470111e6011eb4395e7597c1ed50927b0cef16997d6484545" %} +{% set sha256 = "0a48da6e24e8c0b0d6746914d80991b1662180fcd58b987ae0925326d0007382" %} package: name: binchicken From 99c7d261c74246710f4e1a8c174c37045369ff81 Mon Sep 17 00:00:00 2001 From: Mikhail Kolmogorov Date: Mon, 8 Apr 2024 16:41:01 -0700 Subject: [PATCH 1398/1813] Severus 1.0 (#47040) * severus update to 1.0 * severus max_ping change * sha256 update * add plotly --- recipes/severus/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/severus/meta.yaml b/recipes/severus/meta.yaml index 6fbcfbe6a28f5..313e6ac2f4c3d 100644 --- a/recipes/severus/meta.yaml +++ b/recipes/severus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.2" %} +{% set version = "1.0" %} package: name: severus @@ -6,13 +6,13 @@ package: source: url: https://github.com/KolmogorovLab/Severus/archive/refs/tags/{{ version }}.tar.gz - sha256: 6fd60f673aea6e6ff930a207311be3c533a944c8875e9a677235b99dc18e5135 + sha256: c14b76b4c952f8c68adbdd885e7c59e3500714aad39eaef00302a8c57aea82c7 build: number: 0 noarch: python run_exports: - - {{ pin_subpackage('severus', max_pin='x.x') }} + - {{ pin_subpackage('severus', max_pin='x') }} requirements: host: @@ -31,6 +31,7 @@ requirements: - biopython - numpy - pysam + - plotly extra: skip-lints: From 308a269956ce70a82bad5df6a73eee70426f6f48 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 19:42:54 -0400 Subject: [PATCH 1399/1813] Update vsearch to 2.27.1 (#47024) --- recipes/vsearch/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index 8a16a497c8ed7..4f166d6926624 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.27.0" %} -{% set sha256 = "18d6fc919adce684c01fe57797e2adbf5b4d4f6cf5ef169378ad473797be38ae" %} +{% set version = "2.27.1" %} +{% set sha256 = "54666bcd9434fb7636c5b292a67e7c194e809e631bbe8f4f86b85fb47e863abc" %} package: name: vsearch @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('vsearch', max_pin="x") }} From b55e9e57e1d7aeb55b7bac47f6bce048e2425bfd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 19:43:32 -0400 Subject: [PATCH 1400/1813] Update bioframe to 0.6.4 (#47023) --- recipes/bioframe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioframe/meta.yaml b/recipes/bioframe/meta.yaml index 50aa16011fa1f..b25e8a10778bf 100644 --- a/recipes/bioframe/meta.yaml +++ b/recipes/bioframe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioframe" %} -{% set version = "0.6.3" %} +{% set version = "0.6.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: dfc1e94ae7bbd22e8fe1bb80b28ff4d1fcd6ce791e1166a64a8e7b6db08d61ff + sha256: 17c152fcb45c83ac0041435790e7fcd4344b74e1b09bd8c8d8b3d20c3ac468e9 build: noarch: python From 6d041dced3659ca0d4a03f7179519903ccc793ad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 19:44:22 -0400 Subject: [PATCH 1401/1813] Update snakemake-executor-plugin-googlebatch to 0.3.3 (#47018) * Update snakemake-executor-plugin-googlebatch to 0.3.2 * Update snakemake-executor-plugin-googlebatch to 0.3.3 --- recipes/snakemake-executor-plugin-googlebatch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml index fce87b3ef78b0..4383f0b34e857 100644 --- a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml +++ b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-googlebatch" %} -{% set version = "0.3.1" %} +{% set version = "0.3.3" %} # Upon version update, requirements have to be checked! package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_googlebatch-{{ version }}.tar.gz - sha256: 292c024534e98aecf6a5a2be8a24db104d8038831b6a55fe50c87c1e4fdb28af + sha256: fbc3f3dad6fca51f9d65cd66a6a1272b056213ed3ab03759523f27590c58bcd8 build: noarch: python From d8ad0d61f7013fe7c5ad9c54c7df7e24becb7ec3 Mon Sep 17 00:00:00 2001 From: zhenxian <920596906@qq.com> Date: Tue, 9 Apr 2024 07:45:07 +0800 Subject: [PATCH 1402/1813] Update meta.yaml (#47033) --- recipes/clair3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clair3/meta.yaml b/recipes/clair3/meta.yaml index 038a1a59b7bf1..4775a888628fd 100644 --- a/recipes/clair3/meta.yaml +++ b/recipes/clair3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clair3" %} -{% set version = "1.0.6" %} +{% set version = "1.0.7" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: http://www.bio8.cs.hku.hk/clair3/bioconda/Clair3_v{{ version }}.zip - sha256: 771cc626460bfe1acf9bc535e2d44110e4076622ed900a6867861bb324687b7e + sha256: 4f688f33c4dfac88924da4374ef43c47a6883b57d461388940e649df102c6d4d build: number: 0 From 5fbd9329944cd3b8a92a1017df36cd5311984a8a Mon Sep 17 00:00:00 2001 From: LSTUGA <37195702+LSTUGA@users.noreply.github.com> Date: Tue, 9 Apr 2024 07:45:33 +0800 Subject: [PATCH 1403/1813] Update my recipe SeqSero2 to v1.3.1 lstuga (#47005) * add seqsero2 recipe * files modified * modified salmid dependency * omit salmid * modify recipe * modifed recipe * use noarch: python * update to v1.0.2 * update to v1.0.2 * update to v1.0.2 * update to v1.1.0 * update to v1.1.0 * update to v1.1.1 * update to v1.2.1 * update to seqsero2-v1.3.1 * bump build --------- Co-authored-by: Robert A. Petit III --- recipes/seqsero2/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/seqsero2/meta.yaml b/recipes/seqsero2/meta.yaml index a904b60557fc3..577b4e289f04a 100644 --- a/recipes/seqsero2/meta.yaml +++ b/recipes/seqsero2/meta.yaml @@ -11,7 +11,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation run_exports: @@ -28,10 +28,11 @@ requirements: - samtools >=1.8 - bedtools =2.17.0 - sra-tools >=2.8.0 - - spades >=3.9.0 + - spades >=3.15.5 - sra-tools >=2.8.0 - salmid =0.1.23 - bwa >=0.7.12 + - seqtk >=1.3 test: commands: - SeqSero2_package.py -h From f4cf07df73ca8c6db09f15fe2e56a944a9e53a83 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 20:25:56 -0400 Subject: [PATCH 1404/1813] Update querynator to 0.4.2 (#47066) * Update querynator to 0.4.2 * fix missing_run_exports (#47070) bioconda linting failed because of missing_run_exports. This should fix it. --------- Co-authored-by: Niclas Grote <57624670+HomoPolyethylen@users.noreply.github.com> --- recipes/querynator/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/querynator/meta.yaml b/recipes/querynator/meta.yaml index fdbddc2f8f2f8..137289ca06a6d 100644 --- a/recipes/querynator/meta.yaml +++ b/recipes/querynator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "querynator" %} -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: "{{ name|lower }}" @@ -7,11 +7,13 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 394a48c700ce6c8940cf134ffe0cf1f58f2418fcc8fffef4509a9a08567bda1c + sha256: 869fec02e402428e68c522d0b906a6baaaa6cdecdcd83195f8d775e58ef635a4 build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('querynator', max_pin="x") }} entry_points: - querynator=querynator.__main__:run_querynator script: "{{ PYTHON }} -m pip install . -vv" From 6c40dbfc5587d61f065ad3447044b72c98afa4b4 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Mon, 8 Apr 2024 17:51:32 -0700 Subject: [PATCH 1405/1813] Update ntedit to 2.0.0 (#47068) * Update ntedit to 2.0.0 * Move some dependencies to host section * Correct meson build prefix * Add boost to run * Add CPPFLAG * clean up recipe --------- Co-authored-by: mencian --- recipes/ntedit/build.sh | 19 ++++++------------- recipes/ntedit/meta.yaml | 40 ++++++++++++++++++++++++++++------------ 2 files changed, 34 insertions(+), 25 deletions(-) diff --git a/recipes/ntedit/build.sh b/recipes/ntedit/build.sh index 310cbe6d76b8f..4e5a499abd72a 100644 --- a/recipes/ntedit/build.sh +++ b/recipes/ntedit/build.sh @@ -1,16 +1,9 @@ #!/bin/bash -export CFLAGS="-I$PREFIX/include" -export CPPFLAGS="-I$PREFIX/include" -export CXXFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" -export CPATH=${PREFIX}/include -export C_INCLUDE_PATH=${C_INCLUDE_PATH}:${PREFIX}/include -export LIBRARY_PATH="${PREFIX}/lib" -export LD_LIBRARY_PATH="${PREFIX}/lib" -if [[ "$(uname)" == Darwin ]]; then - export LDFLAGS="$LDFLAGS -headerpad_max_install_names" -fi -make ntedit mkdir -p $PREFIX/bin -mv ntedit $PREFIX/bin + +export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" + +meson setup build --prefix=$PREFIX --strip +cd build +ninja -v install diff --git a/recipes/ntedit/meta.yaml b/recipes/ntedit/meta.yaml index 0c2d71c26f51a..efaab31e1369b 100644 --- a/recipes/ntedit/meta.yaml +++ b/recipes/ntedit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ntedit" %} -{% set version = "1.4.3" %} +{% set version = "2.0.0" %} package: name: {{ name|lower }} @@ -11,31 +11,47 @@ build: - {{ pin_subpackage(name, max_pin="x") }} source: - url: https://github.com/bcgsc/ntEdit/archive/v{{ version }}.tar.gz - sha256: a584a04eb0d6373c4be68b626444600fea8a0bf97931b34fbc4da47c21d7fd27 + url: https://github.com/bcgsc/ntEdit/releases/download/v{{ version }}/ntEdit-{{ version }}.tar.gz + sha256: d7e2fbae0944510b1df1e9f88a5503a85b6a60dee42fdfc5c135698582ea3478 requirements: build: - - make - {{ compiler('cxx') }} - - llvm-openmp # [osx] + - cmake + - make - automake - autoconf - - perl - + - meson + - ninja host: + - perl - zlib + - btllib + - llvm-openmp # [osx] + - boost-cpp run: - - llvm-openmp # [osx] - - zlib - - ntHits ==0.0.1 + - llvm-openmp # [osx] + - nthits >=1.0.0 + - ntcard + - btllib + - snakemake-minimal + - boost-cpp test: commands: - ntedit --help + - run-ntedit --help about: home: https://github.com/bcgsc/ntEdit - license: GPL-3.0 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE - summary: 'ultra fast, scalable genome assembly polishing and snv detection' + summary: 'Ultrafast, lightweight, scalable genome assembly polishing, and SNV detection & annotation' + doc_url: https://github.com/bcgsc/ntEdit/blob/master/README.md + dev_url: https://github.com/bcgsc/ntEdit + +extra: + identifiers: + - doi:10.1093/bioinformatics/btz400 + - biotools:ntEdit From 23cfc6b144e38cdb82cc893343ab58a3fd05cecf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Tue, 9 Apr 2024 02:52:02 +0200 Subject: [PATCH 1406/1813] Bump pychopper (#47075) * Bump pychopper * Add run_export * Fix sha256 * Fixing command --- recipes/pychopper/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/pychopper/meta.yaml b/recipes/pychopper/meta.yaml index 107b6f615ed90..d747c663fb446 100644 --- a/recipes/pychopper/meta.yaml +++ b/recipes/pychopper/meta.yaml @@ -1,18 +1,20 @@ {% set name = "pychopper" %} -{% set version = "2.5.0" %} +{% set version = "2.7.9" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/nanoporetech/pychopper/archive/v{{ version }}.tar.gz - sha256: 1800a2c5e19f2a025da579608e87ec1a802cf5196fc9e8fed936cb09e2e5e465 + url: https://github.com/epi2me-labs/pychopper/archive/v{{ version }}.tar.gz + sha256: 630d644fbafc3199609e111c1522dc47864c1bfde5cc9682d796974acb97ac70 build: noarch: python number: 0 script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage('pychopper', max_pin="x") }} requirements: host: @@ -28,13 +30,15 @@ requirements: - seaborn - six - pandas + - numpy + - pysam test: commands: - - cdna_classifier.py --help + - pychopper --help about: - home: https://github.com/nanoporetech/pychopper - license: MPL2 + home: https://github.com/epi2me-labs/pychopper + license: Mozilla Public License 2.0 summary: A tool to identify, orient and rescue full length cDNA reads from nanopore data. license_file: LICENSE.md From f64b97397f842fe488e308ced61c880ffb0646c4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 21:05:33 -0400 Subject: [PATCH 1407/1813] Update checkatlas to 0.4.7 (#47078) * Update checkatlas to 0.4.4 * Update checkatlas to 0.4.7 * add run_exports --------- Co-authored-by: mencian --- recipes/checkatlas/meta.yaml | 20 +++++++------------- 1 file changed, 7 insertions(+), 13 deletions(-) diff --git a/recipes/checkatlas/meta.yaml b/recipes/checkatlas/meta.yaml index 200cb63dfda15..19464db4eb5b7 100644 --- a/recipes/checkatlas/meta.yaml +++ b/recipes/checkatlas/meta.yaml @@ -1,5 +1,5 @@ {% set name = "checkatlas" %} -{% set version = "0.4.2" %} +{% set version = "0.4.7" %} package: name: "{{ name|lower }}" @@ -7,34 +7,28 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 2bf72a64d383d260dfd33c17f7d823f303973947b339fd32ee39e2a8d54ec241 + sha256: c18fc7014b749377db697f0b163c6913badcf99ecd523f0824f0a3fd10c78e44 build: number: 0 entry_points: - checkatlas = checkatlas.__main__:main - checkatlas-workflow = checkatlas.checkatlas_workflow:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('checkatlas', max_pin="x.x") }} requirements: host: - - llvmlite >=0.39.1,<0.40.0 - - numba >=0.56.4,<0.57.0 - - numpy >=1.23.5,<2.0.0 - pip - - poetry >=1.5.1,<2.0.0 + - poetry-core >=1.5.1,<2.0.0 - python >=3.10 - - rpy2 ==3.5.10 - - scanpy >=1.9.1,<2.0.0 - - scikit-learn >=1.2.1,<2.0.0 - - types-pyyaml >=6.0.12.6,<7.0.0.0 run: + - python >=3.10 - llvmlite >=0.39.1,<0.40.0 - numba >=0.56.4,<0.57.0 - numpy >=1.23.5,<2.0.0 - - poetry >=1.5.1,<2.0.0 - - python >=3.10 - rpy2 ==3.5.10 - scanpy >=1.9.1,<2.0.0 - scikit-learn >=1.2.1,<2.0.0 From 87fa070a286f3bac0b8f8a8e3a472d5dc18a46e5 Mon Sep 17 00:00:00 2001 From: Vedanth Ramji <86137377+Vedanth-Ramji@users.noreply.github.com> Date: Tue, 9 Apr 2024 11:05:52 +1000 Subject: [PATCH 1408/1813] BUG specify pronto version for argnorm (#47081) * BUG specify pronto version for argnorm * Added space between package and version constraints * Increment build number --- recipes/argnorm/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/argnorm/meta.yaml b/recipes/argnorm/meta.yaml index 9cad1351c36e4..3266c5db32433 100644 --- a/recipes/argnorm/meta.yaml +++ b/recipes/argnorm/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - argnorm=argnorm.cli:main script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" @@ -21,15 +21,15 @@ requirements: host: - pandas - pip - - pronto + - pronto >=2.5.6 - pytest - - python + - python >=3.7 - setuptools run: - pandas - - pronto + - pronto >=2.5.6 - pytest - - python + - python >=3.7 - setuptools test: @@ -49,4 +49,4 @@ about: extra: recipe-maintainers: - - Vedanth-Ramji \ No newline at end of file + - Vedanth-Ramji From e511dc9e4275bd6df4b092cfd1b6b7a0de9782e4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 21:21:06 -0400 Subject: [PATCH 1409/1813] Update r-codedepends to 0.6.6 (#47044) * Update r-codedepends to 0.6.6 * add run_exports --------- Co-authored-by: mencian --- recipes/r-codedepends/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/r-codedepends/meta.yaml b/recipes/r-codedepends/meta.yaml index f19f17e98709a..321e8713df784 100644 --- a/recipes/r-codedepends/meta.yaml +++ b/recipes/r-codedepends/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.6.5' %} +{% set version = '0.6.6' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -10,15 +10,17 @@ source: url: - {{ cran_mirror }}/src/contrib/CodeDepends_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/CodeDepends/CodeDepends_{{ version }}.tar.gz - sha256: 18067d49d67c3f8f0cca1f3890680dcee9ffc90a0469561c7da074aec68ef350 + sha256: 7f815b03abe573b95ac9ed2e20caa7c5b5370aff710767e897575c2cf52c5857 build: merge_build_host: True # [win] - number: 4 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-codedepends', max_pin="x.x") }} requirements: build: From d6c23b67566d1676556e079e2e556b5353e06a8c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 21:33:39 -0400 Subject: [PATCH 1410/1813] Update rust-bio-tools to 0.42.1 (#46976) * Update rust-bio-tools to 0.42.1 * add run_exports --------- Co-authored-by: mencian --- recipes/rust-bio-tools/build.sh | 7 +- .../build_failure.linux-64.yaml | 104 ------------------ recipes/rust-bio-tools/meta.yaml | 12 +- 3 files changed, 9 insertions(+), 114 deletions(-) delete mode 100644 recipes/rust-bio-tools/build_failure.linux-64.yaml diff --git a/recipes/rust-bio-tools/build.sh b/recipes/rust-bio-tools/build.sh index 403679dd60ea7..c5cc18c7f9bc5 100644 --- a/recipes/rust-bio-tools/build.sh +++ b/recipes/rust-bio-tools/build.sh @@ -1,11 +1,6 @@ #!/bin/bash -e -# TODO: Remove the following export when pinning is updated and we use -# {{ compiler('rust') }} in the recipe. -export \ - CARGO_NET_GIT_FETCH_WITH_CLI=true \ - CARGO_HOME="${BUILD_PREFIX}/.cargo" - export BINDGEN_EXTRA_CLANG_ARGS="${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" +RUST_BACKTRACE=1 cargo install --no-track --verbose --root "${PREFIX}" --path . diff --git a/recipes/rust-bio-tools/build_failure.linux-64.yaml b/recipes/rust-bio-tools/build_failure.linux-64.yaml deleted file mode 100644 index 26ac40babfcbc..0000000000000 --- a/recipes/rust-bio-tools/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 37fa4d78a2ee8b18065a0bd0f594ad1e9587bb4ac7edf1b4629a9f10fa45d0a5 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - Compiling linear-map v1.2.0 - Running rustc --crate-name linear_map /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/linear-map-1.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=49dea80bcdb65bf0 -C extra-filename=-49dea80bcdb65bf0 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --cap-lints allow - Compiling ieee754 v0.2.6 - Running rustc --crate-name ieee754 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/ieee754-0.2.6/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=3d851bc61679c0fc -C extra-filename=-3d851bc61679c0fc --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --cap-lints allow - Compiling strum v0.23.0 - Running rustc --crate-name strum --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/strum-0.23.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' -C metadata=bd8b155d4a3212cb -C extra-filename=-bd8b155d4a3212cb --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --cap-lints allow - Compiling bio v0.39.2 - Running rustc --crate-name bio --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/bio-0.39.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=bfcb0c8ea87843f8 -C extra-filename=-bfcb0c8ea87843f8 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern anyhow=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libanyhow-8a64e709a9ea7090.rmeta --extern approx=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libapprox-796d96a1d4a24564.rmeta --extern bio_types=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libbio_types-8f2580fc26dc2a4c.rmeta --extern bit_set=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libbit_set-5f69a9e374261aee.rmeta --extern bv=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libbv-c65acac672bf1382.rmeta --extern bytecount=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libbytecount-49ce67f909ab9836.rmeta --extern csv=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libcsv-0a2495576c650dd0.rmeta --extern custom_derive=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libcustom_derive-a31ad87d2c35141e.rmeta --extern enum_map=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libenum_map-e623b86d6eda7738.rmeta --extern fxhash=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libfxhash-b9c70ea26a93b20f.rmeta --extern getset=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libgetset-4a8df41f803195c1.so --extern itertools=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libitertools-f77dc74df281f0e9.rmeta --extern itertools_num=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libitertools_num-2f4a9790e16745e6.rmeta --extern lazy_static=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblazy_static-aef73a8347dc17b1.rmeta --extern multimap=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libmultimap-b0e538eda3526cdf.rmeta --extern ndarray=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libndarray-ef7993ff5859fb97.rmeta --extern newtype_derive=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libnewtype_derive-a5908103a51871d4.rmeta --extern num_integer=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libnum_integer-b03516cba3dc07e2.rmeta --extern num_traits=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libnum_traits-d20b06288d507dcf.rmeta --extern ordered_float=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libordered_float-a04622cb02bc5a6f.rmeta --extern petgraph=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libpetgraph-f249a594137b7f6e.rmeta --extern rand=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/librand-776acd9a3185d913.rmeta --extern regex=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libregex-88299f7761f9c60d.rmeta --extern serde=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libserde-7d6c4f20cee1b377.rmeta --extern serde_derive=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libserde_derive-c1fd716d558cc7fa.so --extern statrs=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libstatrs-9170518eab8196ec.rmeta --extern strum=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libstrum-bd8b155d4a3212cb.rmeta --extern strum_macros=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libstrum_macros-5d4b4ce44430108b.so --extern thiserror=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libthiserror-1d405cc10f35d668.rmeta --extern triple_accel=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libtriple_accel-744d8b0eeecdf446.rmeta --extern vec_map=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libvec_map-daef5ce73b6a7510.rmeta --cap-lints allow - Compiling tempfile v3.5.0 - Running rustc --crate-name tempfile --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/tempfile-3.5.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=984bbc1631ac0d4a -C extra-filename=-984bbc1631ac0d4a --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libcfg_if-1cc625933ee68d00.rmeta --extern fastrand=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libfastrand-ee1f69f245bfe81a.rmeta --extern rustix=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/librustix-e70d1125d1402ad4.rmeta --cap-lints allow - Running rustc --crate-name rgsl /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type dylib --crate-type rlib --emit=dep-info,link -C prefer-dynamic -C opt-level=3 -C embed-bitcode=no --cfg 'feature="v2"' -C metadata=f9a0167cc0ea59a9 -C extra-filename=-f9a0167cc0ea59a9 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern c_vec=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libc_vec-d24918881fb43fb1.so --extern c_vec=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libc_vec-d24918881fb43fb1.rlib --extern libc=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblibc-0731363918231ed5.rlib --cap-lints allow -L native=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -l gsl -l gslcblas -l m -l cblas -l m --cfg 'feature="v2"' - Compiling reqwest v0.9.24 - Running rustc --crate-name reqwest /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/reqwest-0.9.24/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="default-tls"' --cfg 'feature="hyper-tls"' --cfg 'feature="native-tls"' --cfg 'feature="tls"' -C metadata=e5874b3f83f03ba1 -C extra-filename=-e5874b3f83f03ba1 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern base64=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libbase64-a19d784f86588919.rmeta --extern bytes=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libbytes-3e7ae724b77406fb.rmeta --extern cookie=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libcookie-58754e0f73623939.rmeta --extern cookie_store=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libcookie_store-a04b026bdb49d687.rmeta --extern encoding_rs=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libencoding_rs-7b87e74193d0c407.rmeta --extern flate2=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libflate2-70dc71a48c006913.rmeta --extern futures=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libfutures-82cdf9f97ecdab5c.rmeta --extern http=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libhttp-7f8b83c7faa5bad9.rmeta --extern hyper=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libhyper-7943bea2a0ceffab.rmeta --extern hyper_tls=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libhyper_tls-7f8fbc2858a55a76.rmeta --extern log=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblog-6684351ec618d44f.rmeta --extern mime=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libmime-a05a37379b161b05.rmeta --extern mime_guess=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libmime_guess-1b2487e823506fa3.rmeta --extern native_tls=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libnative_tls-e50dec9310c1d4f2.rmeta --extern serde=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libserde-7d6c4f20cee1b377.rmeta --extern serde_json=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libserde_json-89fb4aba726d8fd2.rmeta --extern serde_urlencoded=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libserde_urlencoded-34e063fcff545fb3.rmeta --extern time=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libtime-14a856f0f5513dee.rmeta --extern tokio=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libtokio-7cf2810afdd496d2.rmeta --extern tokio_executor=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libtokio_executor-99a3d933a3bde1bc.rmeta --extern tokio_io=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libtokio_io-7dc5a2eeaf6caba3.rmeta --extern tokio_threadpool=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libtokio_threadpool-2737f5c5fb2b0b23.rmeta --extern tokio_timer=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libtokio_timer-18df72f395af0a55.rmeta --extern url=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liburl-796aa9590a4d4722.rmeta --extern uuid=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libuuid-4f90eabc1e5c34d1.rmeta --cap-lints allow -L native=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/openssl-sys-ee91e98132c0c133/out/openssl-build/install/lib - Compiling tera v1.18.1 - Running rustc --crate-name tera --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/tera-1.18.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="builtins"' --cfg 'feature="chrono"' --cfg 'feature="chrono-tz"' --cfg 'feature="default"' --cfg 'feature="humansize"' --cfg 'feature="percent-encoding"' --cfg 'feature="rand"' --cfg 'feature="slug"' --cfg 'feature="urlencode"' -C metadata=966d160b89ea163c -C extra-filename=-966d160b89ea163c --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern chrono=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libchrono-89a888186eb22b5d.rmeta --extern chrono_tz=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libchrono_tz-b753c3237e3c7fbf.rmeta --extern globwalk=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libglobwalk-61174e9b3ae5e9d7.rmeta --extern humansize=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libhumansize-be7ba658b667f616.rmeta --extern lazy_static=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblazy_static-aef73a8347dc17b1.rmeta --extern percent_encoding=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libpercent_encoding-72cf279d7fef5fd6.rmeta --extern pest=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libpest-438ddbb2964fe264.rmeta --extern pest_derive=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libpest_derive-34cee7d48c31178c.so --extern rand=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/librand-776acd9a3185d913.rmeta --extern regex=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libregex-88299f7761f9c60d.rmeta --extern serde=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libserde-7d6c4f20cee1b377.rmeta --extern serde_json=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libserde_json-89fb4aba726d8fd2.rmeta --extern slug=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libslug-76fec5f36d416b3e.rmeta --extern thread_local=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libthread_local-b464f97d53aac3cd.rmeta --extern unic_segment=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libunic_segment-99bae7b6ba5ce771.rmeta --cap-lints allow - Compiling indicatif v0.11.0 - Running rustc --crate-name indicatif /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/indicatif-0.11.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=06ccea25cd3ff8c1 -C extra-filename=-06ccea25cd3ff8c1 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern console=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libconsole-1d6c5204c86792bd.rmeta --extern lazy_static=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblazy_static-aef73a8347dc17b1.rmeta --extern number_prefix=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libnumber_prefix-539ed0474b8cb3ca.rmeta --extern parking_lot=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libparking_lot-1cf157db8cfd6e1c.rmeta --extern regex=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libregex-88299f7761f9c60d.rmeta --cap-lints allow - Compiling ordered-float v0.5.2 - Running rustc --crate-name ordered_float /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/ordered-float-0.5.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=1ebef4224276407e -C extra-filename=-1ebef4224276407e --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern num_traits=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libnum_traits-6aa76da748f47036.rmeta --extern unreachable=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libunreachable-94a8b606b3e4d516.rmeta --cap-lints allow - Compiling structopt v0.3.26 - Running rustc --crate-name structopt --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/structopt-0.3.26/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' -C metadata=1710fde95804ad58 -C extra-filename=-1710fde95804ad58 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern clap=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libclap-3d4bf005a1c7cfcf.rmeta --extern lazy_static=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblazy_static-aef73a8347dc17b1.rmeta --extern structopt_derive=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libstructopt_derive-f7376ff427964336.so --cap-lints allow - Compiling rand v0.7.3 - Running rustc --crate-name rand --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/rand-0.7.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="getrandom"' --cfg 'feature="getrandom_package"' --cfg 'feature="libc"' --cfg 'feature="std"' -C metadata=3fa9641229006373 -C extra-filename=-3fa9641229006373 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern getrandom_package=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libgetrandom-1fcfb9b16db7f095.rmeta --extern libc=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblibc-0731363918231ed5.rmeta --extern rand_chacha=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/librand_chacha-cc23ecaa15cfa639.rmeta --extern rand_core=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/librand_core-a96d615a8c0dca75.rmeta --cap-lints allow - Compiling rayon v1.7.0 - Running rustc --crate-name rayon --edition=2021 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.7.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=fa12cbfdd336486c -C extra-filename=-fa12cbfdd336486c --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern either=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libeither-22dbb8c1509ff59b.rmeta --extern rayon_core=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/librayon_core-f52a9815ab27f729.rmeta --cap-lints allow - Compiling fern v0.5.9 - Running rustc --crate-name fern --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/fern-0.5.9/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=b34cbfb0b0bdbf78 -C extra-filename=-b34cbfb0b0bdbf78 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern chrono=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libchrono-89a888186eb22b5d.rmeta --extern log=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblog-6684351ec618d44f.rmeta --cap-lints allow - Compiling jsonm v0.1.4 - Running rustc --crate-name jsonm /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/jsonm-0.1.4/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=b04562a7e837d49d -C extra-filename=-b04562a7e837d49d --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern regex=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libregex-88299f7761f9c60d.rmeta --extern serde=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libserde-7d6c4f20cee1b377.rmeta --extern serde_json=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libserde_json-89fb4aba726d8fd2.rmeta --cap-lints allow - Compiling itertools v0.9.0 - Running rustc --crate-name itertools --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/itertools-0.9.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="use_std"' -C metadata=98d11c369e8eac7e -C extra-filename=-98d11c369e8eac7e --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern either=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libeither-22dbb8c1509ff59b.rmeta --cap-lints allow - Compiling streaming-stats v0.2.3 - Running rustc --crate-name stats /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/streaming-stats-0.2.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=841e89977bc962ef -C extra-filename=-841e89977bc962ef --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern num_traits=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libnum_traits-d20b06288d507dcf.rmeta --cap-lints allow - Compiling approx v0.4.0 - Running rustc --crate-name approx /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/approx-0.4.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' -C metadata=cb99626e744706fd -C extra-filename=-cb99626e744706fd --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern num_traits=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libnum_traits-d20b06288d507dcf.rmeta --cap-lints allow - Compiling rustc-serialize v0.3.24 - Running rustc --crate-name rustc_serialize /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/rustc-serialize-0.3.24/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no -C metadata=04bf5da549563244 -C extra-filename=-04bf5da549563244 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --cap-lints allow - Compiling lz-str v0.1.0 - Running rustc --crate-name lz_str --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/lz-str-0.1.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type cdylib --crate-type rlib --emit=dep-info,link -C opt-level=3 -C embed-bitcode=no -C metadata=fa57445c11776e7e -C extra-filename=-fa57445c11776e7e --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --cap-lints allow - Running rustc --crate-name bzip2_sys /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/bzip2-sys-0.1.111.0.8/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="static"' -C metadata=36eb47ca640e666e -C extra-filename=-36eb47ca640e666e --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern libc=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblibc-0731363918231ed5.rmeta --cap-lints allow -L native=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/bzip2-sys-c7eb3073c8ac667e/out/lib -l static=bz2 - Running rustc --crate-name zstd_sys --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/zstd-sys-2.0.8zstd.1.5.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="legacy"' --cfg 'feature="zdict_builder"' -C metadata=0384f761716dfc01 -C extra-filename=-0384f761716dfc01 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern libc=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblibc-0731363918231ed5.rmeta --cap-lints allow -L native=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/zstd-sys-ea5ebf1b5416cf7d/out -l static=zstd - Running /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/librocksdb-sys-f2c64cbc0e46c402/build-script-build - Running rustc --crate-name curl_sys --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/curl-sys-0.4.62curl-8.1.0/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="openssl-sys"' --cfg 'feature="protocol-ftp"' --cfg 'feature="ssl"' --cfg 'feature="static-curl"' --cfg 'feature="static-ssl"' -C metadata=1c22fe32ec4c58ae -C extra-filename=-1c22fe32ec4c58ae --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern libc=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblibc-0731363918231ed5.rmeta --extern libz_sys=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblibz_sys-f37bec32b21ef27e.rmeta --extern openssl_sys=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/libopenssl_sys-e014ce30be3b6ca5.rmeta --cap-lints allow -L native=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/curl-sys-1684153d67f93086/out/build -l static=curl -L native=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/libz-sys-5d58d7855283952d/out/lib -L native=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/openssl-sys-ee91e98132c0c133/out/openssl-build/install/lib --cfg libcurl_vendored --cfg link_libz --cfg link_openssl - Running rustc --crate-name libxlsxwriter_sys --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/libxlsxwriter-sys-1.1.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="no-md5"' --cfg 'feature="use-openssl-md5"' -C metadata=4957ba847f8189c2 -C extra-filename=-4957ba847f8189c2 --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --cap-lints allow -L native=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/libxlsxwriter-sys-f910310a21b7ae2e/out -l static=xlsxwriter - Compiling xlsxwriter v0.3.5 - Running rustc --crate-name xlsxwriter --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/xlsxwriter-0.3.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="no-md5"' --cfg 'feature="use-openssl-md5"' -C metadata=cb61c42d9cf38f2c -C extra-filename=-cb61c42d9cf38f2c --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern libxlsxwriter_sys=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblibxlsxwriter_sys-4957ba847f8189c2.rmeta --cap-lints allow -L native=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/libxlsxwriter-sys-f910310a21b7ae2e/out - error[E0412]: cannot find type size_t in crate libxlsxwriter_sys - --> /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/xlsxwriter-0.3.5/src/worksheet.rs:1126:52 - | - 1126 | buffer.len() as libxlsxwriter_sys::size_t, - | ^^^^^^ help: a type alias with a similar name exists: time_t - | - ::: /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/libxlsxwriter-sys-f910310a21b7ae2e/out/bindings.rs:398:1 - | - 398 | pub type time_t = __time_t; - | --------------- similarly named type alias time_t defined here - - error[E0412]: cannot find type size_t in crate libxlsxwriter_sys - --> /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/xlsxwriter-0.3.5/src/worksheet.rs:1150:52 - | - 1150 | buffer.len() as libxlsxwriter_sys::size_t, - | ^^^^^^ help: a type alias with a similar name exists: time_t - | - ::: /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/libxlsxwriter-sys-f910310a21b7ae2e/out/bindings.rs:398:1 - | - 398 | pub type time_t = __time_t; - | --------------- similarly named type alias time_t defined here - - error[E0063]: missing fields output_buffer and output_buffer_size in initializer of lxw_workbook_options - --> /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/xlsxwriter-0.3.5/src/workbook.rs:90:40 - | - 90 | let mut workbook_options = libxlsxwriter_sys::lxw_workbook_options { - | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ missing output_buffer and output_buffer_size - - Some errors have detailed explanations: E0063, E0412. - For more information about an error, try rustc --explain E0063. - error: could not compile xlsxwriter due to 3 previous errors - - Caused by: - process didn't exit successfully: rustc --crate-name xlsxwriter --edition=2018 /opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/xlsxwriter-0.3.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="no-md5"' --cfg 'feature="use-openssl-md5"' -C metadata=cb61c42d9cf38f2c -C extra-filename=-cb61c42d9cf38f2c --out-dir /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-bio-tools_1685451378291/_build_env/bin/x86_64-conda-linux-gnu-cc -L dependency=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps --extern libxlsxwriter_sys=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/deps/liblibxlsxwriter_sys-4957ba847f8189c2.rmeta --cap-lints allow -L native=/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target/release/build/libxlsxwriter-sys-f910310a21b7ae2e/out (exit status: 1) - warning: build failed, waiting for other jobs to finish... - error: failed to compile rust-bio-tools v0.42.0 (/opt/conda/conda-bld/rust-bio-tools_1685451378291/work), intermediate artifacts can be found at /opt/conda/conda-bld/rust-bio-tools_1685451378291/work/target - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rust-bio-tools_1685451378291/work/conda_build.sh']' returned non-zero exit status 101. -# Last 100 lines of the build log. diff --git a/recipes/rust-bio-tools/meta.yaml b/recipes/rust-bio-tools/meta.yaml index 7e0e2da27e5b6..5d7119d3ce28c 100644 --- a/recipes/rust-bio-tools/meta.yaml +++ b/recipes/rust-bio-tools/meta.yaml @@ -1,22 +1,24 @@ -{% set version = "0.42.0" %} +{% set version = "0.42.1" %} package: name: rust-bio-tools version: {{ version }} build: - number: 1 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('rust-bio-tools', max_pin="x.x") }} source: url: https://github.com/rust-bio/rust-bio-tools/archive/v{{ version }}.tar.gz - sha256: 93642d7ebd4b85da8a043fd394a0c2d3ca112d0d8ecc0620cb8400ae703148ca + sha256: c4759eb3eaec1d491b521172d1ace42feeef57cba0cd0ed0a4e413dcbde1b40f requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - rust >=1.30 + - {{ compiler('rust') }} - clangdev - pkg-config - make @@ -35,9 +37,11 @@ test: about: home: https://github.com/rust-bio/rust-bio-tools license: MIT + license_family: MIT summary: | A growing collection of fast and secure command line utilities for dealing with NGS data implemented on top of Rust-Bio. + dev_url: https://github.com/rust-bio/rust-bio-tools extra: recipe-maintainers: From bae8e7e51bb2e8c0ae6b71464d9c29df0b8dda84 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 21:45:56 -0400 Subject: [PATCH 1411/1813] Update attotree to 0.1.4 (#47082) --- recipes/attotree/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/attotree/meta.yaml b/recipes/attotree/meta.yaml index c470d548d0d3a..29d99d804afab 100644 --- a/recipes/attotree/meta.yaml +++ b/recipes/attotree/meta.yaml @@ -1,5 +1,5 @@ {% set name = "attotree" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 67abe9965a89993481c22af63c6b49e384f0927b373c2c81cb954ed4f249a66a + sha256: b38356b589b6b32e45e8a091ba6c261a0dc511ee74d8b591089e82d9396f98ac build: number: 0 From 201234fd65e87d38375746c726993dffffc49a8a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 21:50:50 -0400 Subject: [PATCH 1412/1813] Update btllib to 1.7.2 (#47077) * Update btllib to 1.7.2 * add run_exports --------- Co-authored-by: mencian --- recipes/btllib/build.sh | 17 ++-- recipes/btllib/build_failure.osx-64.yaml | 104 ----------------------- recipes/btllib/meta.yaml | 24 +++--- 3 files changed, 22 insertions(+), 123 deletions(-) delete mode 100644 recipes/btllib/build_failure.osx-64.yaml diff --git a/recipes/btllib/build.sh b/recipes/btllib/build.sh index d87279c0cadac..c1a093c8ea800 100644 --- a/recipes/btllib/build.sh +++ b/recipes/btllib/build.sh @@ -1,16 +1,15 @@ #!/bin/bash -export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" +export INCLUDES="-I{PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include -D_LIBCPP_DISABLE_AVAILABILITY" -./compile +CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" meson setup --buildtype release --prefix "${PREFIX}" --strip build/ -mkdir -p ${PREFIX}/bin/ -mkdir -p ${PREFIX}/include/ -mkdir -p ${PREFIX}/lib/ +cd build -cp -r install/bin/* ${PREFIX}/bin/ -cp -r install/include/* ${PREFIX}/include/ -cp -r install/lib/* ${PREFIX}/lib/ +ninja -v install # python wrappers: -$PYTHON -m pip install install/lib/btllib/python +$PYTHON -m pip install "${PREFIX}/lib/btllib/python" --no-deps --no-build-isolation -vvv diff --git a/recipes/btllib/build_failure.osx-64.yaml b/recipes/btllib/build_failure.osx-64.yaml deleted file mode 100644 index b1b23121063ba..0000000000000 --- a/recipes/btllib/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b5330eaa8f450048b15b4e0a4ac3067bf62e46a1e378b96516730df6c583866d # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - [58/59] Installing files. - Installing libbtllib.a to $SRC_DIR/install/lib - Skipping RPATH fixing - Installing wrappers/python/_btllib.so to $SRC_DIR/install/lib/btllib/python/btllib - Skipping RPATH fixing - Installing recipes/indexlr to $SRC_DIR/install/bin - Skipping RPATH fixing - Installing recipes/randseq to $SRC_DIR/install/bin - Skipping RPATH fixing - Installing recipes/mi_bf_generate to $SRC_DIR/install/bin - Skipping RPATH fixing - Installing $SRC_DIR/include/btllib/seq_reader_multiline_fastq_module.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/process_pipeline.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/mi_bloom_filter.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/nthash_lowlevel.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/seq_reader_gfa2_module.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/data_stream.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/seq_reader_fastq_module.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/nthash_consts.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/order_queue.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/aahash.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/indexlr.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/status.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/counting_bloom_filter.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/aahash_consts.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/graph.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/bloom_filter.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/randseq.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/seq.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/seq_reader.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/seq_reader_fasta_module.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/nthash.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/seq_reader_multiline_fasta_module.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/util.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/cstring.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/seq_writer.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/include/btllib/seq_reader_sam_module.hpp to $SRC_DIR/install/include/btllib - Installing $SRC_DIR/wrappers/python/btllib.py to $SRC_DIR/install/lib/btllib/python/btllib - Installing /private/tmp/btllib-build-dzadL9GTQASFPuHRFG4M0A/wrappers/python/setup.py to $SRC_DIR/install/lib/btllib/python - Running custom install script '$SRC_DIR/scripts/install-cpptoml' - Running custom install script '$SRC_DIR/scripts/install-sdsl-lite' - - Build finished successfully! - btllib installation can be found at: $SRC_DIR/install - Processing ./install/lib/btllib/python - Preparing metadata (setup.py): started - Preparing metadata (setup.py): finished with status 'done' - Building wheels for collected packages: btllib - Building wheel for btllib (setup.py): started - Building wheel for btllib (setup.py): finished with status 'done' - Created wheel for btllib: filename=btllib-1.6.0-py3-none-any.whl size=673941 sha256=1df681e706445a63e978f5ae5d950166dacf8546ecbedfd7b3a11f89ee9d5142 - Stored in directory: /private/tmp/pip-ephem-wheel-cache-byvyhow3/wheels/fd/de/91/c0ac23923f09e9244ae72dd27c8d91edf6e02332772e8fb05f - Successfully built btllib - Installing collected packages: btllib - Successfully installed btllib-1.6.0 - - Resource usage statistics from building btllib: - Process count: 12 - CPU time: Sys=0:00:14.7, User=0:03:19.7 - Memory: 590.5M - Disk usage: 60.2K - Time elapsed: 0:02:40.9 - - - Packaging btllib - INFO:conda_build.build:Packaging btllib - Packaging btllib-1.6.0-py310hd3d38e4_1 - INFO:conda_build.build:Packaging btllib-1.6.0-py310hd3d38e4_1 - compiling .pyc files... - number of files: 157 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build - newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 1659, in bundle_conda - files = post_process_files(metadata, initial_files) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 1505, in post_process_files - post_build(m, new_files, build_python=python) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/post.py", line 1318, in post_build - post_process_shared_lib(m, f, prefix_files, host_prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/post.py", line 1266, in post_process_shared_lib - mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/post.py", line 397, in mk_relative_osx - names = macho.otool(path, prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/os_utils/macho.py", line 194, in otool - lines = check_output([otool, '-l', path], - File "/opt/mambaforge/envs/bioconda/lib/python3.8/subprocess.py", line 415, in check_output - return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/subprocess.py", line 516, in run - raise CalledProcessError(retcode, process.args, - subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/btllib_1686051065758/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/btllib_1686051065758/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/btllib/python/btllib/_btllib.so']' died with . -# Last 100 lines of the build log. diff --git a/recipes/btllib/meta.yaml b/recipes/btllib/meta.yaml index a01f150fcc8b3..57d7900c785e2 100644 --- a/recipes/btllib/meta.yaml +++ b/recipes/btllib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "btllib" %} -{% set version = "1.7.1" %} +{% set version = "1.7.2" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/bcgsc/btllib/releases/download/v{{ version }}/{{ name|lower }}-{{ version }}.tar.gz - sha256: 7fa600b34a1d46fa4a4dcd214a76c1c5e08c6f7e99a60a61f8bfc477e3fdfdfe + sha256: 4c1bb29fdbd7d9a39f960360a5d4b224d22189862b948027a8e3ecd67c635926 build: - skip: true # [py < 38 or win] + skip: True # [py < 38 or win] number: 0 run_exports: - {{ pin_subpackage('btllib', max_pin="x") }} @@ -18,28 +18,31 @@ build: requirements: build: - {{ compiler('cxx') }} + - cmake + - meson + - ninja host: - python - pip - - wheel - - meson - - ninja - - cmake - llvm-openmp # [osx] - libgomp # [linux] + - samtools + - gcovr + - swig + - doxygen run: - python - samtools + - llvm-openmp # [osx] + - libgomp # [linux] - pigz - - gzip # alternative to pigz + - gzip # alternative to pigz - tar - bzip2 - xz - lrzip - zip - wget - - llvm-openmp # [osx] - - libgomp # [linux] test: commands: @@ -54,6 +57,7 @@ about: license_file: LICENSE summary: 'Bioinformatics common code library in C++ with Python wrappers, from Bioinformatics Technology Lab' doc_url: https://bcgsc.github.io/btllib/ + dev_url: https://github.com/bcgsc/btllib extra: identifiers: From aae51f5af643b0ecae80fda5b74e0dd7a9186b5a Mon Sep 17 00:00:00 2001 From: Yiqian Duan <55238881+cocodyq@users.noreply.github.com> Date: Tue, 9 Apr 2024 09:51:53 +0800 Subject: [PATCH 1413/1813] Add GMSC-mapper v0.1.0 (#46936) * ENH update meta.yaml * Add GMSC-mapper v0.1.0 * Add GMSC-mapper v0.1.0 * Add GMSC-mapper v0.1.0 --- recipes/gmsc-mapper/meta.yaml | 58 +++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 recipes/gmsc-mapper/meta.yaml diff --git a/recipes/gmsc-mapper/meta.yaml b/recipes/gmsc-mapper/meta.yaml new file mode 100644 index 0000000000000..52d5894f99a1a --- /dev/null +++ b/recipes/gmsc-mapper/meta.yaml @@ -0,0 +1,58 @@ +{% set name = "GMSC-mapper" %} +{% set version = "0.1.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://github.com/BigDataBiology/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" + sha256: 30cc09425028969ce9847a7c55d93919921fef7d91a138bfff2b9a1e31bc2921 + +build: + noarch: python + number: 0 + run_exports: + - {{ pin_compatible(name, max_pin="x.x") }} + entry_points: + - gmsc-mapper=gmsc_mapper.main:main + script: {{ PYTHON }} -m pip install --no-deps . -vv + +requirements: + host: + - pip + - python >=3.7 + run: + - atomicwrites + - biopython + - Bottleneck + - certifi + - numexpr + - numpy + - packaging + - pandas + - pyparsing + - pyrodigal + - python-dateutil + - pytz + - six + - python >=3.7 + - mmseqs2 + - diamond >=2.0.13 + +test: + imports: + - gmsc_mapper + commands: + - gmsc-mapper --help + +about: + home: "https://github.com/BigDataBiology/GMSC-mapper" + license: MIT + license_family: MIT + summary: "GMSC-mapper is a command line tool to query the Global Microbial smORFs Catalog (GMSC)." + +extra: + recipe-maintainers: + - luispedro + - cocodyq From e0c1c31cf35ddd94f8c569208ace1af50f22efea Mon Sep 17 00:00:00 2001 From: mencian Date: Mon, 8 Apr 2024 21:16:50 -0500 Subject: [PATCH 1414/1813] Cleanup build failure recipes --- recipes/blast/build_failure.osx-64.yaml | 104 ------------------ recipes/kmc/build_failure.linux-64.yaml | 2 - recipes/meryl/build_failure.osx-64.yaml | 104 ------------------ recipes/moods/build_failure.osx-64.yaml | 104 ------------------ recipes/pairix/build_failure.osx-64.yaml | 104 ------------------ recipes/pyrodigal/build_failure.osx-64.yaml | 104 ------------------ recipes/quast/build_failure.osx-64.yaml | 104 ------------------ recipes/sra-tools/build_failure.linux-64.yaml | 104 ------------------ recipes/tidyp/build_failure.linux-64.yaml | 104 ------------------ recipes/tidyp/build_failure.osx-64.yaml | 104 ------------------ 10 files changed, 938 deletions(-) delete mode 100644 recipes/blast/build_failure.osx-64.yaml delete mode 100644 recipes/kmc/build_failure.linux-64.yaml delete mode 100644 recipes/meryl/build_failure.osx-64.yaml delete mode 100644 recipes/moods/build_failure.osx-64.yaml delete mode 100644 recipes/pairix/build_failure.osx-64.yaml delete mode 100644 recipes/pyrodigal/build_failure.osx-64.yaml delete mode 100644 recipes/quast/build_failure.osx-64.yaml delete mode 100644 recipes/sra-tools/build_failure.linux-64.yaml delete mode 100644 recipes/tidyp/build_failure.linux-64.yaml delete mode 100644 recipes/tidyp/build_failure.osx-64.yaml diff --git a/recipes/blast/build_failure.osx-64.yaml b/recipes/blast/build_failure.osx-64.yaml deleted file mode 100644 index de9e3cf438772..0000000000000 --- a/recipes/blast/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d58ac0e00618c06e1088a1a93035e4adcb36ef78f5f709b2dbb0e437fbc7ec1d # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_islower' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_tolower' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isupper' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_toupper' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_ishexnumber' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isnumber' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isalnum' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isphonogram' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isideogram' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_iscntrl' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isspecial' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isblank' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isascii' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_toascii' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '___wcwidth' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isgraph' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '___istype' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '___isctype' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isrune' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isspace' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '___sputc' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - duplicate symbol '_isalpha' in: - pcretest.o - /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/lib/libregexp.a(pcreposix.o) - ld: 567 duplicate symbols for architecture x86_64 - clang-14: error: linker command failed with exit code 1 (use -v to see invocation) - make[2]: *** [/opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/build/Makefile.app:159: test_pcre] Error 1 - /usr/bin/awk: can't open file make_test_pcre.log.new - source line number 4 - make[1]: *** [/opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/src/build-system/Makefile.meta_l:333: all.nonusr] Error 2 - make: *** [all_l.real] Error 2 - - ------------------------------------------------------ - Current dir: /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/build/util/regexp - - [create_flat_makefile.sh] FAILED (status 2): - make - grep: /opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/blast/c/ReleaseMT/build/Flat.configuration_log: No such file or directory - config.status: error: flat makefile generation failed. - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/blast_1685482928598/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/kmc/build_failure.linux-64.yaml b/recipes/kmc/build_failure.linux-64.yaml deleted file mode 100644 index fc88366e0a16b..0000000000000 --- a/recipes/kmc/build_failure.linux-64.yaml +++ /dev/null @@ -1,2 +0,0 @@ -recipe_sha: abc0774a2c2552b5cc367cf53ea0fd7ea3f67f838a2b3ad526a5a43886553235 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. diff --git a/recipes/meryl/build_failure.osx-64.yaml b/recipes/meryl/build_failure.osx-64.yaml deleted file mode 100644 index 37b4e5de4af67..0000000000000 --- a/recipes/meryl/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 734dbf449636d9f4e478ff96788290d11ba5393ad8dec20baac7580c10ec0e34 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - In file included from meryl/meryl.H:22: - In file included from meryl/merylInput.H:23: - In file included from utility/src/kmers.H:51: - In file included from utility/src/kmers-v2/kmers-writer.H:27: - utility/src/kmers-v2/kmers-files.H:27:20: warning: nested namespace definition is a C17 extension; define each namespace separately [-Wc17-extensions] - namespace merylutil::inline kmers::v2 { - ^~~~~~~~~~~~~~~~~~ - { inline namespace kmers { namespace v2 - utility/src/kmers-v2/kmers-files.H:27:22: warning: inline nested namespace definition is a C20 extension [-Wc20-extensions] - namespace merylutil::inline kmers::v2 { - ^ - utility/src/kmers-v2/kmers-files.H:143:36: warning: format specifies type 'unsigned long' but the argument has type 'uint64' (aka 'unsigned long long') [-Wformat] - toHex(_blockPrefix), _blockPosition, _numKmers, - ^~~~~~~~~~~~~~ - utility/src/kmers-v2/kmers-files.H:143:52: warning: format specifies type 'unsigned long' but the argument has type 'uint64' (aka 'unsigned long long') [-Wformat] - toHex(_blockPrefix), _blockPosition, _numKmers, - ^~~~~~~~~ - utility/src/kmers-v2/kmers-files.H:144:15: warning: format specifies type 'unsigned long' but the argument has type 'off_t' (aka 'long long') [-Wformat] - merylutil::ftell(F), _numKmers nKmers); - ^~~~~~~~~~~~~~~~~~~ - utility/src/kmers-v2/kmers-files.H:144:36: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] - merylutil::ftell(F), _numKmers nKmers); - ^~~~~~~~~~~~~~~~~~ - In file included from meryl/meryl.C:19: - In file included from meryl/meryl.H:22: - In file included from meryl/merylInput.H:23: - In file included from utility/src/kmers.H:51: - In file included from utility/src/kmers-v2/kmers-writer.H:28: - utility/src/kmers-v2/kmers-writer-block.H:32:20: warning: nested namespace definition is a C17 extension; define each namespace separately [-Wc17-extensions] - namespace merylutil::inline kmers::v2 { - ^~~~~~~~~~~~~~~~~~ - { inline namespace kmers { namespace v2 - utility/src/kmers-v2/kmers-writer-block.H:32:22: warning: inline nested namespace definition is a C20 extension [-Wc20-extensions] - namespace merylutil::inline kmers::v2 { - ^ - In file included from meryl/meryl.C:19: - In file included from meryl/meryl.H:22: - In file included from meryl/merylInput.H:23: - In file included from utility/src/kmers.H:51: - In file included from utility/src/kmers-v2/kmers-writer.H:29: - utility/src/kmers-v2/kmers-writer-stream.H:27:20: warning: nested namespace definition is a C17 extension; define each namespace separately [-Wc17-extensions] - namespace merylutil::inline kmers::v2 { - ^~~~~~~~~~~~~~~~~~ - { inline namespace kmers { namespace v2 - utility/src/kmers-v2/kmers-writer-stream.H:27:22: warning: inline nested namespace definition is a C20 extension [-Wc20-extensions] - namespace merylutil::inline kmers::v2 { - ^ - In file included from meryl/meryl.C:19: - In file included from meryl/meryl.H:22: - In file included from meryl/merylInput.H:23: - In file included from utility/src/kmers.H:51: - utility/src/kmers-v2/kmers-writer.H:31:20: warning: nested namespace definition is a C17 extension; define each namespace separately [-Wc17-extensions] - namespace merylutil::inline kmers::v2 { - ^~~~~~~~~~~~~~~~~~ - { inline namespace kmers { namespace v2 - utility/src/kmers-v2/kmers-writer.H:31:22: warning: inline nested namespace definition is a C20 extension [-Wc20-extensions] - namespace merylutil::inline kmers::v2 { - ^ - In file included from meryl/meryl.C:19: - In file included from meryl/meryl.H:22: - In file included from meryl/merylInput.H:23: - In file included from utility/src/kmers.H:52: - utility/src/kmers-v2/kmers-reader.H:27:20: warning: nested namespace definition is a C17 extension; define each namespace separately [-Wc17-extensions] - namespace merylutil::inline kmers::v2 { - ^~~~~~~~~~~~~~~~~~ - { inline namespace kmers { namespace v2 - utility/src/kmers-v2/kmers-reader.H:27:22: warning: inline nested namespace definition is a C20 extension [-Wc20-extensions] - namespace merylutil::inline kmers::v2 { - ^ - In file included from meryl/meryl.C:19: - In file included from meryl/meryl.H:22: - In file included from meryl/merylInput.H:23: - In file included from utility/src/kmers.H:55: - utility/src/kmers-v2/kmers-lookup.H:30:20: warning: nested namespace definition is a C17 extension; define each namespace separately [-Wc17-extensions] - namespace merylutil::inline kmers::v2 { - ^~~~~~~~~~~~~~~~~~ - { inline namespace kmers { namespace v2 - utility/src/kmers-v2/kmers-lookup.H:30:22: warning: inline nested namespace definition is a C20 extension [-Wc20-extensions] - namespace merylutil::inline kmers::v2 { - ^ - 103 warnings generated. - make: Leaving directory '$SRC_DIR/src' - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/meryl_1689693773712/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/moods/build_failure.osx-64.yaml b/recipes/moods/build_failure.osx-64.yaml deleted file mode 100644 index df0004b00581b..0000000000000 --- a/recipes/moods/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 85b12909a78e1bdae24bdf224f6202087b7343518d4e71f8e94bbb76b3837ca1 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - libcxx: 16.0.4-hd57cbcb_0 conda-forge - libiconv: 1.17-hac89ed1_0 conda-forge - libllvm15: 15.0.7-he4b1e75_2 conda-forge - libxml2: 2.11.4-hd95e348_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - llvm-tools: 15.0.7-he4b1e75_2 conda-forge - openssl: 3.1.0-h8a1eda9_3 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.2-hbc0c0cd_6 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: MOODS-python-1.9.4.1_7fd4d634bc.tar.gz - Downloading https://github.com/jhkorhonen/MOODS/releases/download/v1.9.4.1/MOODS-python-1.9.4.1.tar.gz - INFO:conda_build.source:Downloading source to cache: MOODS-python-1.9.4.1_7fd4d634bc.tar.gz - INFO:conda_build.source:Downloading https://github.com/jhkorhonen/MOODS/releases/download/v1.9.4.1/MOODS-python-1.9.4.1.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/moods_1685353906262/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/moods_1685353906262/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/moods_1685353906262/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/moods_1685353906262/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/moods-1.9.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/moods-1.9.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/moods-1.9.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/moods-1.9.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - patching file setup.py - Hunk #1 succeeded at 8 with fuzz 2 (offset 1 line). - Traceback (most recent call last): - File "setup.py", line 7, in - from setuptools import setup, Extension - ModuleNotFoundError: No module named 'setuptools' - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/moods_1685353906262/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/pairix/build_failure.osx-64.yaml b/recipes/pairix/build_failure.osx-64.yaml deleted file mode 100644 index 919f523e493c3..0000000000000 --- a/recipes/pairix/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 171fe0735fef1a9e10a803aefb6b400f711ced35e2783b546dd36d6aeae21f7f # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - int dim = ti_get_sc2(idx)1==0?1:2; - ^~~ - ./pairix.h:209:36: note: passing argument to parameter 'idx' here - int ti_get_sc2(ti_index_t *idx); - ^ - index.c:1219:17: warning: initializing 'char **' with an expression of type 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] - char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list); - ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - index.c:1236:59: warning: passing 'char **' to parameter of type 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] - sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list); - ^~~~~~~ - ./pairix.h:131:73: note: passing argument to parameter 'regs' here - sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs); - ^ - index.c:1242:23: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] - *sp=0; char *chr1 = reg; - ^ ~~~ - index.c:1246:17: warning: initializing 'char **' with an expression of type 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] - char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list); - ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - index.c:1263:59: warning: passing 'char **' to parameter of type 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] - sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list); - ^~~~~~~ - ./pairix.h:131:73: note: passing argument to parameter 'regs' here - sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs); - ^ - index.c:1417:24: error: incompatible pointer to integer conversion returning 'ti_iter_t' (aka 'struct __ti_iter_t *') from a function with result type 'int' [-Wint-conversion] - if (name == 0) return ti_iter_first(); - ^~~~~~~~~~~~~~~ - index.c:1469:20: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] - if( miter->iu = calloc(n,sizeof(iter_unit*))) { - ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - index.c:1469:20: note: place parentheses around the assignment to silence this warning - if( miter->iu = calloc(n,sizeof(iter_unit*))) { - ^ - ( ) - index.c:1469:20: note: use '==' to turn this assignment into an equality comparison - if( miter->iu = calloc(n,sizeof(iter_unit*))) { - ^ - == - index.c:1537:19: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] - miu[i]->s = ti_iter_read(miu[i]->t->fp, miu[i]->iter, miu[i]->len, seqonly); - ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - index.c:1543:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] - miu[0]->s = ti_iter_read(miu[0]->t->fp, miu[0]->iter, miu[0]->len, seqonly); // get next entry for the flushed iter - ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - index.c:1573:11: warning: initializing 'char *' with an expression of type 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] - char *s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0); - ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - index.c:1576:9: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] - s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0); - ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - index.c:1643:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] - seqnames = ti_seqname(tbs[i]->idx,&len); - ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - index.c:1911:34: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] - char *reg2 = flip_region(reg, get_region_split_character(tb)); - ^~~ - index.c:1743:27: note: passing argument to parameter 's' here - char *flip_region ( char* s, char region_split_character) { - ^ - index.c:1971:12: warning: initializing 'char **' with an expression of type 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] - char **seqnames = ti_seqname(idx,&len); - ^ ~~~~~~~~~~~~~~~~~~~~ - index.c:1977:64: warning: passing 'const char *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] - if(ti_get_tid(idx, reg2)!=-1) { free(seqnames); free(reg2); return(0); } // not a triangle - ^~~~ - /Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/stdlib.h:143:18: note: passing argument to parameter here - void free(void *); - ^ - index.c:1978:14: warning: passing 'const char *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] - free(reg2); - ^~~~ - /Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/stdlib.h:143:18: note: passing argument to parameter here - void free(void *); - ^ - 18 warnings and 1 error generated. - make[2]: *** [Makefile:15: index.o] Error 1 - make[2]: Leaving directory '$SRC_DIR/src' - make[1]: *** [Makefile:18: all-recur] Error 1 - make[1]: Leaving directory '$SRC_DIR/src' - cp: bin/pairix: No such file or directory - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/pairix_1685394139065/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/pyrodigal/build_failure.osx-64.yaml b/recipes/pyrodigal/build_failure.osx-64.yaml deleted file mode 100644 index 4f9f326f71367..0000000000000 --- a/recipes/pyrodigal/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: a0eea3e712441dfcfc57db816b9d49d5e2eb5ea661ee696199d496549d6919c2 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #2 - {} is not a Mach-O file - Can't parse the binary at the index #3 - {} is not a Mach-O file - Can't parse the binary at the index #4 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #2 - {} is not a Mach-O file - Can't parse the binary at the index #3 - {} is not a Mach-O file - Can't parse the binary at the index #4 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/en.lproj/InfoPlist.strings', 'vmnet.framework/Versions/A/Resources/Info.plist']' - INFO: sysroot: '/usr/lib/' files: '['zsh/5.8.1/zsh/zselect.so', 'zsh/5.8.1/zsh/zpty.so', 'zsh/5.8.1/zsh/zprof.so', 'zsh/5.8.1/zsh/zleparameter.so']' - INFO: sysroot: '/opt/X11/' files: '[]' - INFO (pyrodigal,lib/python3.10/site-packages/pyrodigal/_pyrodigal.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - WARNING (pyrodigal): interpreter (Python) package conda-forge::python-3.10.11-he7542f4_0_cpython in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) - WARNING (pyrodigal): interpreted library (Python) package conda-forge::setuptools-67.7.2-pyhd8ed1ab_0 in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) - Fixing permissions - Packaged license file/s. - INFO :: Time taken to mark (prefix) - 0 replacements in 0 files was 0.10 seconds - Files containing CONDA_PREFIX - ----------------------------- - bin/pyrodigal (text): Patching - TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/pyrodigal-2.1.0-py310he07d9a1_3.tar.bz2 - Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/work' to '/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/work_moved_pyrodigal-2.1.0-py310he07d9a1_3_osx-64' - shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/work_moved_pyrodigal-2.1.0-py310he07d9a1_3_osx-64) - INFO:conda_build.utils:Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/work' to '/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/work_moved_pyrodigal-2.1.0-py310he07d9a1_3_osx-64' - INFO:conda_build.utils:shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/work_moved_pyrodigal-2.1.0-py310he07d9a1_3_osx-64) - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold - - - The following NEW packages will be INSTALLED: - - bzip2: 1.0.8-h0d85af4_4 conda-forge - ca-certificates: 2023.5.7-h8857fd0_0 conda-forge - libffi: 3.4.2-h0d85af4_5 conda-forge - libsqlite: 3.42.0-h58db7d2_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - ncurses: 6.3-h96cf925_1 conda-forge - openssl: 3.1.0-h8a1eda9_3 conda-forge - pyrodigal: 2.1.0-py310he07d9a1_3 local - python: 3.10.11-he7542f4_0_cpython conda-forge - python_abi: 3.10-3_cp310 conda-forge - readline: 8.2-h9e318b2_1 conda-forge - setuptools: 67.7.2-pyhd8ed1ab_0 conda-forge - tk: 8.6.12-h5dbffcc_0 conda-forge - tzdata: 2023c-h71feb2d_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/test_tmp - import: 'pyrodigal' - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/test_tmp/run_test.py", line 2, in - import pyrodigal - File "/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.10/site-packages/pyrodigal/__init__.py", line 8, in - from . import _pyrodigal - ImportError: dlopen(/opt/mambaforge/envs/bioconda/conda-bld/pyrodigal_1685394321921/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.10/site-packages/pyrodigal/_pyrodigal.cpython-310-darwin.so, 0x0002): symbol not found in flat namespace (_GetX86Info) - Tests failed for pyrodigal-2.1.0-py310he07d9a1_3.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken - WARNING:conda_build.build:Tests failed for pyrodigal-2.1.0-py310he07d9a1_3.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken - TESTS FAILED: pyrodigal-2.1.0-py310he07d9a1_3.tar.bz2 -# Last 100 lines of the build log. diff --git a/recipes/quast/build_failure.osx-64.yaml b/recipes/quast/build_failure.osx-64.yaml deleted file mode 100644 index a7c6bce3f464b..0000000000000 --- a/recipes/quast/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 8237e906909f841e6f9591915ec9d3c10a947f897db59de841e5405f1d688b92 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - adding 'quast_libs/minimap2/python/cmappy.h' - INFO adding 'quast_libs/minimap2/python/cmappy.pxd' - adding 'quast_libs/minimap2/python/cmappy.pxd' - INFO adding 'quast_libs/minimap2/python/mappy.pyx' - adding 'quast_libs/minimap2/python/mappy.pyx' - INFO adding 'quast_libs/minimap2/python/minimap2.py' - adding 'quast_libs/minimap2/python/minimap2.py' - INFO adding 'quast_libs/minimap2/sse2neon/emmintrin.h' - adding 'quast_libs/minimap2/sse2neon/emmintrin.h' - INFO adding 'quast_libs/ra_utils/__init__.py' - adding 'quast_libs/ra_utils/__init__.py' - INFO adding 'quast_libs/ra_utils/argparse.py' - adding 'quast_libs/ra_utils/argparse.py' - INFO adding 'quast_libs/ra_utils/misc.py' - adding 'quast_libs/ra_utils/misc.py' - INFO adding 'quast_libs/ra_utils/vcfToBedpe.py' - adding 'quast_libs/ra_utils/vcfToBedpe.py' - INFO adding 'quast_libs/sambamba/sambamba_linux' - adding 'quast_libs/sambamba/sambamba_linux' - INFO adding 'quast_libs/sambamba/sambamba_osx' - adding 'quast_libs/sambamba/sambamba_osx' - INFO adding 'quast_libs/site_packages/__init__.py' - adding 'quast_libs/site_packages/__init__.py' - INFO adding 'quast_libs/site_packages/_bz2.py' - adding 'quast_libs/site_packages/_bz2.py' - INFO adding 'quast_libs/site_packages/_compression.py' - adding 'quast_libs/site_packages/_compression.py' - INFO adding 'quast_libs/site_packages/bz2.py' - adding 'quast_libs/site_packages/bz2.py' - INFO adding 'quast_libs/site_packages/ordered_dict.py' - adding 'quast_libs/site_packages/ordered_dict.py' - INFO adding 'quast_libs/site_packages/jsontemplate/__init__.py' - adding 'quast_libs/site_packages/jsontemplate/__init__.py' - INFO adding 'quast_libs/site_packages/jsontemplate/jsontemplate.py' - adding 'quast_libs/site_packages/jsontemplate/jsontemplate.py' - INFO adding 'quast-5.2.0.dist-info/LICENSE.txt' - adding 'quast-5.2.0.dist-info/LICENSE.txt' - INFO adding 'quast-5.2.0.dist-info/METADATA' - adding 'quast-5.2.0.dist-info/METADATA' - INFO adding 'quast-5.2.0.dist-info/WHEEL' - adding 'quast-5.2.0.dist-info/WHEEL' - INFO adding 'quast-5.2.0.dist-info/top_level.txt' - adding 'quast-5.2.0.dist-info/top_level.txt' - INFO adding 'quast-5.2.0.dist-info/RECORD' - adding 'quast-5.2.0.dist-info/RECORD' - INFO removing build/bdist.macosx-10.9-x86_64/wheel - removing build/bdist.macosx-10.9-x86_64/wheel - Building wheel for quast (setup.py): finished with status 'done' - Created wheel for quast: filename=quast-5.2.0-py3-none-any.whl size=12996553 sha256=95ee42f38e8b80a8659a77f57f83ff38db5e44342ae493a3b085160b7df6396f - Stored in directory: /private/tmp/pip-ephem-wheel-cache-2t0etpfr/wheels/5f/48/0f/e9fc35a974c2af5e84beac3740c829770b288236193c061309 - Successfully built quast - Installing collected packages: quast - - Successfully installed quast-5.2.0 - Removed build tracker: '/private/tmp/pip-build-tracker-gi2wl7cm' - tail: /opt/mambaforge/envs/bioconda/conda-bld/quast_1685395312261/work/quast_libs/*/make.*: No such file or directory - - Resource usage statistics from building quast: - Process count: 4 - CPU time: Sys=0:00:02.5, User=0:00:05.3 - Memory: 97.0M - Disk usage: 452.0K - Time elapsed: 0:00:17.0 - - - compiling .pyc files... - number of files: 929 - Making absolute symlink relative (bin/quast -> /opt/mambaforge/envs/bioconda/conda-bld/quast_1685395312261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/opt/quast-5.2.0/quast.py :-> ../opt/quast-5.2.0/quast.py) - Making absolute symlink relative (bin/metaquast -> /opt/mambaforge/envs/bioconda/conda-bld/quast_1685395312261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/opt/quast-5.2.0/metaquast.py :-> ../opt/quast-5.2.0/metaquast.py) - Making absolute symlink relative (opt/quast-5.2.0/quast_libs -> /opt/mambaforge/envs/bioconda/conda-bld/quast_1685395312261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.8/site-packages/quast_libs :-> ../../lib/python3.8/site-packages/quast_libs) - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build - newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 1659, in bundle_conda - files = post_process_files(metadata, initial_files) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 1505, in post_process_files - post_build(m, new_files, build_python=python) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/post.py", line 1318, in post_build - post_process_shared_lib(m, f, prefix_files, host_prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/post.py", line 1266, in post_process_shared_lib - mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/post.py", line 397, in mk_relative_osx - names = macho.otool(path, prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/os_utils/macho.py", line 194, in otool - lines = check_output([otool, '-l', path], - File "/opt/mambaforge/envs/bioconda/lib/python3.8/subprocess.py", line 415, in check_output - return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/subprocess.py", line 516, in run - raise CalledProcessError(retcode, process.args, - subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/quast_1685395312261/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/quast_1685395312261/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.8/site-packages/quast_libs/sambamba/sambamba_osx']' died with . -# Last 100 lines of the build log. diff --git a/recipes/sra-tools/build_failure.linux-64.yaml b/recipes/sra-tools/build_failure.linux-64.yaml deleted file mode 100644 index 7d780860f3697..0000000000000 --- a/recipes/sra-tools/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 74068ce82e029b1de83b1336a271611bb232a4f1c51434eb8bb0c9b87a402e99 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/sra-pileup/sam-dump.c: In function 'DumpCGSAM.part.0': - /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/sra-pileup/sam-dump.c:2457:40: warning: 'last_cig_op' may be used uninitialized in this function [-Wmaybe-uninitialized] - 2457 | ciglen = last_ciglen sprintf(dstlast_ciglen,"%d%c",last_cig_oplen,last_cig_op); \ - | ^~~~~~~ - /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/sra-pileup/sam-dump.c:2445:14: note: 'last_cig_op' was declared here - 2445 | char last_cig_op; - | ^~~~~~~~~~~ - [ 68%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump3.c.o - /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/sra-pileup/sam-dump3.c: In function 'KMain': - /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/sra-pileup/sam-dump3.c:510:10: warning: 'mode' may be used uninitialized in this function [-Wmaybe-uninitialized] - 510 | rc = init_out_redir( &redir, mode, opts->outputfile, opts->output_buffer_size ); /* from out_redir.c */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/sra-pileup/sam-dump3.c:502:25: note: 'mode' was declared here - 502 | enum out_redir_mode mode; - | ^~~~ - [ 68%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o - [ 69%] Linking C executable ../../../bin/sam-dump - [ 69%] Built target sam-dump - [ 70%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/helper.c.o - [ 70%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o - [ 70%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o - [ 71%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o - [ 71%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/inspector.c.o - [ 71%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sbuffer.c.o - [ 71%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/err_msg.c.o - [ 72%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_tools.c.o - [ 72%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/var_fmt.c.o - [ 72%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/flex_printer.c.o - [ 72%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_dir.c.o - [ 73%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o - [ 73%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cleanup_task.c.o - [ 73%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/index.c.o - [ 74%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_writer.c.o - [ 74%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_reader.c.o - [ 74%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_file_list.c.o - [ 74%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_value.c.o - [ 75%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_printer.c.o - [ 75%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/merge_sorter.c.o - [ 75%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sorter.c.o - [ 76%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cmn_iter.c.o - [ 76%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o - [ 76%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/special_iter.c.o - [ 76%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fastq_iter.c.o - [ 77%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/db_join.c.o - [ 77%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tbl_join.c.o - [ 77%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_registry.c.o - [ 77%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/copy_machine.c.o - [ 78%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/concatenator.c.o - [ 78%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o - [ 78%] Linking C executable ../../../bin/fasterq-dump - [ 78%] Built target fasterq-dump - [ 79%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o - [ 79%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o - [ 79%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o - In file included from /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/vdb-dump/vdb-dump-tools.c:41: - /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/vdb-dump/vdb-dump-tools.c: In function 'vdt_dump_float_element': - /opt/conda/conda-bld/sra-tools_1685393115370/_build_env/include/cc/gcc/x86_64/bitstr.h:35:20: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] - 35 | #define BSWAP( x ) bswap_32 ( x ) - | ^~~~~~~~ - /opt/conda/conda-bld/sra-tools_1685393115370/_build_env/include/cc/gcc/x86_64/bitstr.h:35:20: warning: 'value' may be used uninitialized in this function [-Wmaybe-uninitialized] - /opt/conda/conda-bld/sra-tools_1685393115370/_build_env/include/cc/gcc/x86_64/bitstr.h:35:20: warning: '*((void *)&value4)' may be used uninitialized in this function [-Wmaybe-uninitialized] - [ 79%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o - [ 80%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o - [ 80%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o - [ 80%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o - [ 80%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o - [ 81%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb_info.c.o - [ 81%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump.c.o - [ 81%] Linking C executable ../../../bin/vdb-dump - [ 81%] Built target vdb-dump - [ 81%] Building C object tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/vdb-validate.c.o - /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/vdb-validate/vdb-validate.c: In function 'kdbcc': - /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/vdb-validate/vdb-validate.c:410:18: error: too many arguments to function 'KTableConsistencyCheck' - 410 | rc = KTableConsistencyCheck ( tbl, 0, level, report, & ctx, platform ); - | ^~~~~~~~~~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/sra-tools_1685393115370/work/sra-tools/tools/external/vdb-validate/vdb-validate.c:41: - /opt/conda/conda-bld/sra-tools_1685393115370/_build_env/include/kdb/consistency-check.h:126:20: note: declared here - 126 | KDB_EXTERN rc_t CC KTableConsistencyCheck ( struct KTable const *self, - | ^~~~~~~~~~~~~~~~~~~~~~ - make[2]: *** [tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/build.make:76: tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/vdb-validate.c.o] Error 1 - make[1]: *** [CMakeFiles/Makefile2:2495: tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/all] Error 2 - make: *** [Makefile:166: all] Error 2 - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/sra-tools_1685393115370/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/tidyp/build_failure.linux-64.yaml b/recipes/tidyp/build_failure.linux-64.yaml deleted file mode 100644 index f3772fe0477fb..0000000000000 --- a/recipes/tidyp/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 5f54a99372501e5b639643248f525296d6bb59524021c5ff02d871c634b5787a # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - - environment location: /opt/conda/conda-bld/tidyp_1685392106059/_build_env - - - The following NEW packages will be INSTALLED: - - _libgcc_mutex: 0.1-conda_forge conda-forge - _openmp_mutex: 4.5-2_gnu conda-forge - binutils_impl_linux-64: 2.39-he00db2b_1 conda-forge - binutils_linux-64: 2.39-h5fc0e48_13 conda-forge - gcc_impl_linux-64: 12.2.0-hcc96c02_19 conda-forge - gcc_linux-64: 12.2.0-h4798a0e_13 conda-forge - kernel-headers_linux-64: 2.6.32-he073ed8_15 conda-forge - ld_impl_linux-64: 2.39-hcc3a1bd_1 conda-forge - libgcc-devel_linux-64: 12.2.0-h3b97bd3_19 conda-forge - libgcc-ng: 12.2.0-h65d4601_19 conda-forge - libgomp: 12.2.0-h65d4601_19 conda-forge - libsanitizer: 12.2.0-h46fd767_19 conda-forge - libstdcxx-ng: 12.2.0-h46fd767_19 conda-forge - make: 4.3-hd18ef5c_1 conda-forge - sysroot_linux-64: 2.12-he073ed8_15 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/conda/conda-bld/src_cache - INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache - Downloading source to cache: 1.04_5f09650411.tar.gz - INFO:conda_build.source:Downloading source to cache: 1.04_5f09650411.tar.gz - Downloading https://github.com/petdance/tidyp/archive/refs/tags/1.04.tar.gz - INFO:conda_build.source:Downloading https://github.com/petdance/tidyp/archive/refs/tags/1.04.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/conda/conda-bld/tidyp_1685392106059/work - export PREFIX=/opt/conda/conda-bld/tidyp_1685392106059/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - export BUILD_PREFIX=/opt/conda/conda-bld/tidyp_1685392106059/_build_env - export SRC_DIR=/opt/conda/conda-bld/tidyp_1685392106059/work - INFO: activate-binutils_linux-64.sh made the following environmental changes: - ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line - AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar - AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as - CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt - ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit - GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof - LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld - LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold - NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm - OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy - OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump - RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib - READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf - SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size - STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings - STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip - INFO: activate-gcc_linux-64.sh made the following environmental changes: - BUILD=x86_64-conda-linux-gnu - CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tidyp-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr - CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot - CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu - CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu - CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp - CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include - DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tidyp-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include - GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc - GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar - GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm - GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib - HOST=x86_64-conda-linux-gnu - LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu - build_alias=x86_64-conda-linux-gnu - host_alias=x86_64-conda-linux-gnu - -BUILD=x86_64-conda_cos6-linux-gnu - -CONDA_BUILD_SYSROOT= - /opt/conda/conda-bld/tidyp_1685392106059/work/conda_build.sh: line 8: ./configure: No such file or directory - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/tidyp_1685392106059/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/tidyp/build_failure.osx-64.yaml b/recipes/tidyp/build_failure.osx-64.yaml deleted file mode 100644 index 030a7aa9ec7f5..0000000000000 --- a/recipes/tidyp/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 5f54a99372501e5b639643248f525296d6bb59524021c5ff02d871c634b5787a # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - cctools_osx-64: 973.0.1-h48a5a9d_13 conda-forge - clang: 15.0.7-h694c41f_2 conda-forge - clang-15: 15.0.7-default_hdb78580_2 conda-forge - clang_osx-64: 15.0.7-h03d6864_3 conda-forge - clangxx: 15.0.7-default_hdb78580_2 conda-forge - compiler-rt: 15.0.7-he1888fc_1 conda-forge - compiler-rt_osx-64: 15.0.7-he1888fc_1 conda-forge - icu: 72.1-h7336db1_0 conda-forge - ld64_osx-64: 609-h8ce0179_13 conda-forge - libclang-cpp15: 15.0.7-default_hdb78580_2 conda-forge - libcxx: 16.0.4-hd57cbcb_0 conda-forge - libiconv: 1.17-hac89ed1_0 conda-forge - libllvm15: 15.0.7-he4b1e75_2 conda-forge - libxml2: 2.11.4-hd95e348_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - llvm-tools: 15.0.7-he4b1e75_2 conda-forge - make: 4.3-h22f3db7_1 conda-forge - openssl: 3.1.0-h8a1eda9_3 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.2-hbc0c0cd_6 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Downloading source to cache: 1.04_5f09650411.tar.gz - INFO:conda_build.source:Downloading https://github.com/petdance/tidyp/archive/refs/tags/1.04.tar.gz - Downloading source to cache: 1.04_5f09650411.tar.gz - Downloading https://github.com/petdance/tidyp/archive/refs/tags/1.04.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/tidyp_1685382282834/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/tidyp_1685382282834/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/tidyp_1685382282834/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/tidyp_1685382282834/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tidyp-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tidyp-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - /opt/mambaforge/envs/bioconda/conda-bld/tidyp_1685382282834/work/conda_build.sh: line 8: ./configure: No such file or directory - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/tidyp_1685382282834/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. From 1907180f8e6bcf05d98505cb78d2486502a97540 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Apr 2024 22:21:21 -0400 Subject: [PATCH 1415/1813] Update clair3-illumina to 1.0.7 (#47036) * Update clair3-illumina to 1.0.7 * try pinning snippy to <1.2.0 * fix meta.yaml formatting * remove snippy pinning --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/clair3-illumina/build.sh | 4 ---- recipes/clair3-illumina/meta.yaml | 14 +++++++++++--- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/recipes/clair3-illumina/build.sh b/recipes/clair3-illumina/build.sh index 91ce406b0b6f3..63c71150a4330 100755 --- a/recipes/clair3-illumina/build.sh +++ b/recipes/clair3-illumina/build.sh @@ -5,7 +5,3 @@ cp -rv preprocess/realign $PREFIX/bin/preprocess cd $PREFIX/bin/preprocess/realign $CXX -std=c++14 -O1 -shared -fPIC -o realigner ssw_cpp.cpp ssw.c realigner.cpp $CXX -std=c++11 -shared -fPIC -o debruijn_graph -O3 debruijn_graph.cpp -I $PREFIX/include -L $PREFIX/lib - - - - diff --git a/recipes/clair3-illumina/meta.yaml b/recipes/clair3-illumina/meta.yaml index 468c6582e9270..08b0896dac355 100644 --- a/recipes/clair3-illumina/meta.yaml +++ b/recipes/clair3-illumina/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clair3-illumina" %} -{% set version = "1.0.6" %} +{% set version = "1.0.7" %} package: name: {{ name }} @@ -7,13 +7,14 @@ package: source: url: https://github.com/HKU-BAL/Clair3/archive/refs/tags/v{{ version }}.zip - sha256: 30821ae909e4d28d5ca01594873b7977690cc2e63f5777b5d6799ec86660e370 + sha256: 4c48146a1a9c0af547444719f443f8f536f5ce51b2f0c426107ef4288b31a4f2 build: number: 0 skip: True # [osx] run_exports: - - {{ pin_subpackage(name, max_pin="x.x") }} + - {{ pin_subpackage(name, max_pin="x") }} + requirements: build: - {{ compiler('cxx') }} @@ -21,6 +22,7 @@ requirements: - boost-cpp run: - clair3 + test: imports: - tensorflow @@ -31,5 +33,11 @@ test: about: home: 'https://github.com/HKU-BAL/Clair3' license: BSD-3-Clause + license_family: BSD license_file: LICENSE.md summary: "Clair3 with libraries to support variant calling using Illumina short-reads. Version in sync with Clair3." + dev_url: 'https://github.com/HKU-BAL/Clair3' + +extra: + identifiers: + - doi:10.1038/s43588-022-00387-x From 624f6b9664dea76b76b776edd8bb8ea91627ee8e Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 12:05:15 +0300 Subject: [PATCH 1416/1813] gmap: add linux-aarch64 build (#47092) * gmap: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Set SIMD level per CPU architecture Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/gmap/build.sh | 14 +++++++++++++- recipes/gmap/meta.yaml | 4 +++- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/recipes/gmap/build.sh b/recipes/gmap/build.sh index 2597b241bce1d..297d0e9a4c1d1 100644 --- a/recipes/gmap/build.sh +++ b/recipes/gmap/build.sh @@ -16,13 +16,25 @@ export LANGUAGE=en_US.UTF-8 export LANG=en_US.UTF-8 export LC_ALL=en_US.UTF-8 +case $(uname -m) in + x86_64) + SIMD_LEVEL="sse42" + ;; + aarch64) + SIMD_LEVEL="arm" + ;; + *) + SIMD_LEVEL="none" + ;; +esac + autoreconf -if ./configure CC="${CC}" CFLAGS="${CFLAGS}" \ CPPFLAGS="${CPPFLAGS}" \ LDFLAGS="${LDFLAGS}" \ --prefix="${PREFIX}" \ --with-gmapdb="${PREFIX}/share" \ - --with-simd-level=sse42 + --with-simd-level=${SIMD_LEVEL} make -j"${CPU_COUNT}" make install diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index 89862ec6db554..be517e1caa9e2 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -13,7 +13,7 @@ source: - single_quote_paths.patch build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('gmap', max_pin=None) }} @@ -46,6 +46,8 @@ about: summary: "Genomic mapping and alignment program for mRNA and EST sequences." extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:gmap - biotools:gsnap From 1e0a608d64b5f6e1b21c6f30ca7bde5f11df51ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 06:32:26 -0400 Subject: [PATCH 1417/1813] Update atlas-gene-annotation-manipulation to 1.1.1 (#47099) * Update atlas-gene-annotation-manipulation to 1.1.1 * Update meta.yaml --------- Co-authored-by: Jonathan Manning --- recipes/atlas-gene-annotation-manipulation/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/atlas-gene-annotation-manipulation/meta.yaml b/recipes/atlas-gene-annotation-manipulation/meta.yaml index 78ccb7f53235b..b950a1054c28a 100644 --- a/recipes/atlas-gene-annotation-manipulation/meta.yaml +++ b/recipes/atlas-gene-annotation-manipulation/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.0" %} +{% set version = "1.1.1" %} package: name: atlas-gene-annotation-manipulation @@ -6,11 +6,13 @@ package: source: url: https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation/archive/v{{ version }}.tar.gz - sha256: 402b8a93a0bcab374c51d24048149b80e3fd7d1d78e6c8c93ca22804d06c59df + sha256: 25df8b43bbdacd7b05534ccae818cc290c1c5159c4d67cc0dafe52050c681480 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage("atlas-gene-annotation-manipulation", max_pin="x") }} requirements: build: From 8d438ef113078e1ef7c9badfc52dd74e1d2ef86e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 07:57:46 -0400 Subject: [PATCH 1418/1813] Update scirpy to 0.16.1 (#47100) --- recipes/scirpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml index fd3cf450186d3..31113a54a3a49 100644 --- a/recipes/scirpy/meta.yaml +++ b/recipes/scirpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scirpy" %} -{% set version = "0.16.0" %} +{% set version = "0.16.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 169d71fcb26da1adac33be0e30541eb09ed9ae32d484f16a194c2fa07bf9a4fb + sha256: b8e5697184c79b6d526bb42f5ce5c5cfd03b827770eaf64aa71a8ba876e6a3f2 folder: "{{ name }}-{{ version }}" build: From a33f6a9095f27487cc09fb9f42abca75a8bbca04 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 10:19:48 -0400 Subject: [PATCH 1419/1813] Update crisprme to 2.1.4 (#47106) --- recipes/crisprme/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/crisprme/meta.yaml b/recipes/crisprme/meta.yaml index 2bb063589ecf3..6997ee9a682b8 100644 --- a/recipes/crisprme/meta.yaml +++ b/recipes/crisprme/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.1.3" %} +{% set version = "2.1.4" %} package: name: crisprme @@ -6,7 +6,7 @@ package: source: url: https://github.com/pinellolab/CRISPRme/archive/refs/tags/v{{ version }}.tar.gz - sha256: f4542accbbf26d4568212e88f7469fec06a8a8c6b52f884160e741d4e9d8bab0 + sha256: a2d8d374365ba90eeb81548b16b589f23bc9ee184cca447306efc12b3d1a97f8 build: run_exports: From 1989b6ed036112e6812e3bbf3a7b5b0744d6d01f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 10:20:00 -0400 Subject: [PATCH 1420/1813] Update checkatlas to 0.4.13 (#47102) --- recipes/checkatlas/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/checkatlas/meta.yaml b/recipes/checkatlas/meta.yaml index 19464db4eb5b7..10e1c40dced61 100644 --- a/recipes/checkatlas/meta.yaml +++ b/recipes/checkatlas/meta.yaml @@ -1,5 +1,5 @@ {% set name = "checkatlas" %} -{% set version = "0.4.7" %} +{% set version = "0.4.13" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c18fc7014b749377db697f0b163c6913badcf99ecd523f0824f0a3fd10c78e44 + sha256: d62a2cd020e88b7142dcf43fde6a0ca7cfcd7e3a0d00343c55899dc40e477780 build: number: 0 From f3611ccd026513abf31aa2b35a145fe319cd1496 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 10:20:25 -0400 Subject: [PATCH 1421/1813] Update matchms to 0.24.3 (#47101) --- recipes/matchms/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 051eb033c05c7..83d0bdff09ba5 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.24.2" %} +{% set version = "0.24.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1fe2b241b7d07e066ee92ddf549b22d135c16634b2755aadb774855a46ff55c3 + sha256: 0ad4d4514d8f2fbd3981f0ba5e7a704261f2db4cf3af63ec42c8a2858384b509 build: number: 0 From 4ceda2f782b8f8ecb196c0b22e525aaa1a74e10c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 10:20:51 -0400 Subject: [PATCH 1422/1813] Update pybiolib to 1.1.1957 (#47093) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 882a362262ffb..52068a7224e24 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1942" %} +{% set version = "1.1.1957" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 814a66825ed4c47857f9891dff7fff75d7f6c39de94f72cbb87e09791af60a70 + sha256: f1908a5129b26ea1d91c762b7f26bbc1356c1211420da138064be60ad199fbc6 build: noarch: python From 8521d14d0c59088002e646dbb66e6ce6f305e16c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 10:21:00 -0400 Subject: [PATCH 1423/1813] Update r-tinyarray to 2.3.3 (#47088) --- recipes/r-tinyarray/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-tinyarray/meta.yaml b/recipes/r-tinyarray/meta.yaml index 2284c61513a42..2c082b48c3bfe 100644 --- a/recipes/r-tinyarray/meta.yaml +++ b/recipes/r-tinyarray/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.3.2' %} +{% set version = '2.3.3' %} package: name: r-tinyarray @@ -8,7 +8,7 @@ source: url: - {{ cran_mirror }}/src/contrib/tinyarray_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/tinyarray/tinyarray_{{ version }}.tar.gz - sha256: 32d74c2e64b88fb973a2ade4162f4a2c3ec9127d41966768301b518cdcac5654 + sha256: 85388351a5811cb6df37a20f3233ed9e1f391800d16a4d56257f1094af44eb00 build: number: 0 From df120ea85889f611f9226f5df80c45b909dfd320 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 17:42:06 +0300 Subject: [PATCH 1424/1813] csvtk: add linux-aarch64 build (#47091) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/csvtk/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/csvtk/meta.yaml b/recipes/csvtk/meta.yaml index 02ffed6b4f62e..75a19c78e343c 100644 --- a/recipes/csvtk/meta.yaml +++ b/recipes/csvtk/meta.yaml @@ -5,15 +5,17 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('csvtk', max_pin='x.x') }} source: - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx] md5: c415255e265ba0cd547806fdbda05652 # [osx] - - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux] - md5: 8f5877d4fbea89609d64bd2679956476 # [linux] + - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux and x86_64] + md5: 8f5877d4fbea89609d64bd2679956476 # [linux and x86_64] + - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_arm64.tar.gz # [linux and aarch64] + md5: 2a6dd840291d23971ff538eaf3de00ec # [linux and aarch64] test: commands: @@ -25,6 +27,8 @@ about: license: MIT extra: + additional-platforms: + - linux-aarch64 skip-lints: - should_be_noarch_generic - should_not_be_noarch_source From 1db31943ee3bf465aca31d045d7007d795f67ddb Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 17:43:04 +0300 Subject: [PATCH 1425/1813] whatshap: add linux-aarch64 build (#47089) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/whatshap/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index f8554c9bb5021..1367cf81832b3 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 4cd34e9b82930c4f42e9e6b7dce2e321e4c81f934fdb980b6093ad91a06ae30a build: - number: 0 + number: 1 script: python -m pip install --no-deps --ignore-installed . run_exports: - {{ pin_subpackage('whatshap', max_pin="x") }} @@ -46,6 +46,8 @@ about: summary: 'phase genomic variants using DNA sequencing reads (haplotype assembly)' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:whatshap - doi:10.1089/cmb.2014.0157 From 84b05a18fe0fabea4874ead2ea58385e6c6185cb Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 18:12:26 +0300 Subject: [PATCH 1426/1813] glimmerhmm: add linux-aarch64 build (#47090) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/glimmerhmm/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/glimmerhmm/meta.yaml b/recipes/glimmerhmm/meta.yaml index 627e2e08693c2..a23cc5efbff1d 100644 --- a/recipes/glimmerhmm/meta.yaml +++ b/recipes/glimmerhmm/meta.yaml @@ -7,7 +7,9 @@ source: url: https://ccb.jhu.edu/software/glimmerhmm/dl/GlimmerHMM-3.0.4.tar.gz build: - number: 6 + number: 7 + run_exports: + - {{ pin_subpackage('glimmerhmm', max_pin="x") }} requirements: build: @@ -28,3 +30,7 @@ about: home: https://ccb.jhu.edu/software/glimmerhmm/ license: Artistic License summary: "GlimmerHMM is a gene finder based on a Generalized Hidden Markov Model (GHMM)" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 1008fc26de34e2def83a2e68a5ad714eb56fe525 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=A3o=20Cavalcante?= Date: Tue, 9 Apr 2024 12:19:18 -0300 Subject: [PATCH 1427/1813] Add MicroView (#47065) * Add MicroView * fix: Update frictionless version Signed-off-by: jvfe * fix: Bump package version Signed-off-by: jvfe * fix: Change hash Signed-off-by: jvfe * fix: Add missing dependencies - decorator and cython (for scikit-bio) * chore: Update description Signed-off-by: jvfe * fix: Change cython build --------- Signed-off-by: jvfe --- recipes/microview/meta.yaml | 61 +++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 recipes/microview/meta.yaml diff --git a/recipes/microview/meta.yaml b/recipes/microview/meta.yaml new file mode 100644 index 0000000000000..592d10aab0fed --- /dev/null +++ b/recipes/microview/meta.yaml @@ -0,0 +1,61 @@ +{% set name = "microview" %} +{% set version = "0.10.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/MicroView-{{ version }}.tar.gz + sha256: c031b0c9405a2eae175d98835f4bd4ada63e0d23128b278ab146b0d3a844036a + +build: + entry_points: + - microview = microview.cli:main + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - python >=3.8 + - pip + - cython + run: + - python >=3.8 + - scipy + - cython + - decorator + - scikit-bio + - pandas + - numpy + - plotly + - jinja2 + - rich + - rich-click + - click-option-group + - frictionless >=4.32.0,<5 + +test: + imports: + - microview + commands: + - pip check + - microview --help + requires: + - pip + +about: + home: https://github.com/jvfe/microview + summary: Generate reports from taxonomic classification data + license: BSD-3-Clause + license_file: LICENSE + +extra: + skip-lints: + - cython_must_be_in_host # Cython needs to be in run as well + recipe-maintainers: + - jvfe From a118c76d409f9386da48b0dcffde0758b3edbe7d Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 18:58:45 +0300 Subject: [PATCH 1428/1813] py2bit: add linux-aarch64 build (#47098) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/py2bit/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/py2bit/meta.yaml b/recipes/py2bit/meta.yaml index d77824737670b..5938010a14d20 100644 --- a/recipes/py2bit/meta.yaml +++ b/recipes/py2bit/meta.yaml @@ -3,7 +3,9 @@ package: version: "0.3.0" build: - number: 8 + number: 9 + run_exports: + - {{ pin_subpackage('py2bit', max_pin='x.x') }} source: url: https://files.pythonhosted.org/packages/53/bb/547a927bed736ead3dc909e1e552d57c9034bb9493eff80544c0cf6e4828/py2bit-0.3.0.tar.gz @@ -27,3 +29,7 @@ about: home: https://github.com/deeptools/py2bit license: 'MIT' summary: 'A package for accessing 2bit files using lib2bit' + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 6cb5afcf88a43cad96ce397e1c2206187a88bc61 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 9 Apr 2024 18:59:02 +0300 Subject: [PATCH 1429/1813] ucsc-wigtobigwig: add linux-aarch64 build (#47096) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-wigtobigwig/htmshell.patch | 11 +++++++++++ recipes/ucsc-wigtobigwig/meta.yaml | 9 ++++++++- 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 recipes/ucsc-wigtobigwig/htmshell.patch diff --git a/recipes/ucsc-wigtobigwig/htmshell.patch b/recipes/ucsc-wigtobigwig/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-wigtobigwig/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-wigtobigwig/meta.yaml b/recipes/ucsc-wigtobigwig/meta.yaml index f5fe88a1de56b..c21b3a9bb7d40 100644 --- a/recipes/ucsc-wigtobigwig/meta.yaml +++ b/recipes/ucsc-wigtobigwig/meta.yaml @@ -12,10 +12,13 @@ source: sha256: {{ sha256 }} patches: - include.patch + - htmshell.patch build: - number: 1 + number: 2 skip: True # [osx] + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} ignore_run_exports: - libpng - libuuid @@ -48,3 +51,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "Convert ascii format wig file (in fixedStep, variableStep)" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From a5cbc693fa7a1c607fd30423d5ceedbc381b35d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 14:44:38 -0400 Subject: [PATCH 1430/1813] Update attotree to 0.1.6 (#47111) --- recipes/attotree/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/attotree/meta.yaml b/recipes/attotree/meta.yaml index 29d99d804afab..9b66f40105c9d 100644 --- a/recipes/attotree/meta.yaml +++ b/recipes/attotree/meta.yaml @@ -1,5 +1,5 @@ {% set name = "attotree" %} -{% set version = "0.1.4" %} +{% set version = "0.1.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b38356b589b6b32e45e8a091ba6c261a0dc511ee74d8b591089e82d9396f98ac + sha256: 9794d2051c007e2e2f38cae53492c2c17b74e6cde2ee5859a8b051dbd65f3a78 build: number: 0 From db8cf4d4aa200889d96469fc1507fe3717d412d2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 14:44:49 -0400 Subject: [PATCH 1431/1813] Update trust4 to 1.1.0 (#47109) --- recipes/trust4/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/trust4/meta.yaml b/recipes/trust4/meta.yaml index 247cf09d8e388..476da155b5c9f 100644 --- a/recipes/trust4/meta.yaml +++ b/recipes/trust4/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.14" %} +{% set version = "1.1.0" %} package: name: trust4 @@ -11,7 +11,7 @@ build: source: url: https://github.com/liulab-dfci/TRUST4/archive/v{{ version }}.tar.gz - sha256: cea1e06976ee3887ba1bd56b6ca86864f7f136076087c7b5c52727ada66f5dfd + sha256: dfb08a2d08badad0d865917d0b034a5bc8db089627157a02b335c28a9500b5ef requirements: build: From 51699ba90a9f81ca083b1124cb49d7ac83ae860b Mon Sep 17 00:00:00 2001 From: Yasas Wijesekara <34155351+Yasas1994@users.noreply.github.com> Date: Tue, 9 Apr 2024 21:16:09 +0200 Subject: [PATCH 1432/1813] Added jaeger-bio 1.1.251 (#47105) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Added jaeger-bio 1.1.251 * Added jaeger-bio 1.1.251 * Added jaeger 1.1.251 * Minor modifications Minor modifications and test to unpin python * Added jaeger-bio bugfix * Added jaeger v1.1.26 * minor changes * minor fix --------- Co-authored-by: Andreas Sjödin --- recipes/jaeger-bio/meta.yaml | 62 ++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 recipes/jaeger-bio/meta.yaml diff --git a/recipes/jaeger-bio/meta.yaml b/recipes/jaeger-bio/meta.yaml new file mode 100644 index 0000000000000..388ff7957b63e --- /dev/null +++ b/recipes/jaeger-bio/meta.yaml @@ -0,0 +1,62 @@ +{% set name = "jaeger-bio" %} +{% set version = "1.1.26" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 7f7d8794cd04185f7787d92a6ccc89fa59bb58acbe0fe929c6bffbee39a90fe4 + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . --no-cache-dir -vvv" + noarch: python + run_exports: + - {{ pin_subpackage('jaeger-bio', max_pin="x.x.x") }} + +requirements: + host: + - python =3 + - pip + run: + - python =3 + - pip + - h5py >=3.8 + - biopython >=1.78 + - kneed >=0.8.5 + - matplotlib-base >=3.7 + - numpy >=1.24 + - pandas >=1.5 + - psutil >=5 + - ruptures >=1.1.9 + - scikit-learn ==1.3.2 + - seaborn >=0.12.2 + - tqdm >=4.64.0 + - tensorflow >=2.15,<2.16 + - parasail-python >=1.3.4 + +test: + imports: + - jaegeraa + - jaegeraa.data + - jaegeraa.nnlib + + commands: + - Jaeger --help + +about: + home: "https://github.com/Yasas1994/Jaeger" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "A quick and precise pipeline for detecting phages in sequence assemblies." + dev_url: https://github.com/Yasas1994/Jaeger + doc_url: https://readthedocs.org/projects/jaeger-docs/ + +extra: + identifiers: + - biotools:jaeger + recipe-maintainers: + - Yasas1994 From 56864afc069808aaa7012f3d72fe16881cdb13dd Mon Sep 17 00:00:00 2001 From: richard-burhans Date: Tue, 9 Apr 2024 15:51:57 -0400 Subject: [PATCH 1433/1813] updating to newer version, reset build number (#47113) Co-authored-by: Richard C. Burhans --- recipes/segalign-full/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/segalign-full/meta.yaml b/recipes/segalign-full/meta.yaml index ead1a962ea78a..500fbccebf7c8 100644 --- a/recipes/segalign-full/meta.yaml +++ b/recipes/segalign-full/meta.yaml @@ -1,11 +1,11 @@ -{% set version = "0.1.2" %} +{% set version = "0.1.2.1" %} package: name: segalign-full version: {{ version }} build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_compatible('segalign-full', max_pin='x.x') }} From 254e770b6681a2bd20d5339026f5f7b6fc89cfed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 15:52:23 -0400 Subject: [PATCH 1434/1813] Update pangu to 0.2.8 (#47112) --- recipes/pangu/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangu/meta.yaml b/recipes/pangu/meta.yaml index bacfeee43db68..e20eb3c1897c3 100644 --- a/recipes/pangu/meta.yaml +++ b/recipes/pangu/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.7" %} -{% set sha256 = "5b0cf818d9bc7a60a6da752ac8bd7ca028aaa382bcf6d622b1d3856da53928a1" %} +{% set version = "0.2.8" %} +{% set sha256 = "4360539dc2a881c3557d43e4c4322326385a7efa929b18f223aabf2e136fdea9" %} package: name: pangu From 26668abbff241f0761c0dc7c0b0b823d8d7ee1c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Tue, 9 Apr 2024 21:53:21 +0200 Subject: [PATCH 1435/1813] Add isonform (#47107) * Add isonform * Add spoa as dependency --- recipes/isonform/meta.yaml | 39 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 recipes/isonform/meta.yaml diff --git a/recipes/isonform/meta.yaml b/recipes/isonform/meta.yaml new file mode 100644 index 0000000000000..8ae2d4739eed3 --- /dev/null +++ b/recipes/isonform/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "isonform" %} +{% set version = "0.3.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/isONform-{{ version }}.tar.gz + sha256: fb96c32e0ce177bf7866b7a19fa6855b1e9fac8f8f164cdccc972e284fbcce47 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage("isonform", max_pin="x.x") }} + +requirements: + host: + - python + - pip + run: + - python + - recordclass >=0.17.2 + - networkx >=2.7.1 + - parasail-python >=1.3.3 + - edlib >=1.1.2 + - spoa + +test: + commands: + - isONform_parallel --help + +about: + home: https://github.com/aljpetri/isONform + summary: De novo construction of isoforms from long-read data + license: GPL-3.0 + license_file: LICENSE From 9e3a50a5d44fff96a44da1ee4fd5d41cf1e694f6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 20:34:59 -0400 Subject: [PATCH 1436/1813] Update arvados-python-client to 2.7.2 (#47114) --- recipes/arvados-python-client/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml index 8c8e710950c0a..0760ed2994b37 100644 --- a/recipes/arvados-python-client/meta.yaml +++ b/recipes/arvados-python-client/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.7.1" %} +{% set version = "2.7.2" %} package: name: arvados-python-client @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz - sha256: c973be949dbb35959d5eeda1d2bad31813484756e8367573e7b2f0149190039e + sha256: 97b064ee9e1fa1340c1742758c9ca7e787585118f8ccf94704033bd9ba5c05ed build: noarch: python From d5a84580c5af2e788e67d49b7d0987fc4252a694 Mon Sep 17 00:00:00 2001 From: Michael Predl <83495351+mpredl@users.noreply.github.com> Date: Wed, 10 Apr 2024 03:15:04 +0200 Subject: [PATCH 1437/1813] Add recipe for pycomo (#47050) * Created a recipe for the pycomo package * Added run_exports statement --- recipes/pycomo/meta.yaml | 50 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 recipes/pycomo/meta.yaml diff --git a/recipes/pycomo/meta.yaml b/recipes/pycomo/meta.yaml new file mode 100644 index 0000000000000..a92c2b57fa40f --- /dev/null +++ b/recipes/pycomo/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "pycomo" %} +{% set version = "0.1.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pycomo-{{ version }}.tar.gz + sha256: be95b8610a3b40ca69dd5ed055356c6bdb838059c66afa796343ea624b07be6c + +build: + entry_points: + - pycomo = pycomo.pycomo_models:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('pycomo', max_pin="x.x") }} + +requirements: + host: + - python >=3.9 + - setuptools + - pip + run: + - python >=3.9 + - cobra >=0.23.0 + - pandas >=1.5.3 + - python-libsbml >=5.20.1 + - numpy >=1.22.4 + +test: + imports: + - pycomo + commands: + - pip check + - pycomo --help + requires: + - pip + +about: + home: https://github.com/univieCUBE/PyCoMo + summary: PyCoMo is a software package for generating and analysing compartmentalized community metabolic models + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - mpredl From 7cc1f01c7eda9abfa3127ef56018d43aafba12bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 21:57:30 -0400 Subject: [PATCH 1438/1813] Update pybedtools to 0.10.0 (#47116) * Update pybedtools to 0.10.0 * update dependencies --------- Co-authored-by: mencian --- recipes/pybedtools/build.sh | 7 +++++-- recipes/pybedtools/meta.yaml | 32 ++++++++++++++++++-------------- 2 files changed, 23 insertions(+), 16 deletions(-) diff --git a/recipes/pybedtools/build.sh b/recipes/pybedtools/build.sh index 9eea3edc58935..c767c7e1d7310 100644 --- a/recipes/pybedtools/build.sh +++ b/recipes/pybedtools/build.sh @@ -1,6 +1,9 @@ #!/bin/bash -export CPATH=${PREFIX}/include -$PYTHON setup.py install --single-version-externally-managed --record=rec.txt + +export C_INCLUDE_PATH="${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" + +${PYTHON} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv # Add more build steps here, if they are necessary. diff --git a/recipes/pybedtools/meta.yaml b/recipes/pybedtools/meta.yaml index a983e247c6501..b9fb582b6ecfb 100644 --- a/recipes/pybedtools/meta.yaml +++ b/recipes/pybedtools/meta.yaml @@ -1,33 +1,33 @@ +{% set name = "pybedtools" %} +{% set version = "0.10.0" %} + package: - name: pybedtools - version: '0.9.1' + name: {{ name }} + version: {{ version }} source: - url: https://files.pythonhosted.org/packages/38/00/f07c17e25f9cc8e2d22b30aace73733e275b1804196f744f0178012a0d16/pybedtools-0.9.1.tar.gz - sha256: 586a626895b1b7215aef877e985c03fd8a908fd6c636e5b9ff8a1a1d09a1d514 + url: https://files.pythonhosted.org/packages/cc/90/cea4197772a029e925bd5d414108b5438d621dfbb1b0cc2627529d1ec524/pybedtools-0.10.0.tar.gz + sha256: 1a6fbaad23b013becc741d7d5922a2df03e391bc44ff92772ffb7dd456711161 build: - skip: True # [py2k] - number: 1 + skip: True # [py < 36] + number: 0 run_exports: - - {{ pin_subpackage("pybedtools", max_pin="x.x.x") }} + - {{ pin_subpackage("pybedtools", max_pin="x.x") }} requirements: build: - {{ compiler('cxx') }} host: - python - - six - #- pysam >=0.16 - - setuptools - #- pandas + - pip + - cython - zlib run: - python - bedtools - - six - - pysam >=0.16 - - pandas + - numpy + - pysam test: imports: @@ -38,7 +38,11 @@ test: about: home: https://github.com/daler/pybedtools license: MIT + license_family: MIT + license_file: LICENSE.txt summary: Wraps BEDTools for use in Python and adds many additional features. + dev_url: https://github.com/daler/pybedtools + doc_url: https://daler.github.io/pybedtools extra: identifiers: From a2295e4545328500a2b429905251f5c4f1e8a231 Mon Sep 17 00:00:00 2001 From: Parham Kazemi Date: Tue, 9 Apr 2024 19:14:24 -0700 Subject: [PATCH 1439/1813] Fix btllib recipe (#47118) * Update meta.yaml * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/btllib/build.sh | 2 +- recipes/btllib/meta.yaml | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/btllib/build.sh b/recipes/btllib/build.sh index c1a093c8ea800..aac83086b89e5 100644 --- a/recipes/btllib/build.sh +++ b/recipes/btllib/build.sh @@ -5,7 +5,7 @@ export LIBPATH="-L${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include -D_LIBCPP_DISABLE_AVAILABILITY" -CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" meson setup --buildtype release --prefix "${PREFIX}" --strip build/ +CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" meson setup --buildtype release --prefix "${PREFIX}" --strip build/ -Db_coverage=false cd build diff --git a/recipes/btllib/meta.yaml b/recipes/btllib/meta.yaml index 57d7900c785e2..e981478394a87 100644 --- a/recipes/btllib/meta.yaml +++ b/recipes/btllib/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [py < 38 or win] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('btllib', max_pin="x") }} @@ -27,7 +27,6 @@ requirements: - llvm-openmp # [osx] - libgomp # [linux] - samtools - - gcovr - swig - doxygen run: From 23d29db46487269ff8f631e727c78b91583c07c4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Apr 2024 23:09:58 -0400 Subject: [PATCH 1440/1813] Update getorganelle to 1.7.7.1 (#46968) * Update getorganelle to 1.7.7.1 * add run_exports * try skipping imports --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/getorganelle/meta.yaml | 32 +++++++++++++++++++++----------- 1 file changed, 21 insertions(+), 11 deletions(-) diff --git a/recipes/getorganelle/meta.yaml b/recipes/getorganelle/meta.yaml index 01453f6f21055..bc62d76f7e438 100644 --- a/recipes/getorganelle/meta.yaml +++ b/recipes/getorganelle/meta.yaml @@ -1,5 +1,5 @@ {% set name = "getorganelle" %} -{% set version = "1.7.7.0" %} +{% set version = "1.7.7.1" %} package: name: {{name}} @@ -7,20 +7,21 @@ package: source: url: https://github.com/Kinggerm/GetOrganelle/archive/{{version}}.tar.gz - sha256: dd351b5cd33688adfcd8bff9794ae0cc0ce01a572dac2bcf6c9d7db77b3e4883 + sha256: cf8e14766de43967182be839de20c9d1709b60fae38a0b3d175742dfad7a5d44 build: number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('getorganelle', max_pin="x") }} requirements: host: - - python + - python >=3.7 - pip - run: - - python + - python >=3.7 - perl - pigz - spades >=3.9 @@ -33,16 +34,25 @@ requirements: - requests test: - imports: - - GetOrganelleLib - + #imports: + #- GetOrganelleLib commands: - get_organelle_from_reads.py -h - get_organelle_from_assembly.py -h - slim_graph.py -h about: - home: http://github.com/Kinggerm/GetOrganelle - license: GPL3 + home: https://github.com/Kinggerm/GetOrganelle + license: "GPL-3.0-or-later" + license_family: GPL3 license_file: LICENSE summary: Get organelle genomes from genome skimming data + dev_url: https://github.com/Kinggerm/GetOrganelle + doc_url: https://github.com/Kinggerm/GetOrganelle/wiki + +extra: + identifiers: + - doi:10.1186/s13059-020-02154-5 + - biotools:getorganelle + - usegalaxy-eu:get_organelle_from_reads + - usegalaxy-eu:get_annotated_regions_from_gb From cb916c72cf45c5a5262386f7471ec304c588d52e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 00:59:17 -0400 Subject: [PATCH 1441/1813] Update fwdpy11 to 0.22.2 (#44099) * Update fwdpy11 to 0.22.1 * add run_exports * add gsl back to host section * Update fwdpy11 to 0.21.3 * Update fwdpy11 to 0.21.4 * Update fwdpy11 to 0.21.5 * Update fwdpy11 to 0.21.6 * add deprecated to run dependencies * Update fwdpy11 to 0.22.0 * Update fwdpy11 to 0.22.2 * add scikit-build-core * enable aarch64 build --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/fwdpy11/build.sh | 12 +++++-- recipes/fwdpy11/meta.yaml | 73 ++++++++++++++++++--------------------- 2 files changed, 44 insertions(+), 41 deletions(-) diff --git a/recipes/fwdpy11/build.sh b/recipes/fwdpy11/build.sh index b03d77ec6e6a5..00d150e289830 100644 --- a/recipes/fwdpy11/build.sh +++ b/recipes/fwdpy11/build.sh @@ -1,8 +1,16 @@ #!/bin/bash +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +if [ `uname` == Darwin ]; then + export HOME=`mktemp -d` +fi + # https://molpopgen.github.io/fwdpy11/misc/developersguide.html # https://doc.rust-lang.org/cargo/commands/cargo-install.html -CARGO_INSTALL_ROOT=$BUILD_PREFIX CARGO_HOME=$BUILD_PREFIX cargo install cbindgen +CARGO_INSTALL_ROOT=$BUILD_PREFIX CARGO_HOME=$CARGO_HOME cargo install cbindgen #CARGO_INSTALL_ROOT=$PREFIX CARGO_HOME=$PREFIX cargo install cbindgen # cmake's "find GSL macro" can barf when conda @@ -10,7 +18,7 @@ CARGO_INSTALL_ROOT=$BUILD_PREFIX CARGO_HOME=$BUILD_PREFIX cargo install cbindgen # fix that: #GSL_ROOT_DIR=$PREFIX $PYTHON -m pip install --no-deps --ignore-installed -vv . # for mac osx need also to add other vars: -CARGO_INSTALL_ROOT=$BUILD_PREFIX CARGO_HOME=$BUILD_PREFIX GSL_ROOT_DIR=$PREFIX $PYTHON -m pip install --no-deps --ignore-installed -vv . +CARGO_INSTALL_ROOT=$BUILD_PREFIX CARGO_HOME=$CARGO_HOME GSL_ROOT_DIR=$PREFIX $PYTHON -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv # on bioconda's Azure it seems that `$PYTHON` variable is not set because get an error: # /opt/conda/conda-bld/fwdpy11_1670108175931/work/conda_build.sh: line 16: -m: command not found # so will hard-code it: diff --git a/recipes/fwdpy11/meta.yaml b/recipes/fwdpy11/meta.yaml index 318a976b8cc25..cfbac7c97ecc0 100644 --- a/recipes/fwdpy11/meta.yaml +++ b/recipes/fwdpy11/meta.yaml @@ -1,74 +1,69 @@ +{% set name = "fwdpy11" %} +{% set version = "0.22.2" %} + package: - name: fwdpy11 - version: "0.21.0" + name: {{ name|lower }} + version: {{ version }} source: - url: https://files.pythonhosted.org/packages/6e/1b/241bdd1278cb9077d81064bd443159ed07962dbacb513388e80d1a047e93/fwdpy11-0.21.0.tar.gz - sha256: cbf5cd42411146e58874baf37b32f3e7a90b5ba18336b73c1be995bd41bbac98 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/fwdpy11-{{ version }}.tar.gz + sha256: 4bdd42d749d3c4e12f728c16d6db8c97bb5d03fff7362fe98b3c8cdfa759841d build: - skip: True # [py27 or py<38] + skip: True # [py < 38 or py > 312] number: 0 + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} + entry_points: + - fwdpy11 = fwdpy11.__main__:main + run_exports: + - {{ pin_subpackage('fwdpy11', max_pin="x.x") }} requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} + - {{ compiler('rust') }} - cmake - make host: - - python - - pkgconfig - python - pip - - numpy >=1.20 - - pybind11 ==2.10.0 - - tskit >=0.5 + - setuptools-scm >=8 + - pybind11 ==2.11.1 - gsl - - openblas - - attrs - - setuptools_scm - - rust >=1.62.1 -# - intervaltree -# - pybind11 >=2.10.0 -# - numpy -# - scipy -# - attrs >=0.19.2 -# - black -# - tskit -# - msprime -# - gsl -# - boost -# - pytest -# - pytest-xdist -# - setuptools_scm -# - demes >=0.2.0 -# - rust >=1.62.1 -# - hypothesis + - scikit-build-core >=0.3.3 run: - python - - numpy >=1.20 - - tskit >=0.5 + - numpy <2.0 + - tskit >=0.5.6 - gsl - openblas - scipy - attrs - black - - demes >=0.2 + - demes >=0.2.2 - intervaltree + - deprecated test: - # Python imports imports: - fwdpy11 + commands: + - fwdpy11 --help about: - home: http://pypi.python.org/pypi/fwdpy11 - license: GNU General Public License v3 or later (GPLv3+) + home: https://github.com/molpopgen/fwdpy11 + license: "GPL-3.0-or-later" + license_family: GPL3 license_file: "COPYING" summary: 'Forward-time population genetic simulation in Python.' + dev_url: https://github.com/molpopgen/fwdpy11 + doc_url: https://molpopgen.github.io/fwdpy11 -extras: +extra: identifiers: - - 10.1534/genetics.114.165019 - - 10.1371/journal.pcbi.1006581 + - doi:10.1534/genetics.114.165019 + - doi:10.1371/journal.pcbi.1006581 + additional-platforms: + - linux-aarch64 From 77add02deb552c39bbd7fc75dd3fd430339e6ef4 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 10 Apr 2024 02:24:44 -0500 Subject: [PATCH 1442/1813] Update ncbi-vdb recipe (#47120) * Update ncbi-vdb recipe * omit aarch64 for now * try OSX patch * edit patch * edit patch * edit build.sh --- recipes/ncbi-vdb/build.sh | 23 ++++++++++++++--------- recipes/ncbi-vdb/env.cmake.patch | 24 ++++++++++++++++++++++++ recipes/ncbi-vdb/meta.yaml | 25 ++++++++++--------------- 3 files changed, 48 insertions(+), 24 deletions(-) create mode 100644 recipes/ncbi-vdb/env.cmake.patch diff --git a/recipes/ncbi-vdb/build.sh b/recipes/ncbi-vdb/build.sh index d8b63767c0d42..9b73fbb271b0e 100644 --- a/recipes/ncbi-vdb/build.sh +++ b/recipes/ncbi-vdb/build.sh @@ -24,13 +24,18 @@ end-of-patch # Execute Make commands from a separate subdirectory. Else: # ERROR: In source builds are not allowed -BUILD_DIR=./build_vdb -mkdir ${BUILD_DIR} -cd ${BUILD_DIR} +#BUILD_DIR="${SRC_DIR}/build_vdb" +#mkdir -p "${BUILD_DIR}" +#cd "${BUILD_DIR}" -export CFLAGS="${CFLAGS} -DH5_USE_110_API" -cmake ../ncbi-vdb/ -DNGS_INCDIR=${PREFIX} \ - -DCMAKE_INSTALL_PREFIX=${PREFIX} \ - -DCMAKE_BUILD_TYPE=Release -cmake --build . -cmake --install . +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include -O3 -D_FILE_OFFSET_BITS=64 -DH5_USE_110_API" + +cmake -S ncbi-vdb/ -B build_vdb \ + -DNGS_INCDIR="${PREFIX}" \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + -DCMAKE_LIBRARY_PATH="${PREFIX}/lib" + +cmake --build build_vdb/ --target install -j 4 -v diff --git a/recipes/ncbi-vdb/env.cmake.patch b/recipes/ncbi-vdb/env.cmake.patch new file mode 100644 index 0000000000000..1a4b4515c6bc4 --- /dev/null +++ b/recipes/ncbi-vdb/env.cmake.patch @@ -0,0 +1,24 @@ +diff --git a/build/env.cmake b/build/env.cmake +index 9527451..7ab041b 100644 +--- a/build/env.cmake ++++ b/build/env.cmake +@@ -106,12 +106,16 @@ else () + endif () + + # create variables based entirely upon OS +-if ( "mac" STREQUAL ${OS} ) +- add_compile_definitions( MAC BSD UNIX ) ++if ( CMAKE_C_COMPILER_ID STREQUAL "AppleClang" ) + set(CMAKE_C_ARCHIVE_CREATE " Scr ") +- set(CMAKE_CXX_ARCHIVE_CREATE " Scr ") + set(CMAKE_C_ARCHIVE_FINISH " -no_warning_for_no_symbols -c ") ++endif() ++if ( CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang" ) ++ set(CMAKE_CXX_ARCHIVE_CREATE " Scr ") + set(CMAKE_CXX_ARCHIVE_FINISH " -no_warning_for_no_symbols -c ") ++endif() ++if ( "mac" STREQUAL ${OS} ) ++ add_compile_definitions( MAC BSD UNIX ) + elseif( "linux" STREQUAL ${OS} ) + add_compile_definitions( LINUX UNIX ) + set( LMCHECK -lmcheck ) diff --git a/recipes/ncbi-vdb/meta.yaml b/recipes/ncbi-vdb/meta.yaml index 30242cd443391..462861a98f263 100644 --- a/recipes/ncbi-vdb/meta.yaml +++ b/recipes/ncbi-vdb/meta.yaml @@ -1,12 +1,12 @@ +{% set name = "ncbi-vdb" %} {% set version = "3.1.0" %} package: - name: ncbi-vdb + name: {{ name }} version: {{ version }} build: - number: 0 - skip: True # [osx] + number: 1 run_exports: - {{ pin_subpackage('ncbi-vdb', max_pin='x') }} @@ -14,22 +14,16 @@ source: url: https://github.com/ncbi/ncbi-vdb/archive/{{ version }}.tar.gz sha256: eec5a64b8353a201bd4cf2c58cfcbb3622327397c3b11696ae59d827fcfcea9d folder: ncbi-vdb + patches: + - env.cmake.patch # [osx] -requirements: +requirements: build: - - {{ compiler('c') }} - {{ compiler('cxx') }} - bison - cmake - flex - make - run: - - ca-certificates - - curl - - ossuuid - - perl - - perl-xml-libxml - - perl-uri about: home: https://github.com/ncbi/ncbi-vdb @@ -38,9 +32,10 @@ about: description: | VDB is the database engine that all SRA tools use. It is a columnar database system with a number of unique features. All SRA objects are stored in VDB. + dev_url: https://github.com/ncbi/ncbi-vdb + doc_url: https://github.com/ncbi/ncbi-vdb/wiki test: commands: - - test -e ${PREFIX}/lib64/libncbi-vdb.so # [not osx] - - test -e ${PREFIX}/lib64/libncbi-vdb.dylib # [osx] - + - test -e ${PREFIX}/lib64/libncbi-vdb.so # [not osx] + - test -e ${PREFIX}/lib64/libncbi-vdb.dylib # [osx] From 0cb9cb72d1bb9482dc9fd3d8976a40cdf3c806a4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 07:02:07 -0400 Subject: [PATCH 1443/1813] Update rust-bio-tools to 0.42.2 (#47126) --- recipes/rust-bio-tools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rust-bio-tools/meta.yaml b/recipes/rust-bio-tools/meta.yaml index 5d7119d3ce28c..169fcf16d2137 100644 --- a/recipes/rust-bio-tools/meta.yaml +++ b/recipes/rust-bio-tools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.42.1" %} +{% set version = "0.42.2" %} package: name: rust-bio-tools @@ -12,7 +12,7 @@ build: source: url: https://github.com/rust-bio/rust-bio-tools/archive/v{{ version }}.tar.gz - sha256: c4759eb3eaec1d491b521172d1ace42feeef57cba0cd0ed0a4e413dcbde1b40f + sha256: 860b29bb917f2d9ca1479d416b43856791c2ca726a0c22df30354bb5c44191c6 requirements: build: From 0a9264d1bc58001aa8917214997dc5b62a48b2c1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 09:04:30 -0400 Subject: [PATCH 1444/1813] Update sourmash to 4.8.8 (#47117) Co-authored-by: C. Titus Brown --- recipes/sourmash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sourmash/meta.yaml b/recipes/sourmash/meta.yaml index 45294de4a0f6a..7a632308a3484 100644 --- a/recipes/sourmash/meta.yaml +++ b/recipes/sourmash/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.8.7" %} +{% set version = "4.8.8" %} package: name: sourmash @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/sourmash/sourmash-{{ version }}.tar.gz - sha256: 0cd18ea49d94ce92f5c85b2337cf7b7328ef3013c33311414db71b29962a93fd + sha256: 667da4b014f003032bdffa43318bb5668edbbc55055fe109dab959a914d69842 build: number: 0 From 34376fea17a320eded0ac54c8bd3b9dd9ac260bf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 09:15:47 -0400 Subject: [PATCH 1445/1813] Update sequali to 0.7.0 (#47129) --- recipes/sequali/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index 288e8d1fc16d8..e4dc25945e90c 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.6.0" %} +{% set version = "0.7.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 29e0d802d2308e5e3d313c56a7ccb8cf2c1c0c86c901f35679566ad48e3d407e + sha256: b1714f90fb62fa56524c9be5a1a96f92ac4b4739cbc5e85874b0890faf6eef8a build: number: 0 From a743ce9638cc88f936105d829752df9b527d6ad6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karel=20B=C5=99inda?= Date: Wed, 10 Apr 2024 18:12:37 +0200 Subject: [PATCH 1446/1813] Add galitime recipe (#47125) --- recipes/galitime/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 recipes/galitime/meta.yaml diff --git a/recipes/galitime/meta.yaml b/recipes/galitime/meta.yaml new file mode 100644 index 0000000000000..f08c8f6cdcd66 --- /dev/null +++ b/recipes/galitime/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "galitime" %} +{% set version = "0.1.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 2815801dd6e2e9add9685f53216abaa718c183bb162c850c41c9d1a2d397794c + +build: + number: 0 + noarch: python + entry_points: + - galitime=galitime.galitime:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('galitime', max_pin="x") }} + +requirements: + host: + - pip + - python >=3 + run: + - python >=3 + +test: + imports: + - galitime + +about: + home: https://github.com/karel-brinda/galitime + license: MIT + license_family: MIT + license_file: LICENSE.txt + doc_url: https://github.com/karel-brinda/galitime + summary: 'benchmarking of scientific computaional experiments' + + From 05a45c2d5d9c0522d5441314c48b76dcaf48469e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 12:41:41 -0400 Subject: [PATCH 1447/1813] Update cutesv to 2.1.1 (#47132) --- recipes/cutesv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cutesv/meta.yaml b/recipes/cutesv/meta.yaml index 957edae2caec5..7f9935d939f64 100644 --- a/recipes/cutesv/meta.yaml +++ b/recipes/cutesv/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.1.0" %} +{% set version = "2.1.1" %} package: name: cutesv @@ -6,7 +6,7 @@ package: source: url: https://github.com/tjiangHIT/cuteSV/archive/cuteSV-v{{ version }}.tar.gz - sha256: c2d072e8c3c1a2a8ec52abe63ffc796d0e023385e850c4ead6e3a18c14f173d3 + sha256: ebba8ffe0943626a9c1606adeed37bec3a4c0816c4fb7af8d6d219d7bee2acd2 build: number: 0 From 9bcb2d3e2d925eabc2b92f7f95598a40af37ca3e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 12:42:20 -0400 Subject: [PATCH 1448/1813] Update oakvar to 2.9.93 (#47128) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 80a6adf5390e4..d929d958fc229 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.92" %} -{% set sha256 = "f12cd22f67d3f84abfa8b8037983f16094d6971f1fa1ed8165e30812cf7d5af9" %} +{% set version = "2.9.93" %} +{% set sha256 = "84b11aaf6f83945c15f48921b1cbb58be3b09732f949d37bdcbb1c5a785ffdce" %} package: name: {{ name|lower }} From 1154127a6b3b25af65c45f86e3fdbc0148866795 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 12:44:44 -0400 Subject: [PATCH 1449/1813] Update checkatlas to 0.4.17 (#47127) * Update checkatlas to 0.4.16 * Update checkatlas to 0.4.17 --- recipes/checkatlas/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/checkatlas/meta.yaml b/recipes/checkatlas/meta.yaml index 10e1c40dced61..3baabf8a06abf 100644 --- a/recipes/checkatlas/meta.yaml +++ b/recipes/checkatlas/meta.yaml @@ -1,5 +1,5 @@ {% set name = "checkatlas" %} -{% set version = "0.4.13" %} +{% set version = "0.4.17" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d62a2cd020e88b7142dcf43fde6a0ca7cfcd7e3a0d00343c55899dc40e477780 + sha256: 3b831f58142cfd3a51fbf0df6a88e588d04f3df40a2a33a69cab7e8d6785b179 build: number: 0 From da1aa9ce8c6791355e13027f788e39f1ef17ac3e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 12:54:57 -0400 Subject: [PATCH 1450/1813] Update mitofinder to 1.4.2 (#47135) * Update mitofinder to 1.4.2 * add run_exports --------- Co-authored-by: mencian --- recipes/mitofinder/build.sh | 2 +- recipes/mitofinder/meta.yaml | 16 ++++++++++++---- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/recipes/mitofinder/build.sh b/recipes/mitofinder/build.sh index afce669dfc433..4d994a1a4c6d3 100644 --- a/recipes/mitofinder/build.sh +++ b/recipes/mitofinder/build.sh @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/bin/bash ./install.sh diff --git a/recipes/mitofinder/meta.yaml b/recipes/mitofinder/meta.yaml index d7df107b87e67..fed796d0e41aa 100644 --- a/recipes/mitofinder/meta.yaml +++ b/recipes/mitofinder/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.1" %} +{% set version = "1.4.2" %} package: name: mitofinder @@ -6,15 +6,21 @@ package: source: url: https://github.com/RemiAllio/MitoFinder/archive/v{{ version }}.tar.gz - sha256: c80a0108c64813dce8c3f653958ed5d6bddc28a0c801fe4d477a173c3a58fe45 + sha256: 2d6d3925fb014777df97f272134143cc518944ae05d000a44ada2862d46ec95a build: - number: 1 - skip: true # [not py2k] + number: 0 + skip: True # [not py2k] + run_exports: + - {{ pin_subpackage('mitofinder', max_pin="x") }} requirements: build: - {{ compiler('c') }} + - make + - autoconf + - automake + - libtool host: - python run: @@ -35,5 +41,7 @@ test: about: home: https://github.com/RemiAllio/MitoFinder license: MIT + license_family: MIT license_file: License/LICENSE summary: Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data. + dev_url: https://github.com/RemiAllio/MitoFinder From 65fbc26cc379892c674f72e2e9c261aab50a741c Mon Sep 17 00:00:00 2001 From: Nate Olson Date: Wed, 10 Apr 2024 14:03:14 -0400 Subject: [PATCH 1451/1813] Update truvari (#47134) * updating dependency versions * linting fix * removing numpy - not specified in pyproject.toml --- recipes/truvari/meta.yaml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/recipes/truvari/meta.yaml b/recipes/truvari/meta.yaml index 1acdd86eb2934..b27d82385cd1e 100644 --- a/recipes/truvari/meta.yaml +++ b/recipes/truvari/meta.yaml @@ -1,17 +1,17 @@ {% set name = "truvari" %} -{% set version = "4.1.0" %} -{% set sha256 = "c30ddee89d0a7107fb0638977cf52aa9751e2f666f109d57026204ca66310ea4" %} +{% set version = "4.2.2" %} +{% set sha256 = "4e7e504e8221b99c321d0825e32299954ef324f382b16fa09c97135aa1e4f872" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/Truvari-{{ version }}.tar.gz + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/truvari-{{ version }}.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: python script: {{ PYTHON }} -m pip install . -vvv entry_points: @@ -21,21 +21,21 @@ build: requirements: host: - - python >=3.6 + - python >=3.8 - pip run: - - python >=3.6 + - python >=3.8 - pywfa >=0.5.1 - rich >=12.5.1 - python-edlib >=1.3.9 - - pysam >=0.15.2 - - intervaltree >=3.0.2 + - pysam >=0.22 + - intervaltree >=3.1 - joblib >=1.2.0 - - numpy - - pytabix - - bwapy - - pandas - - mafft + - pytabix >=0.1 + - bwapy >=0.1.4 + - pandas >=1.5.3 + - pyabpoa >=1.4.3 + - mafft >=7.515 test: imports: From 456fca5d3d762d27ee52dcf1a6ced50b25c3bed7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 14:19:45 -0400 Subject: [PATCH 1452/1813] Update galitime to 0.1.1 (#47136) --- recipes/galitime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galitime/meta.yaml b/recipes/galitime/meta.yaml index f08c8f6cdcd66..718da55cf8a9b 100644 --- a/recipes/galitime/meta.yaml +++ b/recipes/galitime/meta.yaml @@ -1,5 +1,5 @@ {% set name = "galitime" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 2815801dd6e2e9add9685f53216abaa718c183bb162c850c41c9d1a2d397794c + sha256: affa8fbd286d4ac48944b81f803c5b73dab7c4b4ff4cab0795b124b53ab3190d build: number: 0 From 75f70efb5c3870edf23d96fb0b03d27801550bd4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 14:19:53 -0400 Subject: [PATCH 1453/1813] Update panisa to 0.1.7 (#47131) * Update panisa to 0.1.7 * add run_exports --------- Co-authored-by: mencian --- recipes/panisa/meta.yaml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/recipes/panisa/meta.yaml b/recipes/panisa/meta.yaml index c65fdd7f37bab..511cc0e6a3ca8 100644 --- a/recipes/panisa/meta.yaml +++ b/recipes/panisa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "panISa" %} -{% set version = "0.1.6" %} +{% set version = "0.1.7" %} package: name: "{{ name|lower }}" @@ -7,22 +7,22 @@ package: source: url: "https://github.com/bvalot/panISa/archive/refs/tags/{{ version }}.tar.gz" - sha256: 6bb76139cd6e263073f3194ea21712c406e327c273e327c0bb270dcd556cada3 + sha256: 5c9b6c4c30ebe4e43439e2a85ae304b9ed434239165749395232ba06fdbbc44c build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('panisa', max_pin="x.x") }} requirements: host: - pip - - pysam >=0.9 - - python - - requests >=2.12 + - python >=3.7 run: - pysam >=0.9 - - python + - python >=3.7 - requests >=2.12 test: @@ -34,9 +34,11 @@ test: about: home: "https://github.com/bvalot/panISa" - license: "GNU General Public v3 (GPLv3)" + license: "GPL-3.0-or-later" license_family: GPL3 + license_file: LICENSE summary: "panISa is a software to search insertion sequence (IS) on resequencing data (bam file)" + dev_url: "https://github.com/bvalot/panISa" extra: recipe-maintainers: From 64756ef93b8a9efbf7168c6a12ecfdd1f649c06d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Apr 2024 14:20:00 -0400 Subject: [PATCH 1454/1813] Update phyloacc to 2.3.1 (#47115) * Update phyloacc to 2.3.0 * add run_exports * Update phyloacc to 2.3.1 --------- Co-authored-by: mencian --- recipes/phyloacc/build.sh | 11 +++++++---- recipes/phyloacc/meta.yaml | 30 +++++++++++++++--------------- 2 files changed, 22 insertions(+), 19 deletions(-) diff --git a/recipes/phyloacc/build.sh b/recipes/phyloacc/build.sh index 4cc5ed20fac25..449fa686bc283 100644 --- a/recipes/phyloacc/build.sh +++ b/recipes/phyloacc/build.sh @@ -1,7 +1,10 @@ #!/bin/bash -make install CXX=${CXX} -cp src/PhyloAcc-interface/phyloacc.py ${PREFIX}/bin/. -cp src/PhyloAcc-interface/phyloacc_post.py ${PREFIX}/bin/. +mkdir -p ${PREFIX}/bin mkdir -p ${SP_DIR} -cp -R src/PhyloAcc-interface/phyloacc_lib ${SP_DIR}/. + +make install CXX=${CXX} + +cp src/PhyloAcc-interface/phyloacc.py ${PREFIX}/bin/ +cp src/PhyloAcc-interface/phyloacc_post.py ${PREFIX}/bin/ +cp -R src/PhyloAcc-interface/phyloacc_lib ${SP_DIR}/ diff --git a/recipes/phyloacc/meta.yaml b/recipes/phyloacc/meta.yaml index 23e0d0afae9ca..cd1702b9baf67 100644 --- a/recipes/phyloacc/meta.yaml +++ b/recipes/phyloacc/meta.yaml @@ -1,32 +1,34 @@ {% set name = "PhyloAcc" %} -{% set version = "2.2.0" %} -{% set sha256 = "29b13115974545479511bd4074d766c19fd7449412bfa9792721af85f80cbe37" %} +{% set version = "2.3.1" %} +{% set sha256 = "f22dfff721a788b117bb097370402aad0d1a22fb26fec9c6082eb1eb620a553f" %} package: name: {{ name|lower }} version: {{ version }} -source: +source: url: https://github.com/phyloacc/PhyloAcc/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} build: - number: 2 - skip: True # [py < 38] + number: 0 + skip: True # [py < 38] + run_exports: + - {{ pin_subpackage('phyloacc', max_pin="x") }} requirements: build: - {{ compiler('cxx') }} - make - - libgomp # [linux] - - llvm-openmp # [osx] host: + - python - gsl - openblas - blis - liblapack - armadillo - - python + - libgomp # [linux] + - llvm-openmp # [osx] run: - python - blis @@ -34,27 +36,25 @@ requirements: - biopython >=1.79 - numpy >=1.22 - snakemake-minimal >=7.3 + - libgomp # [linux] + - llvm-openmp # [osx] test: commands: - phyloacc.py --version - phyloacc.py --depcheck - phyloacc_post.py -h -# Test commands to run after building and installing about: home: https://phyloacc.github.io/ - license: GNU GPLv3 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE.md summary: 'Bayesian estimation of substitution rate shifts in non-coding regions' description: 'Bayesian estimation of substitution rate shifts in non-coding regions' - doc_url: https://phyloacc.github.io/ + doc_url: https://phyloacc.github.io/readme.html dev_url: https://github.com/phyloacc/PhyloAcc -# Package meta info -# URLs just point to the github page until we update the docs extra: recipe-maintainers: - gwct -# Extra info From 22eef1d6dbf24b5b428db18eacbec75e0d6d0fa5 Mon Sep 17 00:00:00 2001 From: John Palmer <32370730+jpalmer37@users.noreply.github.com> Date: Wed, 10 Apr 2024 11:22:04 -0700 Subject: [PATCH 1455/1813] Add tntblast-2.4 (#46966) * added tntblast-2.4 * modified setup * reverted changes * try different test * new approach * minor edits --------- Co-authored-by: Dan Fornika --- recipes/tntblast/2.4/build.sh | 16 ++++++++++++ recipes/tntblast/2.4/meta.yaml | 48 ++++++++++++++++++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 recipes/tntblast/2.4/build.sh create mode 100644 recipes/tntblast/2.4/meta.yaml diff --git a/recipes/tntblast/2.4/build.sh b/recipes/tntblast/2.4/build.sh new file mode 100644 index 0000000000000..9faf1b0cc953d --- /dev/null +++ b/recipes/tntblast/2.4/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash + +sed -i.bak 's/-DUSE_MPI//g' Makefile +sed -i.bak '/BLAST_DIR =/d' Makefile + +export INCLUDE_PATH="${BUILD_PREFIX}/include" +export LIBRARY_PATH="${BUILD_PREFIX}/lib" +export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BUILD_PREFIX}/lib" + +export LDFLAGS="-lm -lz -L${BUILD_PREFIX}/lib" +export CPPFLAGS="-I${BUILD_PREFIX}/include" + +make CC="${CXX}" INC="${CPPFLAGS}" LIBS="${LDFLAGS}" all + +mkdir -p $PREFIX/bin +cp tntblast $PREFIX/bin diff --git a/recipes/tntblast/2.4/meta.yaml b/recipes/tntblast/2.4/meta.yaml new file mode 100644 index 0000000000000..c4f641810f439 --- /dev/null +++ b/recipes/tntblast/2.4/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "tntblast" %} +{% set version = "2.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage( name|lower, max_pin="x") }} + +source: + url: https://github.com/jgans/thermonucleotideBLAST/archive/61fee4458186cc3f08ec386e18997b5953d5c7e6.zip + sha256: 5a239413a2df7de59d9a28a1bee962e2480b81d5faed3ecfa1e0f9fd84294c0c + +requirements: + build: + - make + - {{ compiler('cxx') }} + - openmp #[linux] + - llvm-openmp #[osx] + - zlib + host: + - openmp #[linux] + - llvm-openmp #[osx] + - zlib + run: + - openmp #[linux] + - llvm-openmp #[osx] + - zlib + +test: + commands: + - '{ tntblast 2>&1 || true; } | grep v.{{ version }}' + +about: + home: https://github.com/jgans/thermonucleotideBLAST + license: BSD License + license_file: LICENSE + license_family: BSD + summary: Searching DNA/RNA sequence databases with PCR and/or probe queries + dev_url: https://github.com/jgans/thermonucleotideBLAST + doc_url: https://github.com/jgans/thermonucleotideBLAST#readme + +extra: + identifiers: + - doi:10.1093/nar/gkn301 From 97c5af8553f0f50c6984b31a232c30ca4e42f136 Mon Sep 17 00:00:00 2001 From: DuyenLe2000 <128071771+DuyenLe2000@users.noreply.github.com> Date: Wed, 10 Apr 2024 22:37:18 +0200 Subject: [PATCH 1456/1813] Update rsv-typer recipe (#47006) * update from 0.2.0 to 0.3.0 * add run_exports * added medaka version dependency * change pyvcf version * reverted changes to medaka and pyvcf dependencies and added longshot and absl-py dependencies --- recipes/rsv-typer/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/rsv-typer/meta.yaml b/recipes/rsv-typer/meta.yaml index 4a2d0f8a78d4f..454e207a3ea42 100644 --- a/recipes/rsv-typer/meta.yaml +++ b/recipes/rsv-typer/meta.yaml @@ -9,7 +9,7 @@ source: sha256: d91607ebe37c305fb3aba4871161d51c6fa2bd7aa43d5d6defcca8d9def74431 build: - number: 0 + number: 1 noarch: python script: python -m pip install . entry_points: @@ -27,6 +27,8 @@ requirements: - minimap2 >=2.17 - muscle =3.8 - pyvcf =0.6.8=py36h9f0ad1d_1002 + - absl-py =1.4.0 + - longshot =0.4.5 test: commands: - rsv-typer -h From cb2eef74c958a493bc392aeee4ceb8b7520f6979 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 00:47:09 -0400 Subject: [PATCH 1457/1813] Update genomad to 1.8.0 (#47147) --- recipes/genomad/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genomad/meta.yaml b/recipes/genomad/meta.yaml index 4ac261bc491b2..8da527e7cdb54 100644 --- a/recipes/genomad/meta.yaml +++ b/recipes/genomad/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genomad" %} -{% set version = "1.7.6" %} +{% set version = "1.8.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a42891daab9cf604c6ed89b3af6fc78b0e20f224844b7ae66f820a1ea155ceca + sha256: 631599f9fea8ea8d07bdc9334e0fc328aed1274968da78f6f5854c0146022233 build: number: 0 From 86e7488a791a450d56e5d5c47f977c1b88f76111 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 03:36:51 -0400 Subject: [PATCH 1458/1813] Update sniffles to 2.3.2 (#47133) * Update sniffles to 2.3 * add run_exports * Update sniffles to 2.3.1 * Update sniffles to 2.3.2 --------- Co-authored-by: mencian --- recipes/sniffles/meta.yaml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/recipes/sniffles/meta.yaml b/recipes/sniffles/meta.yaml index a6fd59a98adda..890bbadf30a6a 100644 --- a/recipes/sniffles/meta.yaml +++ b/recipes/sniffles/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.2" %} -{% set sha256 = "744ee05017e0e95a4b2e21020d7a7277d8fabae2c2c20cd982287bb7775d8ecf" %} +{% set version = "2.3.2" %} +{% set sha256 = "72531b65e479157473bd84dd3ba20118ba38ef27dcd502bf9d53b9d1f2a7d50f" %} package: name: sniffles @@ -12,15 +12,17 @@ source: build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('sniffles', max_pin="x") }} requirements: host: - - python >=3.7 - - setuptools + - python >=3.10 + - pip run: - - python >=3.7 - - pysam + - python >=3.10 + - pysam >=0.21.0 test: commands: @@ -33,3 +35,5 @@ about: license_family: MIT summary: Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore) + doc_url: https://github.com/fritzsedlazeck/Sniffles/wiki + dev_url: https://github.com/fritzsedlazeck/Sniffles From 71d8a097432aabc405436024fc0837b659d22d90 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 10:55:36 -0400 Subject: [PATCH 1459/1813] Update ntedit to 2.0.1 (#47143) --- recipes/ntedit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ntedit/meta.yaml b/recipes/ntedit/meta.yaml index efaab31e1369b..862b8e9ee8fae 100644 --- a/recipes/ntedit/meta.yaml +++ b/recipes/ntedit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ntedit" %} -{% set version = "2.0.0" %} +{% set version = "2.0.1" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ build: source: url: https://github.com/bcgsc/ntEdit/releases/download/v{{ version }}/ntEdit-{{ version }}.tar.gz - sha256: d7e2fbae0944510b1df1e9f88a5503a85b6a60dee42fdfc5c135698582ea3478 + sha256: e686ef5e49139a50dd3983ac2ac8b2771c918e2b3530884fa0f612d811163111 requirements: build: From daaa54a04da9c2622f62fd331447349119fb2e17 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 10:57:42 -0400 Subject: [PATCH 1460/1813] Update galitime to 0.1.2 (#47144) --- recipes/galitime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galitime/meta.yaml b/recipes/galitime/meta.yaml index 718da55cf8a9b..d14db11964b6c 100644 --- a/recipes/galitime/meta.yaml +++ b/recipes/galitime/meta.yaml @@ -1,5 +1,5 @@ {% set name = "galitime" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: affa8fbd286d4ac48944b81f803c5b73dab7c4b4ff4cab0795b124b53ab3190d + sha256: 9789a3beec1ce5d1cd588c6bb56012932f69ae3dedbce02a8f4abc0b86ce601a build: number: 0 From fc6f88f9feeec5b44f184fe47f4064fb0ac550dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 10:59:13 -0400 Subject: [PATCH 1461/1813] Update hostile to 1.1.0 (#47145) --- recipes/hostile/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hostile/meta.yaml b/recipes/hostile/meta.yaml index 88d7df7ebd535..59824376f57ac 100644 --- a/recipes/hostile/meta.yaml +++ b/recipes/hostile/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.0" %} +{% set version = "1.1.0" %} package: name: hostile @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/h/hostile/hostile-{{ version }}.tar.gz - sha256: abe985acf384703ff482d5712cc4b3367e7f777818a66cbd389e7bfc6c6ac76a + sha256: eee390f97ac9f669f10792a3fb487d92b9cec518c0b072338b3654a162965e2e build: noarch: python From 1b7fc055df2f0cec676ea3be6cc750fce28d3c77 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 10:59:23 -0400 Subject: [PATCH 1462/1813] Update oakvar to 2.9.94 (#47146) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index d929d958fc229..abf70229586d9 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.93" %} -{% set sha256 = "84b11aaf6f83945c15f48921b1cbb58be3b09732f949d37bdcbb1c5a785ffdce" %} +{% set version = "2.9.94" %} +{% set sha256 = "c5ffadc8e52accece85ca04a4d52966b8575b55640f542ebfc3906b44f3ccf93" %} package: name: {{ name|lower }} From a45098e5ada8d04f6837211566e085f9b82249ae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 11:37:29 -0400 Subject: [PATCH 1463/1813] Update flams to 1.1.4 (#47164) --- recipes/flams/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/flams/meta.yaml b/recipes/flams/meta.yaml index 4ead7da071881..47602ac18f84f 100644 --- a/recipes/flams/meta.yaml +++ b/recipes/flams/meta.yaml @@ -1,5 +1,5 @@ {% set name = "flams" %} -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/flams-{{ version }}.tar.gz - sha256: b028cd8e131add01eb012ded0ae7c48bf361f36ae14b477a3d193fc0da4ea5fa + sha256: 0d590d0b51f41bd47830136060f1c5d38475c1905d66a7c2ea11e417b7e641b5 build: entry_points: From 1877129d5c8e9a779716b38477d2b542afe6c98c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 11:37:46 -0400 Subject: [PATCH 1464/1813] Update gubbins to 3.3.5 (#47152) --- recipes/gubbins/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml index 7f27a03430d08..2166a683609f3 100644 --- a/recipes/gubbins/meta.yaml +++ b/recipes/gubbins/meta.yaml @@ -1,13 +1,13 @@ {% set name = "gubbins" %} -{% set version = "3.3.4" %} -{% set sha256 = "4176530be756a8b89ad533ca593d14d24742242199dede8469c53d509f229f21" %} +{% set version = "3.3.5" %} +{% set sha256 = "4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 0 skip: True # [py < 38] run_exports: - {{ pin_subpackage('gubbins', max_pin="x") }} From cee5caab993f3e2ed926bc6eb17f5afbf57f670f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 17:45:41 -0400 Subject: [PATCH 1465/1813] Update pbstarphase to 0.9.1 (#47176) --- recipes/pbstarphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml index 2767f8e755965..ee493c0f2c0c3 100644 --- a/recipes/pbstarphase/meta.yaml +++ b/recipes/pbstarphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbstarphase" %} -{% set version = "0.9.0" %} -{% set sha256 = "0a875b66503b234b63c4af33d2537454db78385beddd77147383a6f63d6e0ad9" %} +{% set version = "0.9.1" %} +{% set sha256 = "cfa6696181c54d2aca2e338aec599ba9dc16adc08c6b66d5736e8322a3697823" %} package: name: {{ name }} From 3532c4f6fccb0beebea185468c820cbf5c260f91 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 12 Apr 2024 04:45:16 +0300 Subject: [PATCH 1466/1813] cd-hit: add linux-aarch64 build (#47154) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/cd-hit/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/cd-hit/meta.yaml b/recipes/cd-hit/meta.yaml index 87534475d3ab5..8163e48de1d69 100644 --- a/recipes/cd-hit/meta.yaml +++ b/recipes/cd-hit/meta.yaml @@ -10,7 +10,9 @@ source: sha256: {{ sha256 }} build: - number: 9 + number: 10 + run_exports: + - {{ pin_subpackage('cd-hit', max_pin="x") }} requirements: build: @@ -32,3 +34,7 @@ about: home: https://github.com/weizhongli/cdhit license: GPLv2 summary: Clusters and compares protein or nucleotide sequences + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From cd2935dcc15d31efd2ae43a6243198908fee48b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 22:12:05 -0400 Subject: [PATCH 1467/1813] Update peka to 1.0.1 (#47123) * Update peka to 1.0.1 * add run_exports * edit dependencies --------- Co-authored-by: mencian --- recipes/peka/meta.yaml | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) diff --git a/recipes/peka/meta.yaml b/recipes/peka/meta.yaml index b4b7a6adf5e1f..9a38b52189e86 100644 --- a/recipes/peka/meta.yaml +++ b/recipes/peka/meta.yaml @@ -1,5 +1,5 @@ {% set name = "PEKA" %} -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: "{{ name|lower }}" @@ -7,30 +7,32 @@ package: source: url: "https://github.com/ulelab/peka/archive/refs/tags/v{{ version }}.tar.gz" - sha256: b6e2dffcbb762cc0806025334fbd31f11fa7183aa5896d0630aa08f1c9b7dba5 + sha256: cddbe86774de3de6a7c4ed06b7187d812d736fdc30e19f384170c6bdd77b1174 build: number: 0 entry_points: - peka = peka:main - script: "{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps" + script: "{{ PYTHON }} -m pip install . -vvv --no-build-isolation --no-deps" noarch: python + run_exports: + - {{ pin_subpackage('peka', max_pin="x") }} requirements: host: - pip - - python==3.7 + - python >=3.7 run: - - python==3.7 - - matplotlib-base==3.1.2 - - numpy==1.17.4 - - pybedtools==0.8.0 - - scipy==1.6.2 - - seaborn==0.9.0 - - plumbum==1.6.8 - - scikit-learn==0.21.3 - - pandas==0.24.2 - - textdistance==4.1.3 + - python >=3.7 + - matplotlib-base + - {{ pin_compatible('numpy') }} + - pybedtools + - scipy + - seaborn + - plumbum + - scikit-learn + - pandas + - textdistance test: commands: @@ -38,12 +40,16 @@ test: about: home: "https://github.com/ulelab/peka" - license: GPL-3.0 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: "Analysis of kmers located around locations of interest" + dev_url: "https://github.com/ulelab/peka" extra: recipe-maintainers: - marc-jones - codeprimate123 - kkuret + identifiers: + - doi:10.1186/s13059-022-02755-2 From 095ea3e707ef56be59eb152ebd87a1d8291d4ca0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 22:21:24 -0400 Subject: [PATCH 1468/1813] Update wgd to 2.0.31 (#47179) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index c274a221059fe..b38be15c19f8b 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.30" %} +{% set version = "2.0.31" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: 97abc0f32c05eba6dc98bd50df801164a046c1a423a0fb1be078f381cb2a658b + sha256: 451db487d5584417623b49d8807919173af94c984112cd0812a80484c6719775 build: number: 0 From f1d09a7ad1d2e38d418e8f980b31c9822b530f12 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 22:21:32 -0400 Subject: [PATCH 1469/1813] Update oakvar to 2.9.95 (#47177) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index abf70229586d9..eaf0155aa7c71 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.94" %} -{% set sha256 = "c5ffadc8e52accece85ca04a4d52966b8575b55640f542ebfc3906b44f3ccf93" %} +{% set version = "2.9.95" %} +{% set sha256 = "82323ed140d8c0e8e4631510871ed3fbdaf041fa38112766edf8f1a694c290cb" %} package: name: {{ name|lower }} From aad3640f8da1828c5e0e623284fb5b13d975a525 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 22:22:21 -0400 Subject: [PATCH 1470/1813] Update ont-modkit to 0.2.7 (#47174) --- recipes/ont-modkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml index de4665f2e5551..5b5cb534a641b 100644 --- a/recipes/ont-modkit/meta.yaml +++ b/recipes/ont-modkit/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.6" %} -{% set sha256 = "ca5e864582eb1e3a1277a7ea11745ae9d2b83ff4e5d1efc394b7b81e23aa9ec3" %} +{% set version = "0.2.7" %} +{% set sha256 = "e933e7a69672ad8ac59f99e201010cfdfe23012ecaa7d5b9ba19db59aebe423f" %} package: name: ont-modkit From 5eaf2498e496af298de13e45556cef232194bb88 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 22:22:31 -0400 Subject: [PATCH 1471/1813] Update nda-tools to 0.2.27 (#47173) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/nda-tools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nda-tools/meta.yaml b/recipes/nda-tools/meta.yaml index 1884495f78db8..12325594827f1 100644 --- a/recipes/nda-tools/meta.yaml +++ b/recipes/nda-tools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nda-tools" %} -{% set version = "0.2.26" %} -{% set sha256 = "863bbbf6399aa38bcec6cf8159aca90d3afcb1221eb26b20243f4f41e7eec2fe" %} +{% set version = "0.2.27" %} +{% set sha256 = "79cb91fe4265384287a833911b91747265449e1040a3e88c7c8566d0a561d8a4" %} package: name: {{ name }} From 4551bb1ba158a03f635f8ad1f08ee9f13e330c02 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 22:22:43 -0400 Subject: [PATCH 1472/1813] Update fgsv to 0.2.0 (#47172) --- recipes/fgsv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgsv/meta.yaml b/recipes/fgsv/meta.yaml index ddf5a0053b873..4d064dba5f553 100644 --- a/recipes/fgsv/meta.yaml +++ b/recipes/fgsv/meta.yaml @@ -1,5 +1,5 @@ -{% set version="0.1.1" %} -{% set sha256="e39b24710d80278b7528545b43ce8084e166614054bed55ca898fa79d4be0af9" %} +{% set version="0.2.0" %} +{% set sha256="c2f9536a677e7e99f251cada1338f611cea40477deca144f0c6928505755eb37" %} package: From c7ceb3ab723958c971127e57c7f3c400a17c9197 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 22:22:58 -0400 Subject: [PATCH 1473/1813] Update fgpyo to 0.3.0 (#47170) --- recipes/fgpyo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgpyo/meta.yaml b/recipes/fgpyo/meta.yaml index a95a9fecfe949..724cfe8711b77 100644 --- a/recipes/fgpyo/meta.yaml +++ b/recipes/fgpyo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fgpyo" %} -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/fulcrumgenomics/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: 2555357c1c6d9ca02e1b2335221dcae5edd288d307ba617ab648ee7b10a25ea5 + sha256: 787506e574166c9b2cec80f722db7caa2851d24b787cdd665fae1d42f8a9c9e0 build: noarch: python From 73e7bd3e0bb80a2404253a9c112d1fc6bc32ae56 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 22:23:24 -0400 Subject: [PATCH 1474/1813] Update snakemake-executor-plugin-slurm-jobstep to 0.2.1 (#47169) * Update snakemake-executor-plugin-slurm-jobstep to 0.2.0 * Update snakemake-executor-plugin-slurm-jobstep to 0.2.1 --- recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml b/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml index 6c518d608ee27..1e48b4f3c9c2b 100644 --- a/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm-jobstep" %} -{% set version = "0.1.11" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm_jobstep-{{ version }}.tar.gz - sha256: cafdac937796ab0dfc0354c42380167a44a1db00c4edc98ab736a6ace2201a94 + sha256: 58894d52b5998a34fa6f60ec511ff0bfde4a9ec96714bcaa3cd2f46cf8a33859 build: noarch: python From 48381a4cb0be33643a4f9d1f2e8420f51ccffad3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Apr 2024 22:23:44 -0400 Subject: [PATCH 1475/1813] Update snakemake-interface-common to 1.17.2 (#47153) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 5d1078964b88a..854fad21ef1e9 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.17.1" %} +{% set version = "1.17.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae + sha256: 7a2bba88df98c1a0a5cec89b835c62dd2e6e72c1fb8fd104fe73405c800b87c0 build: noarch: python From 4ae0cc32437b85dd7e2ac9b8d59f7a3ef4b125fa Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 11 Apr 2024 21:46:56 -0500 Subject: [PATCH 1476/1813] ncbi-vdb: enable linux-aarch64 build (#47180) --- recipes/ncbi-vdb/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/ncbi-vdb/meta.yaml b/recipes/ncbi-vdb/meta.yaml index 462861a98f263..2fb4b41232e0e 100644 --- a/recipes/ncbi-vdb/meta.yaml +++ b/recipes/ncbi-vdb/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('ncbi-vdb', max_pin='x') }} @@ -39,3 +39,7 @@ test: commands: - test -e ${PREFIX}/lib64/libncbi-vdb.so # [not osx] - test -e ${PREFIX}/lib64/libncbi-vdb.dylib # [osx] + +extra: + additional-platforms: + - linux-aarch64 From 39bef28c38ca5496fbbe43e9b72ed5bf987086d3 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 12 Apr 2024 07:15:55 +0300 Subject: [PATCH 1477/1813] perl-algorithm-cluster: add linux-aarch64 build (#47166) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/perl-algorithm-cluster/meta.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/perl-algorithm-cluster/meta.yaml b/recipes/perl-algorithm-cluster/meta.yaml index 67a3e26b0738d..b774eb2cfaf6f 100644 --- a/recipes/perl-algorithm-cluster/meta.yaml +++ b/recipes/perl-algorithm-cluster/meta.yaml @@ -10,7 +10,9 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 + run_exports: + - {{ pin_subpackage('perl-algorithm-cluster', max_pin="x") }} requirements: build: @@ -34,3 +36,6 @@ about: license: unknown summary: 'Perl interface to the C Clustering Library' +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 265eb44fa7eec368a87db45ec1e12b08189ce5b4 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 12 Apr 2024 07:16:05 +0300 Subject: [PATCH 1478/1813] gadem: add linux-aarch64 build (#47163) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/gadem/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/gadem/meta.yaml b/recipes/gadem/meta.yaml index 283883945f57a..bf0f5a7c94fa2 100644 --- a/recipes/gadem/meta.yaml +++ b/recipes/gadem/meta.yaml @@ -7,7 +7,9 @@ source: sha256: afe89b8d1ecf7d7dc785b9f59ffdfdb511df68c147934eedc0398873fa2640dc build: - number: 5 + number: 6 + run_exports: + - {{ pin_subpackage('gadem', max_pin="x") }} requirements: build: @@ -23,3 +25,7 @@ about: home: https://www.niehs.nih.gov/research/resources/software/biostatistics/gadem/index.cfm license: GPLv3 summary: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 359b053d115fc67fcf2c2ba871b1fd025eac99ca Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 12 Apr 2024 07:17:37 +0300 Subject: [PATCH 1479/1813] prosampler: add linux-aarch64 build (#47162) * prosampler: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * prosampler: update to v1.5 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- build-fail-blacklist | 1 - recipes/prosampler/build.sh | 2 +- recipes/prosampler/meta.yaml | 12 ++++++++---- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index ff3fedc6f0e8c..bc1cb568f9bee 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -247,7 +247,6 @@ recipes/ngsep recipes/rnabridge-denovo recipes/eval recipes/minorseq -recipes/prosampler recipes/methylextract recipes/blasr recipes/asn2gb diff --git a/recipes/prosampler/build.sh b/recipes/prosampler/build.sh index 2a751024f5a0b..294eb68008e78 100644 --- a/recipes/prosampler/build.sh +++ b/recipes/prosampler/build.sh @@ -1,4 +1,4 @@ #!/bin/bash -$CXX -o ProSampler ProSampler.cc +$CXX -o ProSampler ProSampler_v1.5.cc mkdir -p $PREFIX/bin cp ProSampler $PREFIX/bin diff --git a/recipes/prosampler/meta.yaml b/recipes/prosampler/meta.yaml index 24f5bee0cd1e9..4433e38f225ef 100644 --- a/recipes/prosampler/meta.yaml +++ b/recipes/prosampler/meta.yaml @@ -1,16 +1,18 @@ -{% set version = "1.0" %} -{% set sha256 = "570671cd5effd50c015515b80e0fdafeb0a353cecb626a050a92bb6658a4b69b" %} +{% set version = "1.5" %} +{% set sha256 = "ae75dad4133a5f2d6da487118a3e8e5bcbfc361821edb72c7c36b966419d6187" %} package: name: prosampler version: {{ version }} source: - url: https://github.com/zhengchangsulab/ProSampler/raw/master/PROSAMPLER_01_22_2019.tar.gz + url: https://github.com/zhengchangsulab/ProSampler/raw/master/PROSMPLER_v1.5.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('prosampler', max_pin=None) }} requirements: build: @@ -26,5 +28,7 @@ about: summary: An ultra-fast motif finding program in large ChIP-seq datasets. extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:prosampler From ef598b67db86d8145abaf1608d5d2646b16fe597 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 12 Apr 2024 07:18:34 +0300 Subject: [PATCH 1480/1813] weeder: add linux-aarch64 build (#47160) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/weeder/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/weeder/meta.yaml b/recipes/weeder/meta.yaml index c41db324ee25e..5cbce18083ea8 100644 --- a/recipes/weeder/meta.yaml +++ b/recipes/weeder/meta.yaml @@ -7,8 +7,10 @@ source: md5: 3401675b24ca928b7cc54ce9ebf18b6a build: - number: 8 + number: 9 skip: True # [osx] + run_exports: + - {{ pin_subpackage('weeder', max_pin="x") }} requirements: build: @@ -26,6 +28,8 @@ about: summary: "Motif (transcription factor binding sites) discovery in sequences from coregulated genes of a single species. This is a new Weeder release rewritten to be faster and optimized for large ChIP-Seq data." extra: + additional-platforms: + - linux-aarch64 notes: "Includes a simple wrapper script to be able to run weeder from any directory. It passes arguments transparently to the weeder2 executable." identifiers: - biotools:weeder From 86a73593da7495865fdec3be3dac2f8062f10b4b Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 12 Apr 2024 07:19:36 +0300 Subject: [PATCH 1481/1813] homer: add linux-aarch64 build (#47159) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/homer/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/homer/meta.yaml b/recipes/homer/meta.yaml index a02b6c48e4c32..78bc32e2c14c1 100644 --- a/recipes/homer/meta.yaml +++ b/recipes/homer/meta.yaml @@ -16,10 +16,11 @@ source: - configureHomer.patch build: - number: 8 + number: 9 # Ships pre-built binaries that install_name_tool isn't able to fix. skip: True # [osx] - + run_exports: + - {{ pin_subpackage('homer', max_pin="x") }} # Dependencies according to http://homer.ucsd.edu/homer/introduction/install.html requirements: @@ -52,3 +53,6 @@ about: summary: 'Software for motif discovery and next generation sequencing analysis' maintainer: BioNinja, cokelaer, simonvh, r78v10a07 +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 517158cdebb032819f83dce66bbc49aa60bc9c7e Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 12 Apr 2024 07:19:45 +0300 Subject: [PATCH 1482/1813] dinamo: add linux-aarch64 build (#47157) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/dinamo/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/dinamo/meta.yaml b/recipes/dinamo/meta.yaml index 917619344a1c4..78a2ba7d3cfb2 100644 --- a/recipes/dinamo/meta.yaml +++ b/recipes/dinamo/meta.yaml @@ -14,7 +14,9 @@ source: build: skip: True # [osx] - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: build: @@ -37,6 +39,8 @@ about: summary: An exact and efficient method for IUPAC motif discovery in DNA sequences extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - simonvh identifiers: From ea235c10dfcf19b521e71bc7635e3ae9cb8d8259 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 00:24:07 -0400 Subject: [PATCH 1483/1813] Update pairix to 0.3.8 (#47083) * Update pairix to 0.3.8 * add run_exports * edit tests * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pairix/build.sh | 41 +++++++++++++++----------- recipes/pairix/conda_build_config.yaml | 3 ++ recipes/pairix/meta.yaml | 21 ++++++++----- 3 files changed, 40 insertions(+), 25 deletions(-) create mode 100644 recipes/pairix/conda_build_config.yaml diff --git a/recipes/pairix/build.sh b/recipes/pairix/build.sh index d91603e1fb483..478e63e9afca8 100644 --- a/recipes/pairix/build.sh +++ b/recipes/pairix/build.sh @@ -1,20 +1,27 @@ #!/bin/bash +mkdir -p "${PREFIX}/bin" + # Install both the pairix binaries and the Python extension module -export C_INCLUDE_PATH=${PREFIX}/include -export LIBRARY_PATH=${PREFIX}/lib -make -cp bin/pairix $PREFIX/bin/pairix -cp bin/pairs_merger $PREFIX/bin/pairs_merger -cp bin/streamer_1d $PREFIX/bin/streamer_1d -cp util/column_remover.pl $PREFIX/bin/column_remover.pl -cp util/duplicate_header_remover.pl $PREFIX/bin/duplicate_header_remover.pl -cp util/fragment_4dnpairs.pl $PREFIX/bin/fragment_4dnpairs.pl -cp util/juicer_shortform2pairs.pl $PREFIX/bin/juicer_shortform2pairs.pl -cp util/merge-pairs.sh $PREFIX/bin/merge-pairs.sh -cp util/merged_nodup2pairs.pl $PREFIX/bin/merged_nodup2pairs.pl -cp util/old_merged_nodup2pairs.pl $PREFIX/bin/old_merged_nodup2pairs.pl -cp util/process_merged_nodup.sh $PREFIX/bin/process_merged_nodup.sh -cp util/process_old_merged_nodup.sh $PREFIX/bin/process_old_merged_nodup.sh -cp util/bam2pairs/bam2pairs $PREFIX/bin/bam2pairs -$PYTHON setup.py install --single-version-externally-managed --record=record.txt +export C_INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" + +make CC="${CC}" + +cp ${SRC_DIR}/util/*.pl ${PREFIX}/bin/ +cp ${SRC_DIR}/util/*.sh ${PREFIX}/bin/ +cp ${SRC_DIR}/util/bam2pairs/bam2pairs ${PREFIX}/bin/ + +# Fix perl shebang +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/column_remover.pl +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/duplicate_header_remover.pl +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/fragment_4dnpairs.pl +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/juicer_shortform2pairs.pl +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/merged_nodup2pairs.pl +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/old_merged_nodup2pairs.pl + +cp ${SRC_DIR}/bin/pairix ${PREFIX}/bin/ +cp ${SRC_DIR}/bin/pairs_merger ${PREFIX}/bin/ +cp ${SRC_DIR}/bin/streamer_1d ${PREFIX}/bin/ + +${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir diff --git a/recipes/pairix/conda_build_config.yaml b/recipes/pairix/conda_build_config.yaml new file mode 100644 index 0000000000000..1a582a0844fac --- /dev/null +++ b/recipes/pairix/conda_build_config.yaml @@ -0,0 +1,3 @@ +# current version does not build with newer compilers +c_compiler_version: + - 14 # [osx] diff --git a/recipes/pairix/meta.yaml b/recipes/pairix/meta.yaml index f2d810a4b6cf3..186b41f148112 100644 --- a/recipes/pairix/meta.yaml +++ b/recipes/pairix/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.7" %} +{% set version = "0.3.8" %} package: name: pairix @@ -6,12 +6,14 @@ package: source: url: https://github.com/4dn-dcic/pairix/archive/{{ version }}.tar.gz - md5: a1f9b3c7b13d904dfe736cf5e66c2385 + sha256: 51e349c034eda3bce21d9f89a8e477471d2db5a3ef4424a39999d1ec316e2726 patches: - src_Makefile.patch build: - number: 5 + number: 0 + run_exports: + - {{ pin_subpackage('pairix', max_pin="x.x") }} requirements: build: @@ -19,21 +21,24 @@ requirements: - {{ compiler('c') }} host: - python - - setuptools + - pip - zlib run: - - htslib - python + - perl + - htslib + - samtools test: - imports: - - pypairix + #imports: + #- pypairix commands: - pairix --help about: home: https://github.com/4dn-dcic/pairix license: MIT + license_family: MIT license_file: "LICENSE.txt" summary: 2D indexing on bgzipped text files of paired genomic coordinates - license_family: MIT + dev_url: https://github.com/4dn-dcic/pairix From 45e79780a7cc1b04331a3e582433f5ce60407c21 Mon Sep 17 00:00:00 2001 From: Mike Tisza Date: Thu, 11 Apr 2024 23:51:01 -0500 Subject: [PATCH 1484/1813] Update meta.yaml (#47139) --- recipes/cenote-taker3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cenote-taker3/meta.yaml b/recipes/cenote-taker3/meta.yaml index fd08cffc8d837..63206767586a6 100644 --- a/recipes/cenote-taker3/meta.yaml +++ b/recipes/cenote-taker3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cenote-taker3" %} -{% set version = "3.3.0" %} +{% set version = "3.3.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/mtisza1/{{ name }}/archive/v{{ version }}.tar.gz" - sha256: 43bd01d7cc236d738d98a093fbf688f72a91659718b5380c63eb70856dde420b + sha256: ce595208f3d925f7798e579b2d72b995b192eac802e24bb3d9d0a2ca856b5a99 build: number: 0 From 008957b8510fb8f64f3b78e0741de75c7723e450 Mon Sep 17 00:00:00 2001 From: nickjcroucher Date: Fri, 12 Apr 2024 05:52:19 +0100 Subject: [PATCH 1485/1813] Update to v3.3.5 (#47150) From 571484707dc918d4cceb9fa4fda19cca3aab0e02 Mon Sep 17 00:00:00 2001 From: Jon Puritz Date: Fri, 12 Apr 2024 00:52:27 -0400 Subject: [PATCH 1486/1813] Update vcflib requirement for dDocent (#47178) * Update meta.yaml * Update meta.yaml --- recipes/ddocent/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ddocent/meta.yaml b/recipes/ddocent/meta.yaml index ae926ea5ff7e8..fd0da658b3618 100644 --- a/recipes/ddocent/meta.yaml +++ b/recipes/ddocent/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('ddocent', max_pin="x") }} @@ -30,7 +30,7 @@ requirements: - rainbow - cd-hit - bedtools >=2.26.0 - - vcflib >=0.1.11 + - vcflib >=0.1.11, <1.0.3 - gnuplot - parallel - pear From 7fc4286a5ff0ddaa5c7ebe4b0e06c73ebd5a62cf Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 12 Apr 2024 00:10:37 -0500 Subject: [PATCH 1487/1813] Update KMC to v3.2.4 (#47182) * Update KMC to v3.2.4 * remove linux-aarch64 build --- recipes/kmc/Makefile.patch | 71 -------------------------------------- recipes/kmc/build.sh | 24 +++++-------- recipes/kmc/meta.yaml | 38 +++++++++++--------- 3 files changed, 30 insertions(+), 103 deletions(-) delete mode 100644 recipes/kmc/Makefile.patch diff --git a/recipes/kmc/Makefile.patch b/recipes/kmc/Makefile.patch deleted file mode 100644 index fb9711ad7ff95..0000000000000 --- a/recipes/kmc/Makefile.patch +++ /dev/null @@ -1,71 +0,0 @@ -From 4a29584d69d40a41d2569899b03a5660af85f97c Mon Sep 17 00:00:00 2001 -From: marekkokot -Date: Thu, 20 Jan 2022 19:51:36 +0100 -Subject: [PATCH] makefile for bioconda - ---- - Makefile | 27 ++++++++++++++++++--------- - 1 file changed, 18 insertions(+), 9 deletions(-) - -diff --git a/Makefile b/Makefile -index bc07d35..d2784a7 100644 ---- a/Makefile -+++ b/Makefile -@@ -22,8 +22,8 @@ ifeq ($(UNAME_S),Darwin) - else - CC = g++ - -- CFLAGS = -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -- CLINK = -lm -static -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++14 -+ CFLAGS = -Wall -O3 -m64 -pthread -std=c++14 -+ CLINK = -lm -O3 -std=c++14 - - PY_KMC_API_CFLAGS = -fPIC -Wall -shared -std=c++14 -O3 - endif -@@ -69,13 +69,9 @@ else - $(KMC_MAIN_DIR)/raduls_avx2.o \ - $(KMC_MAIN_DIR)/raduls_avx.o - -- KMC_LIBS = \ -- $(KMC_MAIN_DIR)/libs/libz.a \ -- $(KMC_MAIN_DIR)/libs/libbz2.a -- -- KMC_TOOLS_LIBS = \ -- $(KMC_TOOLS_DIR)/libs/libz.a \ -- $(KMC_TOOLS_DIR)/libs/libbz2.a -+ KMC_LIBS = -lz -lbz2 -lpthread -+ -+ KMC_TOOLS_LIBS = -lz -lbz2 -lpthread - - LIB_KMC_CORE = $(OUT_BIN_DIR)/libkmc_core.a - endif -@@ -90,6 +86,12 @@ $(KMC_API_DIR)/mmer.o \ - $(KMC_API_DIR)/kmc_file.o \ - $(KMC_API_DIR)/kmer_api.o - -+KMC_API_PICO = \ -+$(KMC_API_DIR)/mmer.pico \ -+$(KMC_API_DIR)/kmc_file.pico \ -+$(KMC_API_DIR)/kmer_api.pico -+ -+ - KMC_API_SRC_FILES = $(wildcard $(KMC_API_DIR)/*.cpp) - PY_KMC_API_OBJS = $(patsubst $(KMC_API_DIR)/%.cpp,$(PY_KMC_API_DIR)/%.o,$(KMC_API_SRC_FILES)) - -@@ -110,6 +112,13 @@ $(KMC_TOOLS_DIR)/kff_info_reader.o - $(KMC_CLI_OBJS) $(KMC_CORE_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS) $(KFF_OBJS) $(KMC_TOOLS_OBJS): %.o: %.cpp - $(CC) $(CFLAGS) -c $< -o $@ - -+$(KMC_API_PICO): %.pico: %.cpp -+ $(CC) $(CFLAGS) -fpic -c -o $@ $< -+ -+$(OUT_BIN_DIR)/libkmc_api.so: $(KMC_API_PICO) -+ -mkdir -p $(OUT_BIN_DIR) -+ $(CC) -shared $(LDFLAGS) -o $@ $^ -+ - $(KMC_MAIN_DIR)/raduls_sse2.o: $(KMC_MAIN_DIR)/raduls_sse2.cpp - $(CC) $(CFLAGS) -msse2 -c $< -o $@ - $(KMC_MAIN_DIR)/raduls_sse41.o: $(KMC_MAIN_DIR)/raduls_sse41.cpp --- -2.34.1 - diff --git a/recipes/kmc/build.sh b/recipes/kmc/build.sh index 7cb93486302dd..2b3e4f0ef50b6 100644 --- a/recipes/kmc/build.sh +++ b/recipes/kmc/build.sh @@ -1,23 +1,17 @@ #!/bin/bash -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/lib -mkdir -p $PREFIX/include +mkdir -p ${PREFIX}/bin +mkdir -p ${PREFIX}/lib +mkdir -p ${PREFIX}/include -if [ "$(uname)" == "Darwin" ]; then +if [ "$(uname)" == "Darwin" ]; then mv bin/kmc ${PREFIX}/bin mv bin/kmc_tools ${PREFIX}/bin mv bin/kmc_dump ${PREFIX}/bin else - make CC=${CXX} -j32 all bin/libkmc_api.so - mv bin/kmc $PREFIX/bin - mv bin/kmc_tools $PREFIX/bin - mv bin/kmc_dump $PREFIX/bin - mv bin/libkmc_core.a $PREFIX/lib - mv bin/libkmc_api.so $PREFIX/lib/libkmc.so - mv kmc_api/*.h $PREFIX/include - mv include/kmc_runner.h $PREFIX/include + mv bin/kmc ${PREFIX}/bin + mv bin/kmc_tools ${PREFIX}/bin + mv bin/kmc_dump ${PREFIX}/bin + mv bin/libkmc_core.a ${PREFIX}/lib + mv include/kmc_runner.h ${PREFIX}/include fi - - - diff --git a/recipes/kmc/meta.yaml b/recipes/kmc/meta.yaml index b58633c5e5856..d96d701a183c5 100644 --- a/recipes/kmc/meta.yaml +++ b/recipes/kmc/meta.yaml @@ -1,29 +1,26 @@ -{% set version = "3.2.1" %} -{% set url = "https://github.com/refresh-bio/KMC/archive/v3.2.1.tar.gz" %} # [linux] -{% set sha256 = "7db333091a754508163a097c41720cf32a80abe160bef60f3fc82c8da1d67896" %} # [linux] -{% set url = "https://github.com/refresh-bio/kmc/releases/download/v3.2.1/kmc3.2.1.mac.tar.gz" %} # [osx] -{% set sha256 = "d4bd30d5e16bcbaac7f979f18e49e7447b0148709fb26f754490be9e3e766e73" %} # [osx] - +{% set name = "kmc" %} +{% set version = "3.2.4" %} +{% set url = "https://github.com/refresh-bio/KMC/releases/download/v3.2.4/KMC3.2.4.linux.x64.tar.gz" %} # [linux and x86_64] +{% set sha256 = "158f2084f8d928b3f33b8aaf7d1220fee4183bf46837787e5e6b16bbdf54d31d" %} # [linux and x86_64] +{% set url = "https://github.com/refresh-bio/KMC/releases/download/v3.2.4/KMC3.2.4.mac.x64.tar.gz" %} # [osx] +{% set sha256 = "70d66545d5802cf116469e41acb2a04631271feac81ff5c4d1c299e9407ca326" %} # [osx] package: - name: kmc + name: {{ name }} version: {{ version }} source: url: {{ url }} sha256: {{ sha256 }} - patches: - - Makefile.patch # [linux] build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage("kmc", max_pin="x") }} requirements: build: - make - - bzip2 - - zlib - - {{ compiler('c') }} - {{ compiler('cxx') }} host: - zlib @@ -32,6 +29,10 @@ requirements: - zlib - bzip2 +test: + commands: + - kmc --help + about: home: https://github.com/refresh-bio/kmc summary: "Tools for efficient k-mer counting and filtering of reads based on k-mer content." @@ -39,8 +40,11 @@ about: KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of DNA sequences. KMC tools allow performing various operations on k-mers sets. license: GPL-3 - license_family: GPL + license_family: GPL3 license_file: gpl-3.0.txt -test: - commands: - - kmc --help + dev_url: https://github.com/refresh-bio/kmc + +extra: + identifiers: + - biotools:kmc + - doi:10.1093/bioinformatics/btx304 From 52c5caa028e9b255c8a972fba6daf6a0fef68807 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 12 Apr 2024 07:15:20 +0200 Subject: [PATCH 1488/1813] add mofapy2 recipe (#47175) --- recipes/mofapy2/meta.yaml | 41 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 recipes/mofapy2/meta.yaml diff --git a/recipes/mofapy2/meta.yaml b/recipes/mofapy2/meta.yaml new file mode 100644 index 0000000000000..0b73846286177 --- /dev/null +++ b/recipes/mofapy2/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "mofapy2" %} +{% set version = "0.7.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 937c385e07cebcc20039cff4782b7f7d6ebb7b576c4f5a12f5e74364dcec16c3 +build: + noarch: python + number: 0 + script: python -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage('mofapy2', max_pin="x.x") }} + +requirements: + host: + - python + - pip + - poetry-core + run: + - h5py + - numpy + - pandas + - python + - scipy + - scikit-learn + - anndata + +test: + imports: + - mofapy2 + +about: + home: https://github.com/bioFAM/mofapy2 + license: 'LGPL 3.0' + license_family: LGPL + license_file: LICENSE + summary: Multi-Omics Factor Analysis From 76794693913ab648d37f7c4d2ddc14413dd9d206 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 01:15:41 -0400 Subject: [PATCH 1489/1813] Update parsnp to 2.0.5 (#47181) * Update parsnp to 2.0.5 * Update run_test.sh w/ partition arg --------- Co-authored-by: Bryce Kille --- recipes/parsnp/meta.yaml | 4 ++-- recipes/parsnp/run_test.sh | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index 33ba8ff6a4f39..d99dc6f3bfb79 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.4" %} +{% set version = "2.0.5" %} package: name: parsnp @@ -6,7 +6,7 @@ package: source: url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" - sha256: 04993dcb60034d3c9188fbbbbd6c8209760d1e0d0b0b3efc6458479965ea31b0 + sha256: 1d23695d0d624fa17e02c43b1d730200e526c17a48615593f75ee8fc35402489 build: number: 0 diff --git a/recipes/parsnp/run_test.sh b/recipes/parsnp/run_test.sh index 73e2775eda56a..cb5ae8bb2dba1 100644 --- a/recipes/parsnp/run_test.sh +++ b/recipes/parsnp/run_test.sh @@ -9,4 +9,4 @@ parsnp -r ! -d mers_virus/genomes/*.fna -o test2 --verbose parsnp -g mers_virus/ref/England1.gbk -d mers_virus/genomes/*.fna -p 2 -C 1000 -c -o test --verbose --use-fasttree parsnp -r ! -d mers_virus/genomes/*.fna -o test2 --verbose -p 2 parsnp -r ! -d mers_virus/genomes/*.fna -o test3 --verbose -p 2 --extend-lcbs -parsnp -r ! -d mers_virus/genomes/*.fna -o test4 --verbose -p 2 --partition --partition-size 10 +parsnp -r ! -d mers_virus/genomes/*.fna -o test4 --verbose -p 2 --min-partition-size 10 From f2f95c4e7207a29ae1b61b3cce1383404e1975a5 Mon Sep 17 00:00:00 2001 From: Gabriel Renaud Date: Fri, 12 Apr 2024 12:57:48 +0200 Subject: [PATCH 1490/1813] added soibean to vgan (#47151) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * vgan 2.0 * vgan 2.0 strike2 * vgan 2.0 strike3 * vgan 2.0 strike3 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update recipes/vgan/meta.yaml * fixed minor bug in MCMC for euka Euka had a bug that was committed to 2.0.1, this is fixed now. * Update meta.yaml This a new version of vgan which includes the latest command called soibean to detect species in environmental DNA. * Update meta.yaml run_exports added * Update recipes/vgan/meta.yaml Co-authored-by: Björn Grüning --------- Co-authored-by: James A. Fellows Yates Co-authored-by: Brandon Seah Co-authored-by: Björn Grüning --- recipes/vgan/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/vgan/meta.yaml b/recipes/vgan/meta.yaml index 387e0125543cc..81d26a67d4c0d 100644 --- a/recipes/vgan/meta.yaml +++ b/recipes/vgan/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vgan" %} -{% set version = "2.0.2" %} +{% set version = "3.0.0" %} package: name: {{ name }} @@ -7,11 +7,13 @@ package: source: url: https://github.com/grenaud/vgan/releases/download/v{{ version }}/vgan - sha256: 4340e61ff3c4ca8f8eca388604cc004d23d9399a4df860116f3cab342599d14e + sha256: 7a8fb93618fc0efe49f33e998a4f46fbd004c63c3326fa9c0e414940418c1c7b build: number: 0 skip: true # [osx] + run_exports: + - {{ pin_subpackage('vgan', max_pin="x") }} script: - mkdir -p ${PREFIX}/bin - cp vgan ${PREFIX}/bin/ @@ -19,6 +21,7 @@ build: - mkdir -p ${PREFIX}/share/vgan/ - mkdir -p ${PREFIX}/share/vgan/hcfiles/ - mkdir -p ${PREFIX}/share/vgan/euka_dir/ + - mkdir -p ${PREFIX}/share/vgan/soibean_dir/ - mkdir -p ${PREFIX}/share/vgan/damageProfiles/ - wget -nc -l1 --recursive --no-parent -P ${PREFIX}/share/vgan/ ftp://ftp.healthtech.dtu.dk:/public/haplocart/hcfiles/ - mv -fv ${PREFIX}/share/vgan/ftp.healthtech.dtu.dk/public/haplocart/hcfiles/* ${PREFIX}/share/vgan/hcfiles From 211435de0aacf308368e87579419dd2691c6690e Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Fri, 12 Apr 2024 09:14:29 -0400 Subject: [PATCH 1491/1813] bump build number (#47142) --- recipes/taxonomy/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/taxonomy/meta.yaml b/recipes/taxonomy/meta.yaml index 10c7fb6a093ab..eb6ba753a1b93 100644 --- a/recipes/taxonomy/meta.yaml +++ b/recipes/taxonomy/meta.yaml @@ -12,7 +12,7 @@ source: - pyproject.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('taxonomy', max_pin="x.x") }} From e8e90c7b953f8cc2a3145e759c88d4ad3988fbf6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 09:31:48 -0400 Subject: [PATCH 1492/1813] Update snakemake to 8.10.7 (#47189) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 9d19370e920a6..b41496df85412 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.10.6" %} +{% set version = "8.10.7" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 2b624f033bb020a4763c4274f11eb0b34b51fb3b73cc64598005eaa897f11dd6 + sha256: c64e0ddfe2af6c06f0c50f5451b8cffad0775a829364754e40da418b4c1118d6 build: number: 0 From 5f6fab2a124c56ad0313497377bdd14218d761e5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 09:37:09 -0400 Subject: [PATCH 1493/1813] Update snakemake-interface-executor-plugins to 9.1.1 (#47188) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 0f2ccd84a1dd2..fd5036d4ce8bb 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "9.1.0" %} +{% set version = "9.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: 26da734f7399f5963c5bc7cbcbb51f2d61e3c76298010418d76c48dda92aeb2f + sha256: 357c3b1d633b26241693a4e5ce291fbe198c03a54a30acfa86dd97dc252fa2c6 build: noarch: python From ede342fe0980f22ff143f4bf44b54a4bfe836c31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 09:45:42 -0400 Subject: [PATCH 1494/1813] Update pymzml to 2.5.9 (#47191) --- recipes/pymzml/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pymzml/meta.yaml b/recipes/pymzml/meta.yaml index c5512c2bef155..a50f7ac2305cb 100644 --- a/recipes/pymzml/meta.yaml +++ b/recipes/pymzml/meta.yaml @@ -1,10 +1,10 @@ package: name: pymzml - version: "2.5.6" + version: "2.5.9" source: - url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.6.tar.gz - sha256: 82f7c36c11f4c7e868faf97f5f7a18585fe198142309bfe6a6820b4c764d9e0c + url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.9.tar.gz + sha256: a064aa48bcab79510e564f4d3d93e3546cc2939ceaa89726206ca95c74fccda2 build: number: 0 From 3547c6ef3705e48eaa3a8af77bac72a9feb8f580 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 09:46:02 -0400 Subject: [PATCH 1495/1813] Update pybiolib to 1.1.1971 (#47192) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 52068a7224e24..56fc073830c29 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1957" %} +{% set version = "1.1.1971" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: f1908a5129b26ea1d91c762b7f26bbc1356c1211420da138064be60ad199fbc6 + sha256: 54078e51772e8d88e4fcd4ee8206a57fd15816c03b5fde6ca5ea4fb1838d7edd build: noarch: python From f485cfd23c55a4ac644a26cdf0294087de00ed9e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 09:46:20 -0400 Subject: [PATCH 1496/1813] Update hmftools-orange to 3.4.0 (#47186) --- recipes/hmftools-orange/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-orange/meta.yaml b/recipes/hmftools-orange/meta.yaml index 12b5ae774a8cb..d49445d0d739d 100644 --- a/recipes/hmftools-orange/meta.yaml +++ b/recipes/hmftools-orange/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.3.1" %} -{% set sha256 = "31f0845ab593b7939e02d17605704ba371162f3874ed958b451f9f247ac64847" %} +{% set version = "3.4.0" %} +{% set sha256 = "a9a4da946a938f3964ada5f213514ee65c4991a7cf9f263f48e55cfbed774196" %} package: name: hmftools-orange From 7fd4ae32056a884ff1dfb7e774ec50c60ccf8d15 Mon Sep 17 00:00:00 2001 From: Ralf Gabriels Date: Fri, 12 Apr 2024 16:41:30 +0200 Subject: [PATCH 1497/1813] Add ms2rescore-rs recipe (#47022) * Add ms2rescore-rs recipe * Fix linting errors * Remove unused cxx compiler dependency * Update recipes/ms2rescore-rs/meta.yaml Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ms2rescore-rs/build.sh | 21 ++++++++++++++ recipes/ms2rescore-rs/meta.yaml | 50 +++++++++++++++++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 recipes/ms2rescore-rs/build.sh create mode 100644 recipes/ms2rescore-rs/meta.yaml diff --git a/recipes/ms2rescore-rs/build.sh b/recipes/ms2rescore-rs/build.sh new file mode 100644 index 0000000000000..89752b0073526 --- /dev/null +++ b/recipes/ms2rescore-rs/build.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +# -e = exit on first error +# -x = print every executed command +set -ex + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# Use a custom temporary directory as home on macOS. +# (not sure why this is useful, but people use it in bioconda recipes) +if [ `uname` == Darwin ]; then + export HOME=`mktemp -d` +fi + +# Build the package using maturin - should produce *.whl files. +maturin build --interpreter $PYTHON --release + +# Install *.whl files using pip +$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml new file mode 100644 index 0000000000000..88600a3dc4277 --- /dev/null +++ b/recipes/ms2rescore-rs/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "ms2rescore-rs" %} +{% set version = "0.1.0" %} +{% set sha256 = "8dcf6f44f482c3424358ab88e4a9a84e7fbcde2ebce207f419faaa24c336c60c" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore_rs-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + skip: True # [py < 37] + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('rust') }} + - make + - cmake + host: + - zlib + - python + - maturin >=1.5,<2.0 + - pip + run: + - python + +test: + imports: + - ms2rescore_rs + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/compomics/ms2rescore-rs + summary: "Rust functionality for the MS²Rescore package" + license: Apache-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - CompOmics + - RalfG From d8e3a7d642a257b8627bc960959f6e0366cd4abe Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Fri, 12 Apr 2024 10:53:53 -0400 Subject: [PATCH 1498/1813] fix: Azure for osx, do not force home to be the working directory (#47171) * debug nightly build via PR * bump recipe for testing * fix: do not force home to be the working directory * revert test changes --- azure-pipeline-master.yml | 1 - azure-pipeline-nightly.yml | 1 - 2 files changed, 2 deletions(-) diff --git a/azure-pipeline-master.yml b/azure-pipeline-master.yml index 30030ff694fed..8cf42d62dcb1f 100644 --- a/azure-pipeline-master.yml +++ b/azure-pipeline-master.yml @@ -118,7 +118,6 @@ jobs: conda activate bioconda export OSTYPE="darwin" export CI="true" - export HOME=`pwd` bioconda-utils handle-merged-pr recipes config.yml \ --repo bioconda/bioconda-recipes \ diff --git a/azure-pipeline-nightly.yml b/azure-pipeline-nightly.yml index 439dcdad88a82..eac4139cd5875 100644 --- a/azure-pipeline-nightly.yml +++ b/azure-pipeline-nightly.yml @@ -133,7 +133,6 @@ jobs: conda activate bioconda export OSTYPE="darwin" export CI="true" - export HOME=`pwd` bioconda-utils build recipes config.yml \ --anaconda-upload \ --prelint From d6d411440069a8947c6aa6a08da787c93819ea52 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Fri, 12 Apr 2024 11:00:44 -0400 Subject: [PATCH 1499/1813] ci: specify macos version to control architecture (#47067) --- .github/workflows/Bulk.yml | 2 +- .github/workflows/PR.yml | 2 +- .github/workflows/master.yml | 2 +- .github/workflows/nightly.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index e8eeb8712145d..8a3ec217f3ebb 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -77,7 +77,7 @@ jobs: build-osx: name: Bulk OSX Builds if: "contains(github.event.head_commit.message, '[ci run]')" - runs-on: macOS-latest + runs-on: macos-13 strategy: fail-fast: false max-parallel: 4 diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml index f7bbb0178d3fd..272739ef7b06a 100644 --- a/.github/workflows/PR.yml +++ b/.github/workflows/PR.yml @@ -165,7 +165,7 @@ jobs: build-osx: name: OSX Tests - runs-on: macOS-latest + runs-on: macos-13 strategy: fail-fast: true max-parallel: 4 diff --git a/.github/workflows/master.yml b/.github/workflows/master.yml index 4a3fd95875aab..e698443590e50 100644 --- a/.github/workflows/master.yml +++ b/.github/workflows/master.yml @@ -71,7 +71,7 @@ jobs: build-osx: name: OSX Upload if: github.repository == 'bioconda/bioconda-recipes' - runs-on: macOS-latest + runs-on: macos-13 strategy: fail-fast: false max-parallel: 4 diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml index f2954e626d069..11d48c1154598 100644 --- a/.github/workflows/nightly.yml +++ b/.github/workflows/nightly.yml @@ -65,7 +65,7 @@ jobs: build-osx: name: OSX Tests if: github.repository == 'bioconda/bioconda-recipes' - runs-on: macOS-latest + runs-on: macos-13 strategy: fail-fast: false max-parallel: 4 From af63f464e6e2dbf4c86e47879ac7a2697a9a35ac Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Fri, 12 Apr 2024 11:02:15 -0400 Subject: [PATCH 1500/1813] Bioconductor 3.18 leftovers (#45022) --- .../build_failure.linux-64.yaml | 104 ------------------ recipes/bioconductor-cocoa/meta.yaml | 1 - .../build_failure.linux-64.yaml | 104 ------------------ recipes/bioconductor-enrichtf/meta.yaml | 1 - .../build_failure.linux-64.yaml | 104 ------------------ recipes/bioconductor-otubase/meta.yaml | 1 - .../build_failure.linux-64.yaml | 104 ------------------ 7 files changed, 419 deletions(-) delete mode 100644 recipes/bioconductor-cocoa/build_failure.linux-64.yaml delete mode 100644 recipes/bioconductor-enrichtf/build_failure.linux-64.yaml delete mode 100644 recipes/bioconductor-otubase/build_failure.linux-64.yaml delete mode 100644 recipes/bioconductor-promise/build_failure.linux-64.yaml diff --git a/recipes/bioconductor-cocoa/build_failure.linux-64.yaml b/recipes/bioconductor-cocoa/build_failure.linux-64.yaml deleted file mode 100644 index 65ed04bfcc672..0000000000000 --- a/recipes/bioconductor-cocoa/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: dd85fa037d453102ef61e3f47e51564c9d31f479966d88c0b89e752d33f8ea37 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - bioconda/noarch 100% - pkgs/main/linux-64 - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gbioconda/noarch - [] 1.5s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/linux-64 100% - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 - [] 1.6s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/noarch - [] 1.7s - conda-forge/linux-64 - conda-forge/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.8s - conda-forge/linux-64 - conda-forge/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.9s - conda-forge/linux-64 - conda-forge/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 2.0s - conda-forge/linux-64 - conda-forge/noarch 100% - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 2.1s - conda-forge/linux-64 - conda-forge/noarch 100% - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gconda-forge/noarch - [] 2.2s - conda-forge/linux-64 - pkgs/r/linux-64 - pkgs/r/noarch 100%[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/r/noarch - pkgs/r/linux-64 - [] 2.3s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.5s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.6s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.7s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.8s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.9s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.3s - [2K[1A[2K[0Gconda-forge/linux-64 - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.2MB/s 0.0s - opt/conda/conda-bld/noarch 1.1kB @ 22.3MB/s 0.0s - [?25hTraceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree - test(pkg, config=metadata.config.copy(), stats=stats) - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test - environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, - File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env - display_actions(actions, index) - File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions - actions['LINK'] = [index[d] for d in actions['LINK']] - File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in - actions['LINK'] = [index[d] for d in actions['LINK']] - KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cocoa/meta.yaml b/recipes/bioconductor-cocoa/meta.yaml index 6a4528f450642..f61f932994f3b 100644 --- a/recipes/bioconductor-cocoa/meta.yaml +++ b/recipes/bioconductor-cocoa/meta.yaml @@ -58,4 +58,3 @@ about: summary: 'Coordinate Covariation Analysis' description: 'COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - diff --git a/recipes/bioconductor-enrichtf/build_failure.linux-64.yaml b/recipes/bioconductor-enrichtf/build_failure.linux-64.yaml deleted file mode 100644 index 0885f7bb52630..0000000000000 --- a/recipes/bioconductor-enrichtf/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 1c991de1bbfe0824a102700e267a7f4665d9ce725d1b2ee87b87e8ec4ccbd588 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/linux-64 - pkgs/main/noarch - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.5s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/linux-64 100% - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.6s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/linux-64 100% - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 - [] 1.7s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.8s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/noarch - pkgs/r/noarch - [] 1.9s - conda-forge/linux-64 - conda-forge/noarch - pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0G[] 2.0s - conda-forge/linux-64 - conda-forge/noarch 100% - pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0G[] 2.1s - conda-forge/linux-64 - pkgs/r/linux-64 [2K[1A[2K[1A[2K[0Gconda-forge/noarch - pkgs/r/linux-64 - [] 2.2s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.3s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s - 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conda-forge/linux-64 [2K[1A[2K[0G[] 5.0s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.3s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.4s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.5s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.6s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.7s - [2K[1A[2K[0Gconda-forge/linux-64 - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.1MB/s 0.0s - opt/conda/conda-bld/noarch 1.4kB @ 28.7MB/s 0.0s - [?25hTraceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree - test(pkg, config=metadata.config.copy(), stats=stats) - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test - environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, - File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env - display_actions(actions, index) - File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions - actions['LINK'] = [index[d] for d in actions['LINK']] - File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in - actions['LINK'] = [index[d] for d in actions['LINK']] - KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-enrichtf/meta.yaml b/recipes/bioconductor-enrichtf/meta.yaml index 942370c55322c..5637a45861a28 100644 --- a/recipes/bioconductor-enrichtf/meta.yaml +++ b/recipes/bioconductor-enrichtf/meta.yaml @@ -70,4 +70,3 @@ about: summary: 'Transcription Factors Enrichment Analysis' description: 'As transcription factors (TFs) play a crucial role in regulating the transcription process through binding on the genome alone or in a combinatorial manner, TF enrichment analysis is an efficient and important procedure to locate the candidate functional TFs from a set of experimentally defined regulatory regions. While it is commonly accepted that structurally related TFs may have similar binding preference to sequences (i.e. motifs) and one TF may have multiple motifs, TF enrichment analysis is much more challenging than motif enrichment analysis. Here we present a R package for TF enrichment analysis which combine motif enrichment with the PECA model.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - diff --git a/recipes/bioconductor-otubase/build_failure.linux-64.yaml b/recipes/bioconductor-otubase/build_failure.linux-64.yaml deleted file mode 100644 index ffb92d761f8f5..0000000000000 --- a/recipes/bioconductor-otubase/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 2466376a66b53bb6cdb3dff2c8ae7300a0ed3b25e36f88bb855a119a89b9d177 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - [] 1.2s - conda-forge/linux-64 - conda-forge/noarch - bioconda/linux-64 100% - pkgs/main/linux-64 - pkgs/main/noarch - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gbioconda/linux-64 - [] 1.3s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/linux-64 - pkgs/main/noarch - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.4s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/linux-64 100% - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 - [] 1.5s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.6s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/noarch - [] 1.7s - conda-forge/linux-64 - conda-forge/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.8s - conda-forge/linux-64 - conda-forge/noarch 100% - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gconda-forge/noarch - [] 1.9s - conda-forge/linux-64 - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[0Gpkgs/r/noarch - pkgs/r/linux-64 - [] 2.0s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.1s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.2s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.3s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.5s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.6s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.7s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.8s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.9s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s - [2K[1A[2K[0Gconda-forge/linux-64 - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.6MB/s 0.0s - opt/conda/conda-bld/noarch 922.0 B @ 18.8MB/s 0.0s - [?25hTraceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree - test(pkg, config=metadata.config.copy(), stats=stats) - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test - environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, - File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env - display_actions(actions, index) - File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions - actions['LINK'] = [index[d] for d in actions['LINK']] - File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in - actions['LINK'] = [index[d] for d in actions['LINK']] - KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-otubase/meta.yaml b/recipes/bioconductor-otubase/meta.yaml index 51975ccd38e1e..b6a36eb811848 100644 --- a/recipes/bioconductor-otubase/meta.yaml +++ b/recipes/bioconductor-otubase/meta.yaml @@ -52,4 +52,3 @@ extra: name: bioconductor-otubase path: recipes/bioconductor-otubase version: 1.30.0 - diff --git a/recipes/bioconductor-promise/build_failure.linux-64.yaml b/recipes/bioconductor-promise/build_failure.linux-64.yaml deleted file mode 100644 index cf404d42c073a..0000000000000 --- a/recipes/bioconductor-promise/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 5b781e0fa5e8b6eb7b4e980f15193540530dbd5b63b9a1fb5db07f32907673c6 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.2s - conda-forge/linux-64 - conda-forge/noarch - bioconda/linux-64 - pkgs/main/linux-64 - pkgs/main/noarch - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gbioconda/linux-64 - [] 1.3s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/linux-64 - pkgs/main/noarch - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.4s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/linux-64 100% - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 - [] 1.5s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.6s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.7s - conda-forge/linux-64 - conda-forge/noarch - pkgs/main/noarch - pkgs/r/linux-64 - pkgs/r/noarch 100%[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/r/noarch - pkgs/main/noarch - [] 1.8s - conda-forge/linux-64 - conda-forge/noarch 100% - pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0G[] 1.9s - conda-forge/linux-64 - conda-forge/noarch 100% - pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0Gconda-forge/noarch - pkgs/r/linux-64 - [] 2.0s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.1s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.2s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.3s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s - conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s - conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.5s - conda-forge/linux-64 [2K[1A[2K[0G[] 4.6s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.7s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.8s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.9s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s - conda-forge/linux-64 100%[2K[1A[2K[0Gconda-forge/linux-64 - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.2MB/s 0.0s - opt/conda/conda-bld/noarch 748.0 B @ 15.0MB/s 0.0s - [?25hTraceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree - test(pkg, config=metadata.config.copy(), stats=stats) - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test - environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, - File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env - display_actions(actions, index) - File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions - actions['LINK'] = [index[d] for d in actions['LINK']] - File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in - actions['LINK'] = [index[d] for d in actions['LINK']] - KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) -# Last 100 lines of the build log. From e62ed7fbe9c521fef4e2d7bc0e86098a38f4626c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 11:48:57 -0400 Subject: [PATCH 1501/1813] Update bindash to 2.3 (#47199) --- recipes/bindash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bindash/meta.yaml b/recipes/bindash/meta.yaml index 8944473900559..7c0643e62aca4 100644 --- a/recipes/bindash/meta.yaml +++ b/recipes/bindash/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.2" %} +{% set version = "2.3" %} package: name: bindash @@ -6,7 +6,7 @@ package: source: url: https://github.com/jianshu93/bindash/archive/v{{ version }}.tar.gz - sha256: 0d7cec8c93cd435896ebaee41cee87f5baa8c0feddf8396dba00c1593de3757e + sha256: 6e4bf36fd04195ed0738ea8bf835eca1e400b5ce6eef3902bdf0673955d15166 build: skip: True # [osx] From e3541670517e1d8423e2e893ef444e1329a2f049 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 12:07:20 -0400 Subject: [PATCH 1502/1813] Update cutadapt to 4.8 (#47195) --- recipes/cutadapt/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/cutadapt/meta.yaml b/recipes/cutadapt/meta.yaml index 7931a59bdc867..5b7e6a9e62d14 100644 --- a/recipes/cutadapt/meta.yaml +++ b/recipes/cutadapt/meta.yaml @@ -1,15 +1,15 @@ -{% set version = "4.7" %} +{% set version = "4.8" %} package: name: cutadapt version: {{ version }} source: - url: https://files.pythonhosted.org/packages/92/0f/acf2c1055b31c0cf9edc4a46dd6b900905989d78602aef62293b52057fcb/cutadapt-4.7.tar.gz - sha256: 8738a35b363eaf615665a4e7d1b4beb385cd93fb7ffdcf82cd4ab6457acc879b + url: https://files.pythonhosted.org/packages/c6/a7/7d5399e15747df9d203ecd12f510665db1a38b2bddac4e69eb715f2f90fe/cutadapt-4.8.tar.gz + sha256: ac852f6b5f2d1147d0d34bef2eaa5879776f81c69a35dd328a701aae39ec6034 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" skip: True # [py < 38] run_exports: From 68c45cf49d53552543dbec168d391d48b5035ae7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 13:12:48 -0400 Subject: [PATCH 1503/1813] Update ms2rescore-rs to 0.2.0 (#47198) --- recipes/ms2rescore-rs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml index 88600a3dc4277..bcdfc966cdbb1 100644 --- a/recipes/ms2rescore-rs/meta.yaml +++ b/recipes/ms2rescore-rs/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ms2rescore-rs" %} -{% set version = "0.1.0" %} -{% set sha256 = "8dcf6f44f482c3424358ab88e4a9a84e7fbcde2ebce207f419faaa24c336c60c" %} +{% set version = "0.2.0" %} +{% set sha256 = "561ed92f58fd7ecccc78b3e4b1bc91ffa36d0f2e58d54f7ea317898f3ea55560" %} package: name: {{ name|lower }} From 170fcd32c95a8df695e2e00c0e85e71888bfeaa7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Apr 2024 13:13:00 -0400 Subject: [PATCH 1504/1813] Update orthanq to 1.3.0 (#47194) --- recipes/orthanq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/orthanq/meta.yaml b/recipes/orthanq/meta.yaml index fcd3ab4b27ca6..7d7192a893d7d 100644 --- a/recipes/orthanq/meta.yaml +++ b/recipes/orthanq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.0" %} +{% set version = "1.3.0" %} package: name: orthanq @@ -11,7 +11,7 @@ build: source: url: https://github.com/orthanq/orthanq/archive/v{{ version }}.tar.gz - sha256: dbb7e68ef2c16d23aad479978b5403ae652e05a0b37635f55b59c61e08197477 + sha256: 87097f24321bfb21f109a7d995a4318fba8add9389c7e4c4598a0a70a795283a requirements: build: From 3332163f915dc467ac689f47d97eda9c211c8d64 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Fri, 12 Apr 2024 21:45:13 +0200 Subject: [PATCH 1505/1813] Add awk and sed to merqury dependencies (#47201) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Add awk and sed to merqury dependencies Both are requirements not necessarily present in a working version on host systems and are used in merqury-mash.sh. In particular `awk -v name=$name '{print name"\t"$2"\t"-10*log(1-$1)/log(10)"\t"(1-$1)}'` fails with busybox awk: `Math support is not compiled in` * Bump build number * add run_exports * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/merqury/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/merqury/meta.yaml b/recipes/merqury/meta.yaml index 9949181ef7d8d..583ae7429b8e1 100644 --- a/recipes/merqury/meta.yaml +++ b/recipes/merqury/meta.yaml @@ -11,8 +11,10 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 noarch: generic + run_exports: + - {{ pin_subpackage("merqury", max_pin='x.x') }} requirements: run: @@ -25,6 +27,8 @@ requirements: - bedtools >=2.29.2 - samtools >=1.10 - mscorefonts + - gawk + - sed test: commands: From 774c695ad3985ad40c91efbd3081d774c5d0b5af Mon Sep 17 00:00:00 2001 From: ljmciver Date: Sat, 13 Apr 2024 00:25:30 -0600 Subject: [PATCH 1506/1813] Update Maaslin2 version to use latest from BioC (#46915) * Update meta.yaml Updating Maaslin2 recipe to latest bioC version. * Update build-fail-blacklist Remove maaslin2 from blacklist for PR to build/test * Update meta.yaml to include run_exports * Update meta.yaml reset build number to zero * Update meta.yaml, update sha256 to match * Update meta.yaml, add dependency * Update recipes/maaslin2/meta.yaml, use version variable for url, thank you martin-g Co-authored-by: Martin Grigorov * Update recipes/maaslin2/meta.yaml, use name variable for pin, thank you martin-g Co-authored-by: Martin Grigorov * Update meta.yaml, update license_file and maintainers, thanks to npavlovikj suggestion --------- Co-authored-by: Martin Grigorov --- build-fail-blacklist | 1 - recipes/maaslin2/meta.yaml | 14 ++++++++++---- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index bc1cb568f9bee..a47de0c5488c1 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -696,7 +696,6 @@ recipes/sc3-scripts recipes/riboseqc # Some UnsatisfiableError -recipes/maaslin2 recipes/music-deconvolution # Bulk times out while solving environment diff --git a/recipes/maaslin2/meta.yaml b/recipes/maaslin2/meta.yaml index 08fb4ed966786..faa14bf9d455a 100644 --- a/recipes/maaslin2/meta.yaml +++ b/recipes/maaslin2/meta.yaml @@ -1,19 +1,21 @@ {% set name = "MaAsLin2" %} -{% set version = "0.99.12" %} -{% set sha256 = "694b79550c59ad1d872bc89d68e516b0682ba5ce4a5fdc9dfe3b29a9e7524849" %} +{% set version = "1.16.0" %} +{% set sha256 = "38261a85db7dce552590110eed241e679307f5e6c0b67f1667d68c65c86e25b5" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://bitbucket.org/biobakery/maaslin2/get/0.99.12.tar.gz + url: https://www.bioconductor.org/packages/release/bioc/src/contrib/Maaslin2_{{ version }}.tar.gz sha256: {{ sha256 }} patches: - rpath.patch build: - number: 1 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + number: 0 noarch: generic # This is required to make R link correctly on Linux. rpaths: @@ -41,6 +43,7 @@ requirements: - r-optparse - r-hash - r-cplm + - r-glmmtmb run: - r-base - bioconductor-edger @@ -61,6 +64,7 @@ requirements: - r-optparse - r-hash - r-cplm + - r-glmmtmb test: commands: @@ -70,8 +74,10 @@ test: about: home: http://huttenhower.sph.harvard.edu/maaslin2 license: Custom OSS + license_file: LICENSE summary: "MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata." extra: maintainers: - npavlovikj + - ljmciver From 8edafb7eb857673b6a83f4125dc2537996920cbb Mon Sep 17 00:00:00 2001 From: Ryan Morrison <54183277+ryanmorrison22@users.noreply.github.com> Date: Sat, 13 Apr 2024 18:51:25 +0100 Subject: [PATCH 1507/1813] Add KPop (#46313) * Add KPop * Updated kpop meta.yaml to version 1.1.1 * Update recipes/kpop/meta.yaml Co-authored-by: Ryan Dale * Update build.sh * Implemented all changes discussed in the code review * Reverted to use of should_be_noarch_generic as the "sources" are platform-dependent * Corrected dependency on future version of BiOCamLib :) * Remove BioCamLib dependency --------- Co-authored-by: Ryan Morrison Co-authored-by: Paolo Ribeca Co-authored-by: Ryan Dale --- recipes/kpop/build.sh | 7 ++++++ recipes/kpop/meta.yaml | 50 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 recipes/kpop/build.sh create mode 100644 recipes/kpop/meta.yaml diff --git a/recipes/kpop/build.sh b/recipes/kpop/build.sh new file mode 100644 index 0000000000000..5a56f71b06c0b --- /dev/null +++ b/recipes/kpop/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +cp $SRC_DIR/KPop* $PREFIX/bin + +chmod +x $PREFIX/bin +chmod +x $PREFIX/bin/KPop* diff --git a/recipes/kpop/meta.yaml b/recipes/kpop/meta.yaml new file mode 100644 index 0000000000000..2ed264f8d134b --- /dev/null +++ b/recipes/kpop/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "kpop" %} +{% set version = "1.1.1" %} +{% set sha_linux = "915eb6d4e0b41b4f6409b5fd97188193106b3300734c92131ab8ad0618051e4a" %} +{% set sha_macos = "06c15129e9ecea58092f5e4d5df136a0c227815f011f80f63ad9093d70cc46d3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + - url: https://github.com/PaoloRibeca/KPop/releases/download/v{{ version }}/KPop-{{ version }}-Linux_x86-64.tar.xz # [linux] + sha256: {{ sha_linux }} # [linux] + - url: https://github.com/PaoloRibeca/KPop/releases/download/v{{ version }}/KPop-{{ version }}-MacOS_x86-64.tar.xz # [osx] + sha256: {{ sha_macos }} # [osx] + +build: + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + number: 0 + +requirements: + run: + - r-data.table + - r-ca + +test: + commands: + - KPopCount -V + - KPopCountDB -V + - KPopTwist_ -V + - KPopTwistDB -V + +about: + home: https://github.com/PaoloRibeca/KPop + license: GPL-3.0-only + license_file: LICENSE + summary: 'An assembly-free and scalable method for the comparative analysis of microbial genomes, based on full k-mer spectra and dataset-specific transformations.' + description: + KPop is an assembly-free and scalable method for the comparative analysis of microbial genomes, + based on full k-mer spectra and dataset-specific transformations. It is built using OCaml and R . + dev_url: https://github.com/PaoloRibeca/KPop + +extra: + skip-lints: + - should_be_noarch_generic + identifiers: + - doi:10.1101/2022.06.22.497172 + recipe-maintainers: + - PaoloRibeca + - ryanmorrison22 From 2b4d212d2750a4b1832d34502ba86c42f77549a2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Apr 2024 14:35:45 -0400 Subject: [PATCH 1508/1813] Update perl-parallel-loops to 0.12 (#45142) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update perl-parallel-loops to 0.12 * added run export as required by linter * reset build number to 0 --------- Co-authored-by: Felix Kühnl Co-authored-by: Felix Kuehnl --- recipes/perl-parallel-loops/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/perl-parallel-loops/meta.yaml b/recipes/perl-parallel-loops/meta.yaml index 99eb9562f6bb9..d87e272c6e1db 100644 --- a/recipes/perl-parallel-loops/meta.yaml +++ b/recipes/perl-parallel-loops/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-parallel-loops" %} -{% set version = "0.10" %} -{% set sha256 = "6f967b46e7a363b16871b9991c359e142dc3b2281cfe9b1af39904704c8bd2aa" %} +{% set version = "0.12" %} +{% set sha256 = "b66c8fe2fd519873c8a7b6ad1d1a04df2026912259b5e28a41e51d9c9b154150" %} package: name: {{ name }} @@ -12,7 +12,11 @@ source: build: noarch: generic - number: 1 + number: 0 + run_exports: + weak: + - {{ name }} ={{ version }} + requirements: build: From 7684f034bb65336d4ccf40e42192ca70ba8b242c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Apr 2024 14:44:56 -0400 Subject: [PATCH 1509/1813] Update gffutils to 0.13 (#47211) * Update gffutils to 0.13 * clean up dependencies --------- Co-authored-by: Ryan Dale --- recipes/gffutils/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/gffutils/meta.yaml b/recipes/gffutils/meta.yaml index 30f72adae5628..f57c8e24baa63 100644 --- a/recipes/gffutils/meta.yaml +++ b/recipes/gffutils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gffutils" %} -{% set version = "0.12" %} -{% set sha256 = "b31e261db5bd8737cb712c361c129eb2c373ef62f03b62770320589f10da1983" %} +{% set version = "0.13" %} +{% set sha256 = "b0d52f35c014cc0330fb5c4e3c6fea127c90ccf4c5384a825cdb5c8ff330d4eb" %} package: name: "{{ name|lower }}" @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -25,9 +25,8 @@ requirements: - argcomplete >=1.9.4 - argh >=0.26.2 - pyfaidx >=0.5.5.2 - - python <3.12 + - python - simplejson - - six >=1.12.0 test: imports: From 930dc168ae0b25bd99339c5a71499698b21feb11 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Apr 2024 15:00:28 -0400 Subject: [PATCH 1510/1813] Update nthits to 1.0.3 (#47205) --- recipes/nthits/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nthits/meta.yaml b/recipes/nthits/meta.yaml index 7418b9891adb4..ef933a0b68fd5 100644 --- a/recipes/nthits/meta.yaml +++ b/recipes/nthits/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nthits" %} -{% set version = "1.0.2" %} +{% set version = "1.0.3" %} package: name: nthits @@ -7,7 +7,7 @@ package: source: url: https://github.com/bcgsc/ntHits/releases/download/v{{ version }}/{{ name|lower }}-{{ version }}.tar.gz - sha256: f7b18c9d9510a44cc24cec2f24f3e87312330ea70805b559a4989ea47d530e64 + sha256: ee50e825f2c99f859031fa7e5bfe4cbbc71357108c32863e31b40b950cc077b2 build: number: 0 From e003d957521e919c6ed1cf244b03e6218de512fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Apr 2024 15:00:46 -0400 Subject: [PATCH 1511/1813] Update oakvar to 2.9.96 (#47210) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index eaf0155aa7c71..3db375fc44be0 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.95" %} -{% set sha256 = "82323ed140d8c0e8e4631510871ed3fbdaf041fa38112766edf8f1a694c290cb" %} +{% set version = "2.9.96" %} +{% set sha256 = "7b5926b064c5b2f0bd354f2d294e7cd8ee6c64f95a976405e1aa8bed4dafc5a3" %} package: name: {{ name|lower }} From 39c0d926ee4ba28b8c6ee1089cf336bfabe8275e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Apr 2024 15:01:47 -0400 Subject: [PATCH 1512/1813] Update clipkit to 2.2.6 (#47208) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index 893833b69c120..de6539728c1bd 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.2.5" %} +{% set version = "2.2.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c3b530dcd712c26fff626d9ba55a0a8b1517f9f1fbc46e13888cecf7512cd1fb + sha256: 04564dc5399e1cd41ef812a5dc7865a23912b81ef423cbf07a9476ed4b84067b build: number: 0 From eb0ec416fa565224a31928e07375a07250210901 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Sat, 13 Apr 2024 12:02:53 -0700 Subject: [PATCH 1513/1813] Update ntroot to 1.0.1 (#47203) * Update ntroot to 1.0.1 * Add noarch --- recipes/ntroot/build.sh | 8 +++----- recipes/ntroot/meta.yaml | 23 +++++------------------ recipes/ntroot/ntroot.patch | 10 ---------- 3 files changed, 8 insertions(+), 33 deletions(-) delete mode 100644 recipes/ntroot/ntroot.patch diff --git a/recipes/ntroot/build.sh b/recipes/ntroot/build.sh index 8f8449ef386d5..65498faa460dd 100644 --- a/recipes/ntroot/build.sh +++ b/recipes/ntroot/build.sh @@ -1,9 +1,7 @@ #!/bin/bash -export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" -# Build ntRoot mkdir -p ${PREFIX}/bin -meson setup build --prefix ${PREFIX} -cd build -ninja install +cp ntroot ${PREFIX}/bin +cp ntRootAncestryPredictor.pl ${PREFIX}/bin +cp ntroot_run_pipeline.smk ${PREFIX}/bin diff --git a/recipes/ntroot/meta.yaml b/recipes/ntroot/meta.yaml index af7861de8eb89..f61a5fa7999eb 100644 --- a/recipes/ntroot/meta.yaml +++ b/recipes/ntroot/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ntRoot" %} -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: {{ name|lower }} @@ -7,41 +7,28 @@ package: source: url: https://github.com/bcgsc/ntRoot/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: 0de1e98bc9ac4a3eb1d3265358ac866d031190dd2375fa644ac5b34bb71f4795 - patches: - - ntroot.patch + sha256: dd7a72cc0a2d92163a7ff7135e99e034d0831a6da16d3d8731039fff275502b5 build: number: 0 + noarch: generic run_exports: - {{ pin_subpackage("ntroot", max_pin="x") }} requirements: - build: - - {{ compiler('cxx') }} - - cmake host: - python - - meson - - ninja - - llvm-openmp # [osx] - - libgomp # [linux] - - btllib >=1.7.0 - - boost-cpp - - cmake + - perl run: - python - - btllib - snakemake - samtools - - ntcard - - nthits >=1.0.2 + - ntedit >=2.0.1 - perl test: commands: - ntroot -h - - make_genome_bf -h about: home: https://github.com/bcgsc/ntroot diff --git a/recipes/ntroot/ntroot.patch b/recipes/ntroot/ntroot.patch deleted file mode 100644 index 927f59539c481..0000000000000 --- a/recipes/ntroot/ntroot.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- subprojects/ntEdit/meson.build 2024-03-26 15:01:23.000000000 -0700 -+++ subprojects/ntEdit/meson.build.patch 2024-03-26 15:03:25.000000000 -0700 -@@ -32,6 +32,7 @@ - 'ntedit.cpp', - dependencies: dependencies, - include_directories: 'lib', -+ link_args : link_args, - install: true, - ) - From 4fa8512fe8f6b8b52ac93cbd5fdec0fb4e1d7782 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Apr 2024 15:03:16 -0400 Subject: [PATCH 1514/1813] Update sigprofilerplotting to 1.3.22 (#47202) --- recipes/sigprofilerplotting/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sigprofilerplotting/meta.yaml b/recipes/sigprofilerplotting/meta.yaml index 22cc7d698df97..0487d51de9645 100644 --- a/recipes/sigprofilerplotting/meta.yaml +++ b/recipes/sigprofilerplotting/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SigProfilerPlotting" %} -{% set version = "1.3.21" %} +{% set version = "1.3.22" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sigProfilerPlotting-{{ version }}.tar.gz - sha256: 2b7805adc9d00c275bc7cb9af16a732ea3d7cccea68dc8ea3f96b4cd2a405550 + sha256: a14a11504b01fa11f4fade4931818052f42d00fa5eabf107804442f1af066d28 build: entry_points: From bc49185e27ca71bbfd407b0dbdd99b622ca48e12 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Apr 2024 15:03:35 -0400 Subject: [PATCH 1515/1813] Update bed2gff to 0.1.5 (#47209) --- recipes/bed2gff/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bed2gff/meta.yaml b/recipes/bed2gff/meta.yaml index f7e17ea6ec0dd..43a1e954c68bf 100644 --- a/recipes/bed2gff/meta.yaml +++ b/recipes/bed2gff/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bed2gff" %} -{% set version = "0.1.4" %} +{% set version = "0.1.5" %} package: name: bed2gff @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz - sha256: 171c4e334faf50bd7a75d47faaf7e0adda52b820f9af02db282b185af000a0a0 + sha256: 250333a3388a90d0a2f5a927eef220def95f7556e0c7d2344f0f7a37b3efa327 build: number: 0 From 113dbe5e69dd9f06ecf998e5dc520c356550d84e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Apr 2024 15:03:54 -0400 Subject: [PATCH 1516/1813] Update bed2gtf to 1.9.2 (#47207) --- recipes/bed2gtf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bed2gtf/meta.yaml b/recipes/bed2gtf/meta.yaml index 90543d51d327f..8647a4c928c8c 100644 --- a/recipes/bed2gtf/meta.yaml +++ b/recipes/bed2gtf/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bed2gtf" %} -{% set version = "1.9.1" %} +{% set version = "1.9.2" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz - sha256: 7acf7dff631a4d724420110a7a4e28a8324ae9040311567c0feeeec6a33fe661 + sha256: 38bd7528a5a643a4ade316838af36085809bf6476d1b8f37f126d7678fb7e15f build: number: 0 From 1c5b036e8bb6f1cf9f8162d198f012515c62436a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 14 Apr 2024 07:19:26 -0400 Subject: [PATCH 1517/1813] Update deeplcretrainer to 0.2.12 (#47216) --- recipes/deeplcretrainer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/deeplcretrainer/meta.yaml b/recipes/deeplcretrainer/meta.yaml index e3ad13723e94d..635792b35745b 100644 --- a/recipes/deeplcretrainer/meta.yaml +++ b/recipes/deeplcretrainer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLCRetrainer" %} -{% set version = "0.2.11" %} -{% set sha256 = "99b1b2f41abb8d79638cc0731095e4b12bb7ca07ab1d64d87923e6b00154996b" %} +{% set version = "0.2.12" %} +{% set sha256 = "bd31124518f6b5d1f1ec2f0983c0885b44e235b93134cc61c5eab52e2519bdff" %} package: name: {{ name|lower }} From 706c9dd2be7b5395a150c8b8af7fd95ed8b6d506 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 14 Apr 2024 07:24:34 -0400 Subject: [PATCH 1518/1813] Update matchms to 0.24.4 (#47212) --- recipes/matchms/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 83d0bdff09ba5..c61d978f84e73 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.24.3" %} +{% set version = "0.24.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 0ad4d4514d8f2fbd3981f0ba5e7a704261f2db4cf3af63ec42c8a2858384b509 + sha256: 012afda1e28ea0f06592e3b7fab07748ed348d31349416869b35af25859d7619 build: number: 0 From 7cebbe83e921e7e15eef4bd85977f6bf7876a578 Mon Sep 17 00:00:00 2001 From: RolandFaure <64131971+RolandFaure@users.noreply.github.com> Date: Sun, 14 Apr 2024 13:27:33 +0200 Subject: [PATCH 1519/1813] Update HairSplitter version (#47190) * added hairsplitter * correct linting * corrected hairsplitter recipe * updated hairsplitter version to correct bugs in installation * update hairsplitter version --- recipes/hairsplitter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hairsplitter/meta.yaml b/recipes/hairsplitter/meta.yaml index 1f7c712cd742a..1cec99b38b7c2 100644 --- a/recipes/hairsplitter/meta.yaml +++ b/recipes/hairsplitter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "HairSplitter" %} -{% set version = "1.7.14" %} -{% set sha256 = "4bfb058ad7d0b0ea760c1791bd8179a3a5b75b314f3034cb2979f1a26290a3d3" %} +{% set version = "1.7.15" %} +{% set sha256 = "9c713999298c857cf21b964318d6119fc8f2fb6a212a8d907a20e4f0535d7706" %} package: name: {{ name|lower }} From 121000aeed65628285111f58f1ce0fe0217b9b45 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Sun, 14 Apr 2024 14:28:13 +0300 Subject: [PATCH 1520/1813] pairix: add linux-aarch64 build (#47184) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/pairix/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/pairix/meta.yaml b/recipes/pairix/meta.yaml index 186b41f148112..5a39beae8b866 100644 --- a/recipes/pairix/meta.yaml +++ b/recipes/pairix/meta.yaml @@ -11,7 +11,7 @@ source: - src_Makefile.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('pairix', max_pin="x.x") }} @@ -42,3 +42,7 @@ about: license_file: "LICENSE.txt" summary: 2D indexing on bgzipped text files of paired genomic coordinates dev_url: https://github.com/4dn-dcic/pairix + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 88da89ba196e76f583d44c6e0e8637343db834cc Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Sun, 14 Apr 2024 14:31:26 +0300 Subject: [PATCH 1521/1813] hyphy: add linux-aarch64 build (#47183) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/hyphy/build.sh | 13 ++++++++++++- recipes/hyphy/meta.yaml | 4 +++- 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/recipes/hyphy/build.sh b/recipes/hyphy/build.sh index 133335196642c..50ac0f9bd45ef 100644 --- a/recipes/hyphy/build.sh +++ b/recipes/hyphy/build.sh @@ -1,3 +1,14 @@ -cmake -DCMAKE_INSTALL_PREFIX=$PREFIX -DNOAVX=ON . +#!/usr/bin/env bash + +case $(uname -m) in + aarch64) + HYPHY_OPTS="" + ;; + *) + HYPHY_OPTS="-DNOAVX=ON" + ;; +esac + +cmake -DCMAKE_INSTALL_PREFIX=$PREFIX ${HYPHY_OPTS} . make hyphy HYPHYMPI make install diff --git a/recipes/hyphy/meta.yaml b/recipes/hyphy/meta.yaml index 580e79c6c74df..eaa7cacaec924 100644 --- a/recipes/hyphy/meta.yaml +++ b/recipes/hyphy/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("hyphy", max_pin="x.x") }} requirements: @@ -45,5 +45,7 @@ about: dev_url: https://github.com/veg/hyphy extra: + additional-platforms: + - linux-aarch64 container: extended-base: true From cb0aed51e4a716c4c6c18250b595da2467dcf0c8 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Sun, 14 Apr 2024 14:36:55 +0300 Subject: [PATCH 1522/1813] xxmotif: add linux-aarch64 build (#47161) * xxmotif: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Remove xxmotif from the blacklisted recipes Signed-off-by: Martin Tzvetanov Grigorov * Set GCC/G++ to v9 for Linux Signed-off-by: Martin Tzvetanov Grigorov * Try to build with GCC/G++ 7.x Signed-off-by: Martin Tzvetanov Grigorov * Fix the build for xxmotif by implementing == and != for Pool_alloc Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- build-fail-blacklist | 1 - recipes/xxmotif/conda_build_config.yaml | 5 ++++ recipes/xxmotif/fix-build.patch | 32 +++++++++++++++++++++++++ recipes/xxmotif/meta.yaml | 10 +++++++- 4 files changed, 46 insertions(+), 2 deletions(-) create mode 100644 recipes/xxmotif/conda_build_config.yaml create mode 100644 recipes/xxmotif/fix-build.patch diff --git a/build-fail-blacklist b/build-fail-blacklist index a47de0c5488c1..f1582c697e8fa 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -321,7 +321,6 @@ recipes/bam-readcount recipes/mqc recipes/roprofile recipes/chanjo -recipes/xxmotif recipes/phylip recipes/gqt recipes/diamond_add_taxonomy diff --git a/recipes/xxmotif/conda_build_config.yaml b/recipes/xxmotif/conda_build_config.yaml new file mode 100644 index 0000000000000..8caf245450f76 --- /dev/null +++ b/recipes/xxmotif/conda_build_config.yaml @@ -0,0 +1,5 @@ +c_compiler_version: + - 10 # [linux] + +cxx_compiler_version: + - 10 # [linux] diff --git a/recipes/xxmotif/fix-build.patch b/recipes/xxmotif/fix-build.patch new file mode 100644 index 0000000000000..def99e58bc24e --- /dev/null +++ b/recipes/xxmotif/fix-build.patch @@ -0,0 +1,32 @@ +diff --git CMakeLists.txt CMakeLists.txt +index 85c64b6..100a843 100644 +--- CMakeLists.txt ++++ CMakeLists.txt +@@ -9,7 +9,7 @@ set(XXMOTIF_PATCH_VERSION 6) + set(XXMOTIF_VERSION ${XXMOTIF_MAJOR_VERSION}.${XXMOTIF_MINOR_VERSION}.${XXMOTIF_PATCH_VERSION}) + + +-set(CMAKE_CXX_FLAGS "-std=c++11 -DLOG_MAX_LEVEL=0 -D__GXX_EXPERIMENTAL_CXX0X__ -O3 -g3 -pedantic -pedantic-errors -Wall -fmessage-length=0 -fno-strict-aliasing -Wconversion") ++set(CMAKE_CXX_FLAGS "-std=c99 -DLOG_MAX_LEVEL=0 -D__GXX_EXPERIMENTAL_CXX0X__ -O3 -g3 -pedantic -pedantic-errors -Wall -fmessage-length=0 -fno-strict-aliasing -Wconversion") + + set(CMAKE_C_FLAGS "-D__GXX_EXPERIMENTAL_CXX0X__ -O3 -pedantic -pedantic-errors -Wall -fmessage-length=0 -Wconversion") + +diff --git src/memoryPool/pool_alloc.h src/memoryPool/pool_alloc.h +index c1fe05b..925f31d 100644 +--- src/memoryPool/pool_alloc.h ++++ src/memoryPool/pool_alloc.h +@@ -90,4 +90,14 @@ private: + + template Pool Pool_alloc::mem(sizeof(T)); + ++template ++inline bool operator==(const Pool_alloc& a, const Pool_alloc& b){ ++ return &a == &b; ++} ++ ++template ++inline bool operator!=(const Pool_alloc& a, const Pool_alloc& b){ ++ return &a != &b; ++} ++ + #endif /* POOL_ALLOC_H */ diff --git a/recipes/xxmotif/meta.yaml b/recipes/xxmotif/meta.yaml index 8b48a8ae15c6d..d5711f3c9b718 100644 --- a/recipes/xxmotif/meta.yaml +++ b/recipes/xxmotif/meta.yaml @@ -7,10 +7,14 @@ package: source: url: https://github.com/soedinglab/xxmotif/archive/{{ version }}.tar.gz sha256: 235eb8ad562c4757a549751bb290f443ff70c29a142edbff0f03440f097b61cb + patches: + - fix-build.patch build: - number: 3 + number: 4 skip: True # [osx] + run_exports: + - {{ pin_subpackage('xxmotif', max_pin="x") }} requirements: build: @@ -29,3 +33,7 @@ about: test: commands: - test -f ${PREFIX}/bin/XXmotif + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From a3bc36dcdfbf33326ff84167e416ebaa2643c3ee Mon Sep 17 00:00:00 2001 From: Shuai WANG <48624090+wshuai294@users.noreply.github.com> Date: Sun, 14 Apr 2024 19:39:23 +0800 Subject: [PATCH 1523/1813] add localhgt (#47121) * add localhgt * g++ * refine meta.yaml * delete aarch64 * Update recipes/localhgt/meta.yaml Co-authored-by: Martin Grigorov * revision as suggested * some new revisions * change sha256 * add module --------- Co-authored-by: Martin Grigorov --- recipes/localhgt/build.sh | 9 +++++++ recipes/localhgt/meta.yaml | 53 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 recipes/localhgt/build.sh create mode 100644 recipes/localhgt/meta.yaml diff --git a/recipes/localhgt/build.sh b/recipes/localhgt/build.sh new file mode 100644 index 0000000000000..a2d8631a97701 --- /dev/null +++ b/recipes/localhgt/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +make + +mkdir -p $PREFIX/bin + +cp $SRC_DIR/scripts/*py $PREFIX/bin +cp $SRC_DIR/scripts/*sh $PREFIX/bin +cp $SRC_DIR/scripts/extract_ref $PREFIX/bin diff --git a/recipes/localhgt/meta.yaml b/recipes/localhgt/meta.yaml new file mode 100644 index 0000000000000..1ed3dd5aa3c37 --- /dev/null +++ b/recipes/localhgt/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.1" %} + +package: + name: localhgt + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("localhgt", max_pin="x") }} + entry_points: + - localhgt = localhgt:main + +source: + url: https://github.com/deepomicslab/LocalHGT/archive/refs/tags/v{{ version }}.tar.gz + sha256: f06c83372c8ffe9c220f0c4e8cdc1eaec82d52104fe5b32f178555b4a5babfbb + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + run: + - python >=3.7.12 + - scikit-bio >=0.5.6 + - networkx >=2.6.3 + - typing-extensions >=4.11.0 + - pyfaidx + - pysam + - biopython + - scikit-learn + - scipy + - numpy + - pandas + - samtools >=1.11 + - seqkit >=2.6.1 + - bwa >=0.7.17 + - fastp >=0.23.2 + +about: + home: https://github.com/samtools/samtools + license: MIT + summary: Tools for dealing with SAM, BAM and CRAM files + +test: + commands: + - localhgt --help + +extra: + identifiers: + - biotools:localhgt + recipe-maintainers: + - wshuai294 From 675687e65d3eedc1372263a86f0a10cea5c80938 Mon Sep 17 00:00:00 2001 From: Xavier Pastor Date: Sun, 14 Apr 2024 13:41:52 +0200 Subject: [PATCH 1524/1813] Add recipe for igfinder (#47064) * Add igfinder * Updated sources * Added run_exports, corrected versions --------- Co-authored-by: Xavier Pastor --- recipes/igfinder/build.sh | 12 ++++++++++++ recipes/igfinder/meta.yaml | 39 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 recipes/igfinder/build.sh create mode 100644 recipes/igfinder/meta.yaml diff --git a/recipes/igfinder/build.sh b/recipes/igfinder/build.sh new file mode 100644 index 0000000000000..399e98c07b4a2 --- /dev/null +++ b/recipes/igfinder/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +set -x -e + +export LIBRARY_PATH="${PREFIX}/lib" +cp igfinder.py ${LIBRARY_PATH} + +export BINARY_HOME="${PREFIX}/bin" +script=${BINARY_HOME}/igfinder + +echo "#!/bin/bash" > $script +echo "python2 ${LIBRARY_PATH}/igfinder.py \$@" >> $script diff --git a/recipes/igfinder/meta.yaml b/recipes/igfinder/meta.yaml new file mode 100644 index 0000000000000..10c40ce484fd1 --- /dev/null +++ b/recipes/igfinder/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "igfinder" %} +{% set version = "1.0" %} +{% set sha256 = "dc5f65e7e6661c4cd424d7e43ef82e00cd335f688bc0a9f076946d117f57349a" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://tx.bioreg.kyushu-u.ac.jp/igfinder/igfinder.py + sha256: {{ sha256 }} + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('igfinder', max_pin="x.x") }} + +requirements: + build: + - python =2.7 + - biopython + + host: + - python <3 + + run: + - python =2.7 + - biopython + - numpy + +test: + commands: + - "igfinder -h" + +about: + home: https://tx.bioreg.kyushu-u.ac.jp/igfinder + license: MIT + summary: A tool to extract Igh and Igl/Igk gene sequences from assembled transcripts From 0990e5d496a56ba9317ac998c3108bfb772008a3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 14 Apr 2024 07:42:06 -0400 Subject: [PATCH 1525/1813] Update ms2rescore to 3.0.3 (#47071) * Update ms2rescore to 3.0.3 * add ms2rescore-rs --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian --- recipes/ms2rescore/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index c561cb34e5e8d..47c1ca6c892a4 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms2rescore" %} -{% set version = "3.0.2" %} +{% set version = "3.0.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz - sha256: 6049cdf2afdd70244552a47ee369ca89ff3a851440f56e181b01e5f9691fbc12 + sha256: d2ecbe0dd3c23ce598265b265c83c84e515f50fef849c0deac3963c49ba93c77 build: number: 0 @@ -18,7 +18,7 @@ build: - ms2rescore = ms2rescore.__main__:main - ms2rescore-gui = ms2rescore.gui.__main__:main - ms2rescore-report = ms2rescore.report.__main__:main - script: "{{ PYTHON }} -m pip install . --no-deps -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" requirements: host: @@ -34,6 +34,7 @@ requirements: - pyopenms - lxml >=4.5 - ms2pip >=4.0.0-dev8 + - ms2rescore-rs - click >=7 - cascade-config >=0.4.0 - deeplc >=2.2 @@ -56,19 +57,18 @@ test: imports: - ms2rescore commands: - - pip check - ms2rescore --help # - ms2rescore-gui --help - ms2rescore-report --help - requires: - - pip about: home: https://compomics.github.io/projects/ms2rescore/ summary: 'MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and retention times.' dev_url: https://github.com/compomics/ms2rescore license: Apache-2.0 + license_family: APACHE license_file: LICENSE + doc_url: https://ms2rescore.readthedocs.io/en/stable/ extra: container: From d4390f742d35a7547f4819ab7975c444c5712419 Mon Sep 17 00:00:00 2001 From: TPOB <19909103+TTTPOB@users.noreply.github.com> Date: Sun, 14 Apr 2024 19:43:25 +0800 Subject: [PATCH 1526/1813] Add primers recipe (#47047) * Add primers recipe * fix: add run_exports for primers * workaround packaging issue by patch * replace patch with a more standardized one --- ...ectly-write-requirements-in-setup.py.patch | 26 ++++++++++++ recipes/primers/meta.yaml | 40 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 recipes/primers/0001-directly-write-requirements-in-setup.py.patch create mode 100644 recipes/primers/meta.yaml diff --git a/recipes/primers/0001-directly-write-requirements-in-setup.py.patch b/recipes/primers/0001-directly-write-requirements-in-setup.py.patch new file mode 100644 index 0000000000000..bdbba3ec8a854 --- /dev/null +++ b/recipes/primers/0001-directly-write-requirements-in-setup.py.patch @@ -0,0 +1,26 @@ +From d1878dbc60b3e4db625f2b3b320c031fe8bfabb6 Mon Sep 17 00:00:00 2001 +From: tpob +Date: Mon, 8 Apr 2024 19:39:30 +0800 +Subject: [PATCH] directly write requirements in setup.py + +--- + setup.py | 3 +-- + 1 file changed, 1 insertion(+), 2 deletions(-) + +diff --git a/setup.py b/setup.py +index 2750b76..94ac0bf 100644 +--- a/setup.py ++++ b/setup.py +@@ -7,8 +7,7 @@ from setuptools import setup, find_packages + with open("README.md", "r") as fh: + long_description = fh.read() + +-with open("requirements.txt") as f: +- requirements = f.read().splitlines() ++requirements = ["seqfold>=0.7.3"] + + try: + require("setuptools>=38.3") +-- +2.31.1 + diff --git a/recipes/primers/meta.yaml b/recipes/primers/meta.yaml new file mode 100644 index 0000000000000..da109904de0c9 --- /dev/null +++ b/recipes/primers/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "primers" %} +{% set version = "0.5.4" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 6ad13316985a59bba3763a803dbddfbf67a2336a7a51cdaef86d61eabaf434ba + patches: + - 0001-directly-write-requirements-in-setup.py.patch + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('primers', max_pin="x.x") }} + +requirements: + host: + - pip + - python =3 + - setuptools + + run: + - python =3 + - seqfold >=0.7.3 + +test: + imports: + - primers + +about: + home: "https://github.com/Lattice-Automation/primers" + license: MIT + license_file: LICENSE + summary: "This is a small, straightforward tool for creating PCR primers. Its target use-case is DNA assembly." + doc_url: "https://github.com/Lattice-Automation/primers" From dbb57fae8bf3f36e980d56ba5f7b689af0aeb427 Mon Sep 17 00:00:00 2001 From: mm36 <1010170266@qq.com> Date: Sun, 14 Apr 2024 19:45:19 +0800 Subject: [PATCH 1527/1813] add dmtools (#46903) * add new * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up * up --- recipes/dmtools/build.sh | 24 +++++++++++++ recipes/dmtools/conda_build_config.yaml | 7 ++++ recipes/dmtools/meta.yaml | 45 +++++++++++++++++++++++++ 3 files changed, 76 insertions(+) create mode 100644 recipes/dmtools/build.sh create mode 100644 recipes/dmtools/conda_build_config.yaml create mode 100644 recipes/dmtools/meta.yaml diff --git a/recipes/dmtools/build.sh b/recipes/dmtools/build.sh new file mode 100644 index 0000000000000..d52244b3f4425 --- /dev/null +++ b/recipes/dmtools/build.sh @@ -0,0 +1,24 @@ +#!/bin/bash + +export C_INCLUDE_PATH=${PREFIX}/include +export CPLUS_INCLUDE_PATH=${PREFIX}/include +export LIBRARY_PATH=${PREFIX}/lib +export LD_LIBRARY_PATH=${PREFIX}/lib + +##echo make CXX=$CXX CPP=$CXX CC=$CC CFLAGS="-g -w -O3 -Wsign-compare -I$BUILD_PREFIX/include" +make CXX=$CXX CPP=$CXX CC=$CC +#CFLAGS="-g -w -O3 -Wsign-compare -I$PREFIX/include -L$PREFIX/lib" +##export CFLAGS="-I$BUILD_PREFIX/include" +##export LDFLAGS="-L$BUILD_PREFIX/lib" +##CFLAGS="${CFLAGS} -fcommon" +##LDFLAGS="" +##make CXX=$CXX CPP=$CXX CC=$CC LDLIBS="-L$PREFIX/lib -lz -lzstd -ltbb -ltbbmalloc -lpthread" WITH_ZSTD=1 + +mkdir -p $PREFIX/bin +cp dmtools $PREFIX/bin +cp genome2cg $PREFIX/bin +cp genomebinLen $PREFIX/bin +cp dmalign $PREFIX/bin +cp bam2dm $PREFIX/bin +cp dmDMR $PREFIX/bin +cp libBinaMeth.so $PREFIX/lib diff --git a/recipes/dmtools/conda_build_config.yaml b/recipes/dmtools/conda_build_config.yaml new file mode 100644 index 0000000000000..1271f9dfbd295 --- /dev/null +++ b/recipes/dmtools/conda_build_config.yaml @@ -0,0 +1,7 @@ +# current version does not build with newer compilers +cxx_compiler_version: + - 10 # [linux] + - 14 # [osx] +c_compiler_version: + - 10 # [linux] + - 14 # [osx] diff --git a/recipes/dmtools/meta.yaml b/recipes/dmtools/meta.yaml new file mode 100644 index 0000000000000..478f477f896f6 --- /dev/null +++ b/recipes/dmtools/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "dmtools" %} +{% set version = "0.2.6" %} +{% set sha256 = "7492be776a73ed0aea639ec73d78726a37cfa45d6d31baa12dc7ecb7589d41e9" %} + +package: + name: "{{ name|lower }}" + version: {{ version }} + +source: + url: https://github.com/ZhouQiangwei/dmtools/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('dmtools', max_pin="x.x") }} + skip: True # [osx] + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: + - curl + - zlib + - libcurl + - htslib + - gsl + run: + - htslib + - zlib + - gsl + - libcurl + - perl + +test: + commands: + - dmtools + +about: + home: 'https://github.com/ZhouQiangwei/dmtools' + license: MIT + summary: 'BS-seq, WGBS, NOMe-Seq, RRBS data storage and analysis tool dmtools' + doc_url: 'https://dmtools-docs.readthedocs.io/en/latest/index.html' From 0f305c4321c2885d3edfa078c67cbd394b3405cc Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Sun, 14 Apr 2024 14:55:19 +0300 Subject: [PATCH 1528/1813] iow: add linux-aarch64 build (#46804) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/iow/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/iow/meta.yaml b/recipes/iow/meta.yaml index 3e2c487b8cf80..22163552ec6cb 100644 --- a/recipes/iow/meta.yaml +++ b/recipes/iow/meta.yaml @@ -10,8 +10,10 @@ source: sha256: 6b3ddb08f7ec1dec265de4a0f6025c7a4c81df5aa613f3ead5633073b0fe2271 build: - number: 3 + number: 4 skip: True # [py2k] + run_exports: + - {{ pin_subpackage('iow', max_pin='x') }} requirements: build: @@ -50,5 +52,7 @@ about: dev_url: https://github.com/biocore/improved-octo-waddle extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - wasade From 6d518f2ed6be9874b61370d377ed284a8c41b28f Mon Sep 17 00:00:00 2001 From: ChangqingW <87298334+ChangqingW@users.noreply.github.com> Date: Sun, 14 Apr 2024 22:13:13 +1000 Subject: [PATCH 1529/1813] Add seqsizzle (#46415) --- recipes/seqsizzle/LICENSE.md | 662 +++++++++++++++++++++++++++++++++++ recipes/seqsizzle/build.sh | 7 + recipes/seqsizzle/meta.yaml | 40 +++ 3 files changed, 709 insertions(+) create mode 100644 recipes/seqsizzle/LICENSE.md create mode 100644 recipes/seqsizzle/build.sh create mode 100644 recipes/seqsizzle/meta.yaml diff --git a/recipes/seqsizzle/LICENSE.md b/recipes/seqsizzle/LICENSE.md new file mode 100644 index 0000000000000..fe6b9036ba181 --- /dev/null +++ b/recipes/seqsizzle/LICENSE.md @@ -0,0 +1,662 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. + diff --git a/recipes/seqsizzle/build.sh b/recipes/seqsizzle/build.sh new file mode 100644 index 0000000000000..397f07f5695be --- /dev/null +++ b/recipes/seqsizzle/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX diff --git a/recipes/seqsizzle/meta.yaml b/recipes/seqsizzle/meta.yaml new file mode 100644 index 0000000000000..04e45be842289 --- /dev/null +++ b/recipes/seqsizzle/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "0.1.4" %} +{% set sha256 = "8c8fd6ff9c3752676fa6673fe3cdab32220033c0b5790828740430f8890f20e3" %} + +package: + name: seqsizzle + version: {{ version }} + +source: + url: https://github.com/ChangqingW/SeqSizzle/archive/v{{version}}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('seqsizzle', max_pin="x") }} + +requirements: + build: + - {{ compiler("c") }} + - rust + - pkg-config + host: + - xz + - zlib + - bzip2 + run: + - xz + - zlib + - bzip2 + +test: + commands: + - seqsizzle -h + +about: + home: https://github.com/ChangqingW/SeqSizzle + license: AGPL-3.0-or-later + licence_family: AGPL + license_file: LICENSE.md + summary: A pager for viewing FASTQ files with fuzzy adaptor matching and coloring. From 535b2f515e452be4e5e5b1403097685c6414b892 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 14 Apr 2024 10:08:26 -0400 Subject: [PATCH 1530/1813] Update pybbi to 0.4.0 (#47217) --- recipes/pybbi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybbi/meta.yaml b/recipes/pybbi/meta.yaml index 398f334dbcfd6..6277bd7c5c715 100644 --- a/recipes/pybbi/meta.yaml +++ b/recipes/pybbi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybbi" %} -{% set version = "0.3.6" %} +{% set version = "0.4.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "1733b49a86c56848bbdc286b653da7ecfdeb72164516bfac10e54f0f1d49fc2a" + sha256: "afafbc23f16f789344a454fce619af5556a67a2e11b7c36de8fc6f091e2478fc" build: number: 0 From 062e5a716e52f0943e13c2573f586fa7f8209baa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 14 Apr 2024 11:43:12 -0400 Subject: [PATCH 1531/1813] Update ribotricer to 1.4.0 (#47213) * Update ribotricer to 1.4.0 * Update meta.yaml --------- Co-authored-by: Saket Choudhary --- recipes/ribotricer/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/ribotricer/meta.yaml b/recipes/ribotricer/meta.yaml index 5c4100c7a633f..d3195bd2c29fe 100644 --- a/recipes/ribotricer/meta.yaml +++ b/recipes/ribotricer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ribotricer" %} -{% set version = "1.3.3" %} +{% set version = "1.4.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0724fd0acea601a15078e8e3b51e2df5f6b735c276dd978b139619a159f51f75 + sha256: f0f612796f65460f58639cafe297afb1350d6fe7f50d06ea38f372447bdbc63b build: number: 0 @@ -15,6 +15,9 @@ build: entry_points: - ribotricer=ribotricer.cli:cli script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + run_exports: + - {{ pin_subpackage('ribotricer', max_pin="x.x") }} + requirements: host: From 053cac0d4a5684f8d1f9a6d33855efbb70f57b4c Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 15 Apr 2024 10:27:48 +1200 Subject: [PATCH 1532/1813] Added HelitronScanner (#46992) * Added HelitronScanner * Added a wrapper for HelitronScanner.jar * Now using SPDX identifier for lic --- recipes/helitronscanner/HelitronScanner.sh | 64 ++++++++++++++++++++++ recipes/helitronscanner/build.sh | 28 ++++++++++ recipes/helitronscanner/meta.yaml | 31 +++++++++++ 3 files changed, 123 insertions(+) create mode 100644 recipes/helitronscanner/HelitronScanner.sh create mode 100644 recipes/helitronscanner/build.sh create mode 100644 recipes/helitronscanner/meta.yaml diff --git a/recipes/helitronscanner/HelitronScanner.sh b/recipes/helitronscanner/HelitronScanner.sh new file mode 100644 index 0000000000000..1e028d8f50b7e --- /dev/null +++ b/recipes/helitronscanner/HelitronScanner.sh @@ -0,0 +1,64 @@ +#!/bin/bash +# HelitronScanner executable shell script, adapted from bazam shell script +jar_name="HelitronScanner.jar" + +set -eu -o pipefail + +set -o pipefail +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR + +java=java + +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + pass_args="$pass_args $arg" + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/$jar_name" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/$jar_name" $pass_args +fi +exit diff --git a/recipes/helitronscanner/build.sh b/recipes/helitronscanner/build.sh new file mode 100644 index 0000000000000..ba789741a2457 --- /dev/null +++ b/recipes/helitronscanner/build.sh @@ -0,0 +1,28 @@ +#!/bin/sh +set -x -e + +HELITRONSCANNER_DIR=${PREFIX}/share/HelitronScanner +HELITRONSCANNER_TRAININGSET_PATH=${HELITRONSCANNER_DIR}/TrainingSet + +mkdir -p ${PREFIX}/bin +mkdir -p ${HELITRONSCANNER_DIR} +mkdir -p ${HELITRONSCANNER_TRAININGSET_PATH} + +cp -r HelitronScanner/* ${HELITRONSCANNER_DIR} +cp -r TrainingSet/* ${HELITRONSCANNER_TRAININGSET_PATH} + +cp ${RECIPE_DIR}/HelitronScanner.sh ${HELITRONSCANNER_DIR}/HelitronScanner +chmod +x ${HELITRONSCANNER_DIR}/HelitronScanner +ln -s ${HELITRONSCANNER_DIR}/HelitronScanner ${PREFIX}/bin + +## Set HelitronScanner variables on env activation for training set access +mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d +cat <> ${PREFIX}/etc/conda/activate.d/helitronscanner.sh +export HELITRONSCANNER_PATH=${HELITRONSCANNER_DIR} +export HELITRONSCANNER_TRAININGSET_PATH=${HELITRONSCANNER_TRAININGSET_PATH} +EOF + +cat <> ${PREFIX}/etc/conda/deactivate.d/helitronscanner.sh +unset HELITRONSCANNER_PATH +unset HELITRONSCANNER_TRAININGSET_PATH +EOF diff --git a/recipes/helitronscanner/meta.yaml b/recipes/helitronscanner/meta.yaml new file mode 100644 index 0000000000000..015f10c62f4d1 --- /dev/null +++ b/recipes/helitronscanner/meta.yaml @@ -0,0 +1,31 @@ +{% set name = "HelitronScanner" %} +{% set version = "1.0" %} +{% set sha256 = "936accf4a129bc36b38d10472a5b7295dd00f68cc275952e50fff9d9fa685815" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://sourceforge.net/projects/HelitronScanner/files/HelitronScanner_V{{ version }}.zip + sha256: {{ sha256 }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('helitronscanner', max_pin='x') }} + +requirements: + run: + - openjdk + +test: + commands: + - HelitronScanner scanHead -Xmx2g --help | grep 'Scan for Helitron 5' + - cat "${HELITRONSCANNER_TRAININGSET_PATH}/head.lcvs" | grep 'TCCATAATA' + +about: + home: 'https://sourceforge.net/projects/helitronscanner' + license: GPL-3.0-or-later + summary: HelitronScanner uncovers a large overlooked cache of Helitron transposons in many genomes From 7110cf610a07024d68887d5f7acbbc0d7bc012a7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 00:55:27 -0400 Subject: [PATCH 1533/1813] Update snakefmt to 0.10.1 (#47221) * Update snakefmt to 0.10.1 * Update min. black version --------- Co-authored-by: Michael Hall --- recipes/snakefmt/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/snakefmt/meta.yaml b/recipes/snakefmt/meta.yaml index a86a8e347327b..91ea56d632d39 100644 --- a/recipes/snakefmt/meta.yaml +++ b/recipes/snakefmt/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.10.0" %} +{% set version = "0.10.1" %} package: name: snakefmt @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakefmt/snakefmt-{{ version }}.tar.gz - sha256: 53eae69fc81425e2192684eba76171bd648b05dcba93c9d5f45746d3fadb8617 + sha256: b04a34fc5481b15667c8bc7f23b5722b98ef827b27c6fd6dfbab8b34b245e32b build: number: 0 @@ -19,14 +19,14 @@ build: requirements: host: - - black >=24.1,<25.0 + - black >=24.3,<25.0 - click >=8.0.0,<9.0.0 - pip - python >=3.8 - toml >=0.10.2,<0.11.0 - poetry >=1.3,<2.0 run: - - black >=24.1,<25.0 + - black >=24.3,<25.0 - click >=8.0.0,<9.0.0 - python >=3.8 - toml >=0.10.2,<0.11.0 From 0d1b0333851a36850b74d5164a4db73e86a840df Mon Sep 17 00:00:00 2001 From: Yongze Yin Date: Mon, 15 Apr 2024 01:05:54 -0500 Subject: [PATCH 1534/1813] add tmhg (#47214) * add tmhg * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/tmhg/meta.yaml | 44 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 recipes/tmhg/meta.yaml diff --git a/recipes/tmhg/meta.yaml b/recipes/tmhg/meta.yaml new file mode 100644 index 0000000000000..39414bccf2f77 --- /dev/null +++ b/recipes/tmhg/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "tmhg" %} +{% set version = "1.0.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: 'https://github.com/yongze-yin/tMHG-Finder/archive/refs/tags/v{{version}}.tar.gz' + sha256: a05df84ca80674154cb78f63148e26f023b88af26fa95cc2fa54e34f105efcac + +build: + run_exports: + - {{ pin_subpackage('tmhg', max_pin="x") }} + noarch: generic + number: 0 + script: "{{ PYTHON }} -m pip install ." + +requirements: + host: + - python >=3.6 + run: + - biopython + - blast + - dendropy + - numpy >=1.11 + - pandas >=1.1.3 + - networkx + - biopython + - bedtools >=2.31.1 + - pathos + - mash + - mafft + +test: + commands: + - tmhgf find --help + - tmhgf add --help + +about: + home: https://github.com/yongze-yin/tMHG-Finder/ + license: MIT + summary: tMHG-Finder is a tree-guided tool to partition whole genomes into maximal homologous groups. + From 4d63206e0d6e2672a6a05126755c2eb05c7129d1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 04:42:58 -0400 Subject: [PATCH 1535/1813] Update bwa to 0.7.18 (#47224) Drop superseded patch; add run_exports & additional-platforms; remove redundant zlib `run` dependency. Co-authored-by: John Marshall --- recipes/bwa/Makefile.patch | 16 ---------------- recipes/bwa/build.sh | 5 +---- recipes/bwa/meta.yaml | 13 +++++++------ 3 files changed, 8 insertions(+), 26 deletions(-) delete mode 100644 recipes/bwa/Makefile.patch diff --git a/recipes/bwa/Makefile.patch b/recipes/bwa/Makefile.patch deleted file mode 100644 index 5a26928815dc6..0000000000000 --- a/recipes/bwa/Makefile.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff --git a/Makefile b/Makefile -index 7151435..2f0a4fe 100644 ---- a/Makefile -+++ b/Makefile -@@ -1,9 +1,9 @@ --CC= gcc -+#CC= gcc - #CC= clang --analyze - CFLAGS= -g -Wall -Wno-unused-function -O2 - WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS - AR= ar --DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) -+DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) $(LDFLAGS) - LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \ - QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o - AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ diff --git a/recipes/bwa/build.sh b/recipes/bwa/build.sh index a8ff3c2d2b692..6bdafb538cade 100644 --- a/recipes/bwa/build.sh +++ b/recipes/bwa/build.sh @@ -1,9 +1,6 @@ #!/bin/bash -export C_INCLUDE_PATH=${PREFIX}/include -export LIBRARY_PATH=${PREFIX}/lib - -make CFLAGS="${CFLAGS} -fcommon" +make CC="$CC" CFLAGS="$CFLAGS" CPPFLAGS="$CPPFLAGS" LDFLAGS="$LDFLAGS" mkdir -p $PREFIX/bin mkdir -p $PREFIX/share/man/man1 cp bwa $PREFIX/bin diff --git a/recipes/bwa/meta.yaml b/recipes/bwa/meta.yaml index b781e21c89e93..c4b7f382317b3 100644 --- a/recipes/bwa/meta.yaml +++ b/recipes/bwa/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.17" %} -{% set sha256 = "980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd" %} +{% set version = "0.7.18" %} +{% set sha256 = "194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870" %} package: name: bwa @@ -8,11 +8,11 @@ package: source: url: https://github.com/lh3/bwa/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} - patches: - - Makefile.patch build: - number: 11 + number: 0 + run_exports: + - {{ pin_subpackage("bwa", max_pin="x.x") }} requirements: build: @@ -21,7 +21,6 @@ requirements: host: - zlib run: - - zlib - perl test: @@ -37,6 +36,8 @@ about: summary: The BWA read mapper. extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:bwa - usegalaxy-eu:bwa_mem From 67c1c5f5cdb32f16c8eebf0dd86e9ab1ceffef4b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 05:47:22 -0400 Subject: [PATCH 1536/1813] Update snakemake-executor-plugin-slurm to 0.4.3 (#47187) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake-executor-plugin-slurm to 0.4.3 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 57c874c53a5b3..9d831ade072b6 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.4.2" %} +{% set version = "0.4.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 265ffff24cdaa7929769bdbe822c39d8ac059b0642e92fc6fa9e55c9cdc7d018 + sha256: 976367aa2c444ab169b263c7951294b25b54fcddba88e64210d52876ad132586 build: noarch: python @@ -24,8 +24,8 @@ requirements: run: - python >=3.11.0,<4.0.0 - snakemake-interface-common >=1.13.0,<2.0.0 - - snakemake-interface-executor-plugins >=9.0.0,<10.0.0 - - snakemake-executor-plugin-slurm-jobstep >=0.1.10,<0.2.0 + - snakemake-interface-executor-plugins >=9.1.1,<10.0.0 + - snakemake-executor-plugin-slurm-jobstep >=0.2.0,<0.3.0 - throttler >=1.2.2,<2.0.0 test: From 8590a869ebe5af103cc6f7710b4c8bc92455b5d1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 12:14:46 -0400 Subject: [PATCH 1537/1813] Update monopogen to 1.6.0 (#47225) --- recipes/monopogen/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/monopogen/meta.yaml b/recipes/monopogen/meta.yaml index 9470742aac938..fee69ee522e3c 100644 --- a/recipes/monopogen/meta.yaml +++ b/recipes/monopogen/meta.yaml @@ -1,6 +1,6 @@ {% set name = "Monopogen" %} -{% set version = "1.5.0" %} -{% set sha256 = "dc13817d34a7d5e1294e5b6318fd12e8490c56216fc84ab7ea0f229e96e00053" %} +{% set version = "1.6.0" %} +{% set sha256 = "c0783c3296aed13017d337f2d7b9c7e55d72ac7f0397e83ba0d1c14fe38cb91b" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage('monopogen', max_pin="x") }} From 6c1e4866a24d2f642b504729013db4942aada7bf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 13:34:42 -0400 Subject: [PATCH 1538/1813] Update crispresso2 to 2.3.0 (#47148) * Update crispresso2 to 2.3.0 * Remove flash and trimmomatic dependencies and replace with fastp for CRISPResso2 * Revert changes to crispresso recipe * Remove flash and trimmomatic from CRISPResso2 recipe, replace with fastp * Remove extra space from crispresso recipe * Add run_exports to CRISPResso2 recipe * Add jinja_partials dependency --------- Co-authored-by: Cole Lyman --- recipes/crispresso2/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/crispresso2/meta.yaml b/recipes/crispresso2/meta.yaml index 73a70bc89da04..877e9f4483714 100644 --- a/recipes/crispresso2/meta.yaml +++ b/recipes/crispresso2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.2.14" %} +{% set version = "2.3.0" %} package: name: crispresso2 @@ -7,10 +7,12 @@ package: build: skip: True # [py2k] number: 0 + run_exports: + - {{ pin_subpackage('crispresso2', max_pin='x') }} source: url: https://github.com/pinellolab/CRISPResso2/archive/v{{ version }}.tar.gz - sha256: ec9c5ff4069a651601dd980ef20c60bf14467ec97324c92673f6dcd698b9f844 + sha256: ccbb1c8e27139a10562d154c510149d833841f92370755914020d71e49bcfa33 requirements: build: @@ -29,8 +31,8 @@ requirements: - plotly - matplotlib-base - jinja2 - - trimmomatic - - flash + - jinja_partials + - fastp - samtools - bowtie2 - seaborn-base From 9954b0091989f3f991f53f2ffb9e171c6da5103a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 14:52:44 -0400 Subject: [PATCH 1539/1813] Update htslib to 1.20 (#47235) --- recipes/htslib/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml index 31e786232b9da..0ed226673ba88 100644 --- a/recipes/htslib/meta.yaml +++ b/recipes/htslib/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "1.19.1" %} +{% set version = "1.20" %} package: name: htslib version: {{ version }} build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('htslib', max_pin='x.x') }} source: url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 - sha256: 222d74d3574fb67b158c6988c980eeaaba8a0656f5e4ffb76b5fa57f035933ec + sha256: e52d95b14da68e0cfd7d27faf56fef2f88c2eaf32a2be51c72e146e3aa928544 patches: - arm_hwcap.patch From a89b371aee6fbf18bf87435da18422ab343deb64 Mon Sep 17 00:00:00 2001 From: Charlotte Capitanchik Date: Mon, 15 Apr 2024 19:18:14 +0000 Subject: [PATCH 1540/1813] fix clippy install (#47200) * fix clippy install In newer numpy distributions numpy-base is a part of numpy so looking for it like this causes errors. * linting fix fix linting * Update meta.yaml change run_exports * Update meta.yaml white space * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/clippy/meta.yaml | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/recipes/clippy/meta.yaml b/recipes/clippy/meta.yaml index d0948b1f86c5b..53f2af39d28f4 100644 --- a/recipes/clippy/meta.yaml +++ b/recipes/clippy/meta.yaml @@ -10,29 +10,33 @@ source: sha256: 1fc00fd3df22524cb28974b7aae2d5fc20c6c23c5b84312dbc09ea275cebcf86 build: - number: 0 + number: 1 entry_points: - clippy = clip:main script: "{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps" noarch: python + run_exports: + - {{ pin_subpackage("clippy", max_pin='x.x') }} requirements: host: - pip - - python>=3.8 + - python >=3.8 + - openssl run: - - python>=3.8 - - bedtools=2.26.0 - - numpy>=1.19.0,<1.20.3 - - numpy-base>=1.19.0,<1.20.3 + - python >=3.8 + - bedtools =2.26.0 + - samtools =1.9 + - openssl + - numpy >=1.19.0,<1.20.3 - numpydoc - pandas - pybedtools - scipy - matplotlib-base - - dash=1.20.0 - - dash-bootstrap-components=0.11.3 - - werkzeug=2.0.0 + - dash =1.20.0 + - dash-bootstrap-components =0.11.3 + - werkzeug =2.0.0 test: imports: From b5803e875a5a87e39b3a480652a93f1735a5609c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 17:01:29 -0400 Subject: [PATCH 1541/1813] Update bcftools to 1.20 (#47243) --- recipes/bcftools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index d419fce55b866..6641ea2aeb54d 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -1,17 +1,17 @@ -{% set version="1.19" %} +{% set version="1.20" %} package: name: bcftools version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage("bcftools", max_pin="x") }} source: url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 - sha256: 782b5f1bc690415192231e82213b3493b047f45e630dc8ef6f154d6126ab3e68 + sha256: 312b8329de5130dd3a37678c712951e61e5771557c7129a70a327a300fda8620 requirements: build: From f09588e4cb59bd0929348991dfa9170e49c99bcc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 17:02:33 -0400 Subject: [PATCH 1542/1813] Update samtools to 1.20 (#47244) --- recipes/samtools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index 8b2987bf9ce72..f098279936380 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "1.19.2" %} +{% set version = "1.20" %} package: name: samtools version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage("samtools", max_pin="x") }} source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - sha256: 71f60499668e4c08e7d745fbff24c15cc8a0977abab1acd5d2bb419bdb065e96 + sha256: c71be865e241613c2ca99679c074f1a0daeb55288af577db945bdabe3eb2cf10 requirements: build: From 4ec613efedee4aa6b8d4daf95fb73b58c688f3fe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 19:15:26 -0400 Subject: [PATCH 1543/1813] Update pybiolib to 1.1.1974 (#47241) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 56fc073830c29..896a55fbece51 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1971" %} +{% set version = "1.1.1974" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 54078e51772e8d88e4fcd4ee8206a57fd15816c03b5fde6ca5ea4fb1838d7edd + sha256: c93c0ee7b8fe8296ce3e8a6cac684affa465f31db4f5d777098bf0b22b80aad3 build: noarch: python From f1b60e4fc4df9c3005671de22a6e6947d55b7773 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 19:15:55 -0400 Subject: [PATCH 1544/1813] Update itsxpress to 2.1.0 (#47237) --- recipes/itsxpress/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/itsxpress/meta.yaml b/recipes/itsxpress/meta.yaml index 728781e65e5e5..2ecd49b405f60 100644 --- a/recipes/itsxpress/meta.yaml +++ b/recipes/itsxpress/meta.yaml @@ -1,8 +1,8 @@ {% set name = "itsxpress" %} -{% set version = "2.0.2" %} +{% set version = "2.1.0" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "f89b17cb74b5194fd57e310af53c6973832b91c2183da8fa5b6ed80530a2f1f1" %} +{% set hash_value = "608e5c55526d4c084f8ea552c7bd2d232505ae83751fc517c8ceabb2eb483aed" %} package: name: '{{ name|lower }}' From 007b2609049a380813d55b63ebe393ad4270073b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 19:16:01 -0400 Subject: [PATCH 1545/1813] Update ebi-eva-common-pyutils to 0.6.6 (#47236) --- recipes/ebi-eva-common-pyutils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ebi-eva-common-pyutils/meta.yaml b/recipes/ebi-eva-common-pyutils/meta.yaml index be5d7171e3bb3..5e11341ad5529 100644 --- a/recipes/ebi-eva-common-pyutils/meta.yaml +++ b/recipes/ebi-eva-common-pyutils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ebi-eva-common-pyutils" %} -{% set version = "0.6.5" %} +{% set version = "0.6.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ebi_eva_common_pyutils-{{ version }}.tar.gz - sha256: 4ef517d1dc594510b46b7cc6e039f1c9ee67af6d6810bcad866265e05df89b13 + sha256: 9f55b4482b52fad605e7fbca061f200b82277bfac967fbf55688f5724dd76348 build: script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation From 561468725c9df691a63ca981a483afbf67d5e270 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 19:16:10 -0400 Subject: [PATCH 1546/1813] Update tissuumaps to 3.2.1.5 (#47220) --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index f5db72adfd1e0..0e538a5c241be 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.1.4" %} +{% set version = "3.2.1.5" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 765decbd743ffae399ad35ffff1f925defc26969a1db3512183c7fcb64c9ceb2 + sha256: 0166a573b70e65d8d77fe13d9caf5e804a924313f9e555568b2cc965ee00873e build: number: 0 From 0266c7a1af48a3bb8488ca2c8d4d4a8dc91a7762 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 19:16:42 -0400 Subject: [PATCH 1547/1813] Update snakemake-interface-storage-plugins to 3.2.0 (#47233) --- recipes/snakemake-interface-storage-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-storage-plugins/meta.yaml b/recipes/snakemake-interface-storage-plugins/meta.yaml index 9efb00584f492..2203d95e3e6a7 100644 --- a/recipes/snakemake-interface-storage-plugins/meta.yaml +++ b/recipes/snakemake-interface-storage-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-storage-plugins" %} -{% set version = "3.1.1" %} +{% set version = "3.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_storage_plugins-{{ version }}.tar.gz - sha256: d4d2b72ac964f12c5ba343639499c797316d6368dda471fba63610aec8e77cbb + sha256: 84f9a48d8a413f3d301a645379b79c2aeb1f453016389b140043ba046e37c4f8 build: noarch: python From 352755145010d81bc73ef782ae129d7c05371c96 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Tue, 16 Apr 2024 11:32:27 +1200 Subject: [PATCH 1548/1813] Bump bioconda-repodata-patches for new htslib and libdeflate releases (#47240) --- recipes/bioconda-repodata-patches/gen_patch_json.py | 4 ++-- recipes/bioconda-repodata-patches/meta.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bioconda-repodata-patches/gen_patch_json.py b/recipes/bioconda-repodata-patches/gen_patch_json.py index 7c729627c9df0..21de6d0ce0aa4 100755 --- a/recipes/bioconda-repodata-patches/gen_patch_json.py +++ b/recipes/bioconda-repodata-patches/gen_patch_json.py @@ -169,13 +169,13 @@ def _gen_new_index(repodata, subdir): if has_dep(record, 'htslib'): # skip deps prior to 1.10, which was the first with soversion 3 # TODO adjust replacement (exclusive) upper bound with each new compatible HTSlib - _pin_looser(fn, record, 'htslib', min_lower_bound='1.10', upper_bound='1.20') + _pin_looser(fn, record, 'htslib', min_lower_bound='1.10', upper_bound='1.21') # future libdeflate versions are compatible until they bump their soversion; relax dependencies accordingly if record_name in ['htslib', 'staden_io_lib', 'fastp'] and has_dep(record, 'libdeflate'): # skip deps that allow anything <1.3, which contained an incompatible library filename # TODO adjust the replacement (exclusive) upper bound each time a compatible new libdeflate is released - _pin_looser(fn, record, 'libdeflate', min_lower_bound='1.3', upper_bound='1.20') + _pin_looser(fn, record, 'libdeflate', min_lower_bound='1.3', upper_bound='1.21') # nanosim <=3.1.0 requires scikit-learn<=0.22.1 if record_name.startswith('nanosim') and has_dep(record, "scikit-learn") and version <= "3.1.0": diff --git a/recipes/bioconda-repodata-patches/meta.yaml b/recipes/bioconda-repodata-patches/meta.yaml index 71e65ad66f5eb..311f06f50de80 100644 --- a/recipes/bioconda-repodata-patches/meta.yaml +++ b/recipes/bioconda-repodata-patches/meta.yaml @@ -1,6 +1,6 @@ package: name: bioconda-repodata-patches - version: 20240112 # ensure that this is the "current" date, and always higher than the latest version in master + version: 20240416 # ensure that this is the "current" date, and always higher than the latest version in master source: path: . From 939af968d4126eb01ca261d62e9c7025fe01fe2e Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 16 Apr 2024 02:33:22 +0300 Subject: [PATCH 1549/1813] sorted_nearest: add linux-aarch64 build (#47227) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/sorted_nearest/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/sorted_nearest/meta.yaml b/recipes/sorted_nearest/meta.yaml index 613fe31b6243f..8cd37892ae730 100644 --- a/recipes/sorted_nearest/meta.yaml +++ b/recipes/sorted_nearest/meta.yaml @@ -14,8 +14,10 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 0 + number: 1 script: python setup.py install --single-version-externally-managed --record=record.txt + run_exports: + - {{ pin_subpackage(name|lower, max_pin='x.x') }} requirements: build: @@ -36,3 +38,7 @@ about: home: https://github.com/endrebak/sorted_nearest license: BSD summary: Find nearest interval. + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 9a63ea8dc5fb6228602ec4219a968af1f3bdb89b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Apr 2024 20:12:37 -0400 Subject: [PATCH 1550/1813] Update cnvkit to 0.9.11 (#47204) * Update cnvkit to 0.9.11 * add run_exports --------- Co-authored-by: mencian --- recipes/cnvkit/meta.yaml | 59 +++++++++++++++++++++++++++++----------- 1 file changed, 43 insertions(+), 16 deletions(-) diff --git a/recipes/cnvkit/meta.yaml b/recipes/cnvkit/meta.yaml index b4fce96ae4f94..f39326c930829 100644 --- a/recipes/cnvkit/meta.yaml +++ b/recipes/cnvkit/meta.yaml @@ -1,37 +1,43 @@ -{% set version="0.9.10" %} +{% set name = "cnvkit" %} +{% set version = "0.9.11" %} + package: - name: cnvkit + name: {{ name }} version: {{ version }} source: url: https://github.com/etal/cnvkit/archive/v{{ version }}.tar.gz - sha256: 56739496f1f59511661107e662d81e5fd8af413571e853b0a1b34d882a19349a + sha256: 1763936427184270108fd51219ebc82f542e28339bdec587579b8745f61179a8 build: noarch: python number: 0 - script: {{ PYTHON }} -m pip install . --no-deps -vv + entry_points: + - cnvkit.py = cnvlib.cnvkit:main + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv + run_exports: + - {{ pin_subpackage('cnvkit', max_pin="x.x") }} requirements: host: - - python >=3.5 + - python >=3.8 - pip run: - - python >=3.5 + - python >=3.8 - bioconductor-dnacopy - - biopython >=1.62 - - joblib <1.0 - - matplotlib-base >=1.3.1 + - biopython >=1.80 + - matplotlib-base >=3.5.2 - networkx >=2.4 - - numpy >=1.9 - - pandas >=0.23.3 - - pomegranate >=0.9.0 - - pyfaidx >=0.4.7 - - pysam >=0.16.0 + - numpy >=1.24.2 + - pandas >=1.5.3 + - pomegranate >=0.14.8,<=0.14.9 + - pyfaidx >=0.7.1 + - pysam >=0.20.0 - r-base >=3.4.1 - r-cghflasso - - reportlab >=3.0 - - scipy >=0.15.0 + - reportlab >=3.6.12 + - scikit-learn >=1.1.0 + - scipy >=1.10.1 test: imports: @@ -45,9 +51,30 @@ test: about: home: https://github.com/etal/cnvkit license: Apache-2.0 + license_family: APACHE + license_file: LICENSE summary: Copy number variant detection from high-throughput sequencing + dev_url: https://github.com/etal/cnvkit + doc_url: https://cnvkit.readthedocs.io/en/stable/ extra: identifiers: - biotools:cnvkit - doi:10.1371/journal.pcbi.1004873 + - usegalaxy-eu:cnvkit_access + - usegalaxy-eu:cnvkit_antitarget + - usegalaxy-eu:cnvkit_autobin + - usegalaxy-eu:cnvkit_batch + - usegalaxy-eu:cnvkit_call + - usegalaxy-eu:cnvkit_coverage + - usegalaxy-eu:cnvkit_diagram + - usegalaxy-eu:cnvkit_fix + - usegalaxy-eu:cnvkit_heatmap + - usegalaxy-eu:cnvkit_reference + - usegalaxy-eu:cnvkit_scatter + - usegalaxy-eu:cnvkit_segment + - usegalaxy-eu:cnvkit_target + - usegalaxy-eu:cnvkit_breaks + - usegalaxy-eu:cnvkit_genemetrics + - usegalaxy-eu:cnvkit_segmetrics + - usegalaxy-eu:cnvkit_sex From f664ea98306c8a10af7fb792f33e0e03817465b0 Mon Sep 17 00:00:00 2001 From: Luis Paulin Date: Mon, 15 Apr 2024 23:35:36 -0600 Subject: [PATCH 1551/1813] Update sniffles requirements (#47242) * Update sniffles requirments * Update meta.yaml * Update meta.yaml --- recipes/sniffles/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/sniffles/meta.yaml b/recipes/sniffles/meta.yaml index 890bbadf30a6a..981b06693c8d7 100644 --- a/recipes/sniffles/meta.yaml +++ b/recipes/sniffles/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{sha256}}' build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" run_exports: @@ -23,6 +23,8 @@ requirements: run: - python >=3.10 - pysam >=0.21.0 + - edlib >=1.3.9 + - psutil >=5.9.4 test: commands: From 9784ab9114846099f0c3114904e44eb223234d12 Mon Sep 17 00:00:00 2001 From: Charlie Date: Tue, 16 Apr 2024 03:48:46 -0400 Subject: [PATCH 1552/1813] Add unassigner recipe (#47167) * Init unassigner recipe * Add vsearch as requirement * Add necessary run requirements Co-authored-by: Thanh Lee * Install script ignore installed Co-authored-by: Thanh Lee * Update license to GPLv2+ * Fix run requirements * update license identifier https://spdx.org/licenses/GPL-2.0-or-later.html * Remove unused 'about' fields --------- Co-authored-by: Thanh Lee --- recipes/unassigner/meta.yaml | 46 ++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/unassigner/meta.yaml diff --git a/recipes/unassigner/meta.yaml b/recipes/unassigner/meta.yaml new file mode 100644 index 0000000000000..e3b7bce47b243 --- /dev/null +++ b/recipes/unassigner/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "unassigner" %} +{% set version = "1.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 0a79a0fdf88318a2583e2a46deffb6f6ff4ce612c55b470c007eed7bb9aa2194 + +build: + number: 0 + noarch: python + entry_points: + - unassigner = unassigner.command:main + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + run_exports: + - {{ pin_subpackage('unassigner', max_pin="x") }} + +requirements: + host: + - pip + - python + run: + - python + - vsearch + - biopython + - scipy + +test: + imports: + - unassigner + commands: + - unassigner --help + +about: + home: https://github.com/PennChopMicrobiomeProgram/unassigner + license: GPL-2.0-or-later + license_family: GPL + summary: "Type strain identification for 16S reads" + dev_url: https://github.com/PennChopMicrobiomeProgram/unassigner + +extra: + recipe-maintainers: + - Ulthran From fbef6a2d77ff642545fcb7cf6be60534a9ae56e9 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 16 Apr 2024 13:28:19 +0300 Subject: [PATCH 1553/1813] ucsc-gtftogenepred: add linux-aarch64 build (#47254) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-gtftogenepred/htmshell.patch | 11 +++++++++++ recipes/ucsc-gtftogenepred/meta.yaml | 9 ++++++++- 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 recipes/ucsc-gtftogenepred/htmshell.patch diff --git a/recipes/ucsc-gtftogenepred/htmshell.patch b/recipes/ucsc-gtftogenepred/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-gtftogenepred/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-gtftogenepred/meta.yaml b/recipes/ucsc-gtftogenepred/meta.yaml index e3c78d48bc2a7..87ed2f492e9cb 100644 --- a/recipes/ucsc-gtftogenepred/meta.yaml +++ b/recipes/ucsc-gtftogenepred/meta.yaml @@ -12,13 +12,16 @@ source: sha256: {{ sha256 }} patches: - include.patch + - htmshell.patch build: - number: 0 + number: 1 skip: True # [osx] ignore_run_exports: - libpng - libuuid + run_exports: + - {{ pin_subpackage(package|lower, max_pin=None) }} requirements: build: @@ -48,3 +51,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "Convert a GTF file to a genePred" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From d173f30b8d3531e375faac14b7d407dd961e38dd Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 16 Apr 2024 13:38:40 +0300 Subject: [PATCH 1554/1813] pyrle: add linux-aarch64 build (#47251) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/pyrle/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/pyrle/meta.yaml b/recipes/pyrle/meta.yaml index 5dc32645ae5d5..22700d4dda1c5 100644 --- a/recipes/pyrle/meta.yaml +++ b/recipes/pyrle/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5 build: - number: 0 + number: 1 skip: True # [py2k] script: python setup.py install --single-version-externally-managed --record=record.txt run_exports: @@ -43,5 +43,7 @@ about: summary: Genomic Rle-objects for Python extra: + additional-platforms: + - linux-aarch64 skip-lints: - uses_setuptools From dbe406f26a67b2bb6ca720c8adccf902640393ba Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 16 Apr 2024 13:38:57 +0300 Subject: [PATCH 1555/1813] mawk: add linux-aarch64 build (#47252) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/mawk/meta.yaml | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/recipes/mawk/meta.yaml b/recipes/mawk/meta.yaml index 28545184f83bf..90a8f6efb736d 100644 --- a/recipes/mawk/meta.yaml +++ b/recipes/mawk/meta.yaml @@ -4,20 +4,31 @@ package: name: mawk version: "1.3.4" + source: url: https://invisible-mirror.net/archives/mawk/mawk-{{ version }}-{{ date }}.tgz sha256: db17115d1ed18ed1607c8b93291db9ccd4fe5e0f30d2928c3c5d127b23ec9e5b + build: - number: 7 + number: 8 + run_exports: + - {{ pin_subpackage('mawk', max_pin="x") }} + requirements: build: - make - {{ compiler('c') }} run: + test: commands: - mawk -W usage + about: home: http://invisible-island.net/mawk/ license: Copyright (c) 2009-2014,2015 by Thomas E. Dickey summary: mawk is an interpreter for the AWK Programming Language. + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 955fc1e74c96162defdb51a50dc94989ab562ec4 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 16 Apr 2024 13:39:15 +0300 Subject: [PATCH 1556/1813] grabix: add linux-aarch64 build (#47253) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/grabix/meta.yaml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/recipes/grabix/meta.yaml b/recipes/grabix/meta.yaml index 83e16c66f818a..c08d290d74b4e 100644 --- a/recipes/grabix/meta.yaml +++ b/recipes/grabix/meta.yaml @@ -4,11 +4,14 @@ package: version: "0.1.8" build: - number: 9 + number: 10 + run_exports: + - {{ pin_subpackage('grabix', max_pin="x.x") }} source: url: https://github.com/arq5x/grabix/archive/{{ revision }}.tar.gz md5: eb8805bed149ef56669ef19abba19b80 + requirements: build: - {{ compiler('cxx') }} @@ -16,10 +19,16 @@ requirements: - zlib run: - zlib + test: commands: - grabix + about: home: https://github.com/arq5x/grabix summary: a wee tool for random access into BGZF files. license: MIT + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From c70a9b9d8761eb5119765611430fa619fad68c1e Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 16 Apr 2024 13:40:21 +0300 Subject: [PATCH 1557/1813] mageck: add linux-aarch64 build (#47255) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/mageck/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/mageck/meta.yaml b/recipes/mageck/meta.yaml index 9ed1fab66174c..d711f9765c5dc 100644 --- a/recipes/mageck/meta.yaml +++ b/recipes/mageck/meta.yaml @@ -7,7 +7,9 @@ source: sha256: b06a18036da63959cd7751911a46727aefe2fb1d8dd79d95043c3e3bdaf1d93a build: - number: 3 + number: 4 + run_exports: + - {{ pin_subpackage('mageck', max_pin="x.x") }} requirements: build: @@ -32,3 +34,7 @@ about: home: http://mageck.sourceforge.net license: BSD License summary: MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data. + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 730290d71d3526ea848288ee63b67844f30f3705 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Apr 2024 06:48:59 -0400 Subject: [PATCH 1558/1813] Update poly-qtlseq to 1.0.1 (#47247) --- recipes/poly-qtlseq/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/poly-qtlseq/meta.yaml b/recipes/poly-qtlseq/meta.yaml index b08bcc23379d1..11953504d4dab 100644 --- a/recipes/poly-qtlseq/meta.yaml +++ b/recipes/poly-qtlseq/meta.yaml @@ -1,13 +1,13 @@ {% set name = "polyQtlseq" %} -{% set version = "1.0.0" %} -{% set sha256 = "800b669bdd89c89d2cc2218f842b419ff5aac29747b8f1dfd32ecba5f961543e" %} +{% set version = "1.0.1" %} +{% set sha256 = "bc6a7c3ddac1191b697084a003336aab06d7530538f4a6963d572cd1a6f679bc" %} package: name: poly-qtlseq version: {{ version }} source: - url: https://github.com/TatsumiMizubayashi/PolyploidQtlSeq/releases/download/v1.0.0/polyQtlseq-1.0.0.zip + url: https://github.com/TatsumiMizubayashi/PolyploidQtlSeq/releases/download/v1.0.1/polyQtlseq-1.0.1.zip sha256: {{ sha256 }} build: From 57565eab16e2e807fa1efd70bdae2dc83b72fb2b Mon Sep 17 00:00:00 2001 From: Andrea Telatin <15690844+telatin@users.noreply.github.com> Date: Tue, 16 Apr 2024 13:32:54 +0100 Subject: [PATCH 1559/1813] Add Canopy (#47245) * Add Canopy * Create build.sh * pin * Rename main.yaml to meta.yaml [WHAT DID I DO] * set name * Update meta.yaml * Update meta.yaml * Apply suggestions from code review Co-authored-by: Martin Grigorov * test fix for macos https://github.com/bioconda/bioconda-recipes/issues/8869 * Update license Thanks @Thanhleviet Co-authored-by: Thanh Lee --------- Co-authored-by: Martin Grigorov Co-authored-by: Thanh Lee --- recipes/canopy/build.sh | 6 ++++++ recipes/canopy/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 recipes/canopy/build.sh create mode 100644 recipes/canopy/meta.yaml diff --git a/recipes/canopy/build.sh b/recipes/canopy/build.sh new file mode 100644 index 0000000000000..0754372e7255c --- /dev/null +++ b/recipes/canopy/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +echo "Compiling Canopy" +mkdir -p ${PREFIX}/bin +make +mv cc.bin ${PREFIX}/bin/ diff --git a/recipes/canopy/meta.yaml b/recipes/canopy/meta.yaml new file mode 100644 index 0000000000000..8906c6773dc28 --- /dev/null +++ b/recipes/canopy/meta.yaml @@ -0,0 +1,36 @@ +{% set version="0.25" %} +{% set name="canopy" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/hildebra/canopy2/archive/refs/tags/v{{ version }}.tar.gz + sha256: 6ea391021dc81ff1981bb69b0ec27a56a17bd23e01c25a27b86808366d62061f + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - make + - llvm-openmp + host: + - zlib + run: + - zlib + - llvm-openmp + +test: + commands: + - cc.bin --version | grep {{ version }} + +about: + home: https://github.com/hildebra/canopy2/ + license: GPL-2.0-or-later + license_file: LICENSE + summary: 'Canopy - Metagenomics Canopy Clustering Implementation' From 0e0f40fac8811b66c9e0d3ee294b520c22c7f867 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 16 Apr 2024 15:36:01 +0300 Subject: [PATCH 1560/1813] seqfu: add linux-aarch64 build (#47230) * seqfu: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Remove zlib from build deps Signed-off-by: Martin Tzvetanov Grigorov * Export CXXFLAGS with -L$PREFIX/lib to find -lz Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/seqfu/build.sh | 2 ++ recipes/seqfu/meta.yaml | 4 +++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/seqfu/build.sh b/recipes/seqfu/build.sh index 3857c7e750166..0b5b964b47460 100644 --- a/recipes/seqfu/build.sh +++ b/recipes/seqfu/build.sh @@ -27,6 +27,8 @@ if [[ $OSTYPE == "darwin"* ]]; then else # Trying to fix build when gcc or g++ are required echo "LINUX: Patching makefile" + sed -i 's/gcc/gcc $(LDFLAGS)/g' Makefile + sed -i 's/g++/g++ $(LDFLAGS)/g' Makefile sed -i 's/gcc/$(GCC)/g' Makefile sed -i 's/g++/$(GXX)/g' Makefile sed -i '1iGCC ?= gcc' Makefile diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml index 9d494a364ba0b..13b66f49d86fe 100644 --- a/recipes/seqfu/meta.yaml +++ b/recipes/seqfu/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -48,6 +48,8 @@ about: Tools to interleave and deinterleave, to calculate stats, and extract portions of sequence datasets. extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - telatin identifiers: From 31a4af48855bf84b5745b619b491fe7eeafbca17 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 16 Apr 2024 16:43:30 +0300 Subject: [PATCH 1561/1813] staden_io_lib: add linux-aarch64 build (#47259) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/staden_io_lib/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/staden_io_lib/meta.yaml b/recipes/staden_io_lib/meta.yaml index 281cfd3b3d0e7..ed1200fa9c0ff 100644 --- a/recipes/staden_io_lib/meta.yaml +++ b/recipes/staden_io_lib/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ hash }} build: - number: 7 + number: 8 skip: True # [osx] run_exports: - {{ pin_subpackage('staden_io_lib', max_pin='x.x') }} @@ -42,3 +42,7 @@ about: license: BSD license_file: COPYRIGHT summary: 'Staden io_lib is a library of file reading and writing code e.g. for SAM/BAM/CRAM' + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From d4d6f498233eabc3a6d63a86004a4c42ebdda4dc Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Tue, 16 Apr 2024 06:45:38 -0700 Subject: [PATCH 1562/1813] Update ntedit build (#47239) --- recipes/ntedit/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/ntedit/meta.yaml b/recipes/ntedit/meta.yaml index 862b8e9ee8fae..bfca8d2deb1dd 100644 --- a/recipes/ntedit/meta.yaml +++ b/recipes/ntedit/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -29,6 +29,7 @@ requirements: - btllib - llvm-openmp # [osx] - boost-cpp + - python >=3.9 run: - llvm-openmp # [osx] - nthits >=1.0.0 From f6a384ed95a2e185002afd48a8906875564dadfa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Apr 2024 10:36:39 -0400 Subject: [PATCH 1563/1813] Update pybiolib to 1.1.1979 (#47266) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 896a55fbece51..4f947b7f8a974 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1974" %} +{% set version = "1.1.1979" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: c93c0ee7b8fe8296ce3e8a6cac684affa465f31db4f5d777098bf0b22b80aad3 + sha256: f038b9dac4e5661ae22e96b17314fcf56b5625f59fce49c1e987f18453510888 build: noarch: python From 3657b6e5d774eaf90c6e617a11aae3d8792a10cb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Apr 2024 10:37:28 -0400 Subject: [PATCH 1564/1813] Update locityper to 0.14.5 (#47257) --- recipes/locityper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/locityper/meta.yaml b/recipes/locityper/meta.yaml index b785fc0a3b164..1849ec8e9da84 100644 --- a/recipes/locityper/meta.yaml +++ b/recipes/locityper/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.4" %} +{% set version = "0.14.5" %} package: name: locityper @@ -11,7 +11,7 @@ build: source: url: https://github.com/tprodanov/locityper/archive/refs/tags/v{{ version }}.tar.gz - sha256: 83381d3600d4ad5b08f03c579bdd1ac5dcb149edd966a39516fa6d12192cd16d + sha256: 968e984f757c3985caa7a02ff87f82b859e0f7c5cf2b2fa80f0393b2e2e9545a requirements: build: From cf9cedeb767dfb04e99322d0b76a85d18ca910fd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Apr 2024 19:20:40 -0400 Subject: [PATCH 1565/1813] Update instrain to 1.8.1 (#47272) --- recipes/instrain/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/instrain/meta.yaml b/recipes/instrain/meta.yaml index bb970379926a2..b3390694f6173 100644 --- a/recipes/instrain/meta.yaml +++ b/recipes/instrain/meta.yaml @@ -1,5 +1,5 @@ {% set name = "inStrain" %} -{% set version = "1.8.0" %} +{% set version = "1.8.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b3d88c885658a9db393be7ce201e89454c3ea593128fdb673521640e5c1ecae4 + sha256: 0eab49f8f4bd64037f4314c228a193f6dfeaf37dec96eee81cf63851adeb9a59 build: noarch: python From 9d58c0b1efe198cc36ef8569c03f01f6180d32e7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Apr 2024 20:28:10 -0400 Subject: [PATCH 1566/1813] Update jbrowse2 to 2.11.0 (#47276) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 46d52e91923e0..c4d285c98c707 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.10.3" %} +{% set version = "2.11.0" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 0257ff74f7c4dd1502158e32238dbe362098292e6825b99b0f95f96c5b3cbce4 + sha256: e6bed6c3043ef5b87bcda83944c30e869d2a8b5c7ee224692a928f1d6624f515 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From 3cc5ae9c4375171dc2e593a9a3f22cc8466ba9d9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Apr 2024 20:28:18 -0400 Subject: [PATCH 1567/1813] Update straglr to 1.5.0 (#47274) * Update straglr to 1.5.0 * add run_exports --------- Co-authored-by: mencian --- recipes/straglr/meta.yaml | 28 +++++++++++++++++----------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/recipes/straglr/meta.yaml b/recipes/straglr/meta.yaml index ea5ed75c81eaf..572fb1c829da6 100644 --- a/recipes/straglr/meta.yaml +++ b/recipes/straglr/meta.yaml @@ -1,32 +1,36 @@ -{% set version = "1.4.1" %} +{% set name = "straglr" %} +{% set version = "1.5.0" %} package: - name: straglr + name: {{ name }} version: {{ version }} source: - url: https://github.com/bcgsc/straglr/archive/refs/tags/v1.4.1.tar.gz - sha256: 6c37a5f5cd91b81d766f0a524170fcf96fb288d184f796bfabb6bda335212f9e + url: https://github.com/bcgsc/straglr/archive/refs/tags/v1.5.0.tar.gz + sha256: 9daab4251a640959e3caa59e9ebfec1fbd0384c78730b4e71fd5a81d7fa23f58 build: noarch: python number: 0 - script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('straglr', max_pin="x") }} requirements: host: - python >=3.7 - pip run: + - python >=3.7 - trf - blast - pysam >=0.14.0 - - pybedtools >=0.7.9 + - pybedtools >=0.9.0 - intspan >=1.5.8 - - numpy >=1.14.2 + - numpy >=1.22.3 - pathos >=0.2.3 - - scikit-learn >=0.19.0 - - scipy >=1.0.1 + - scikit-learn >=1.1 + - scipy >=1.8.0 test: commands: @@ -34,10 +38,12 @@ test: about: home: https://github.com/bcgsc/straglr - license: MIT License + license: GPL-3.0-or-later summary: 'Short-tandem repeat genotyping using long reads ' license_family: GPL3 - + license_file: LICENSE + dev_url: https://github.com/bcgsc/straglr + extra: recipe-maintainers: - wdecoster From 48fce805e39f8a918af529dabaf997e96ea6330e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Apr 2024 20:28:32 -0400 Subject: [PATCH 1568/1813] Update psm-utils to 0.8.3 (#47273) * Update psm-utils to 0.8.3 * edit dependencies --------- Co-authored-by: mencian --- recipes/psm-utils/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index 4448df6ee1330..3a2b480bec129 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.8.2" %} -{% set sha256 = "b225f70caacccd6cec3838083fd6c3ff77052c4589e455bd789d900ec2f80baa" %} +{% set version = "0.8.3" %} +{% set sha256 = "99ce675b551dc76bd82074a5b4a45e18ea40cd7e38ef1e34a7345d7471ae4a80" %} package: name: {{ name|lower }} @@ -23,10 +23,9 @@ requirements: host: - pip - python >=3.7 - - flit-core run: - python >=3.7 - - pyteomics >=4 + - pyteomics >=4,<4.7 - pyopenms - lxml - psims From f3f68bf04c4f815244e8379724ad82d89e517fb6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Apr 2024 20:28:39 -0400 Subject: [PATCH 1569/1813] Update ppx to 1.4.2 (#47270) * Update ppx to 1.4.2 * add run_exports --------- Co-authored-by: mencian --- recipes/ppx/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/ppx/meta.yaml b/recipes/ppx/meta.yaml index 645d249430539..7666042599d38 100644 --- a/recipes/ppx/meta.yaml +++ b/recipes/ppx/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ppx" %} -{% set version = "1.3.0" %} +{% set version = "1.4.2" %} package: name: "{{ name|lower }}" @@ -7,22 +7,24 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a94f94071fca29e98fc13e4a306fc0c4c1deee2306dea9680e8a292a5c8b4376 + sha256: 4136286d6095ab07930b7df74cf450a938878b2c0e262cbc1987ac03166a16eb build: number: 0 noarch: python entry_points: - ppx = ppx.ppx:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('ppx', max_pin="x") }} requirements: host: - pip - - python >=3.7 + - python >=3.10 - setuptools_scm >=6.4.2 run: - - python >=3.7 + - python >=3.10 - requests >=2.23.0 - tqdm >=4.60.0 - cloudpathlib >=0.7.1 @@ -36,6 +38,7 @@ test: about: home: "https://github.com/wfondrie/ppx" license: MIT + license_family: MIT license_file: LICENSE summary: "A Python interface to proteomics data repositories" doc_url: "https://ppx.readthedocs.io" From 38927fef057fa75edc248eccd7e7e421ed9b49d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 00:18:16 -0400 Subject: [PATCH 1570/1813] Update spaln to 3.0.4 (#45188) * Update spaln to 3.0.3 * edit sha256 * Update spaln to 3.0.4 * edit dependencies * edit build.sh * edit build.sh * enable aarch64 build * disable aarch64 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: joshuazhuang7 Co-authored-by: Brandon Seah --- recipes/spaln/build.sh | 28 +++++++++++++++++++++++----- recipes/spaln/makefile.patch | 12 ++++++++++-- recipes/spaln/meta.yaml | 24 +++++++++++++----------- 3 files changed, 46 insertions(+), 18 deletions(-) diff --git a/recipes/spaln/build.sh b/recipes/spaln/build.sh index 516965f0874e8..d660fa42671ea 100644 --- a/recipes/spaln/build.sh +++ b/recipes/spaln/build.sh @@ -1,6 +1,24 @@ -(cd src && \ - ./configure --exec_prefix=${PREFIX}/bin --table_dir=${PREFIX}/share/spaln/table --alndbs_dir=${PREFIX}/share/spaln/alndbs --use_zlib=1 && \ - make AR="${AR:-ar} rc" LDFLAGS="-L${PREFIX}/lib" && make install) +#!/bin/bash -#(cd ${SRC_DIR}/perl && perl Makefile.PL && \ -# sed -i -s '1s^#!/usr/bin/perl^#!/usr/bin/env perl^' *.pl && make && make install && chmod u+w ${PREFIX}/bin/*.pl) +mkdir -p "${PREFIX}/bin" + +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" + +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SRC_DIR}/perl/*.pl +rm -rf ${SRC_DIR}/perl/*.bak +cp -rf ${SRC_DIR}/perl/*.pl "${PREFIX}/bin" + +cd src + +./configure --exec_prefix="${PREFIX}/bin" --table_dir="${PREFIX}/share/spaln/table" \ + --alndbs_dir="${PREFIX}/share/spaln/alndbs" + +make CFLAGS="${CFLAGS}" AR="${AR:-ar} rc" LDFLAGS="${LDFLAGS}" -j4 +make install + +make clearall diff --git a/recipes/spaln/makefile.patch b/recipes/spaln/makefile.patch index d58ad71183684..05b4085926c03 100644 --- a/recipes/spaln/makefile.patch +++ b/recipes/spaln/makefile.patch @@ -1,6 +1,8 @@ +diff --git a/src/Makefile.in b/src/Makefile.in +index ed5cb96..2d837d0 100644 --- a/src/Makefile.in +++ b/src/Makefile.in -@@ -1,14 +1,14 @@ +@@ -1,19 +1,19 @@ # Makefile.in for splan/sortgrcd # Copyright(c) Osamu Gotoh <> @@ -14,10 +16,16 @@ +CXX = $(CXX) #CXX = clang++ -CFLAGS = -O3 -march=native -+CFLAGS = -O3 -march=native -I$(PREFIX)/include ++CFLAGS += -O3 RANLIB = ranlib -LD = g++ +LD = $(CXX) AR = ar ru DEL = rm -f DEFLT = -DM_THREAD=1 + +-CXX := $(CXX) $(CFLAGS) $(DEFLT) ++CXX := $(CXX) $(CFLAGS) $(CPPFLAGS) $(DEFLT) + + .SUFFIXES: .o .cc .h .sh + diff --git a/recipes/spaln/meta.yaml b/recipes/spaln/meta.yaml index a127680c665c8..98884708d7d91 100644 --- a/recipes/spaln/meta.yaml +++ b/recipes/spaln/meta.yaml @@ -1,6 +1,6 @@ {% set name = "spaln" %} -{% set version = "3.0.1" %} -{% set sha256 = "efb7d492c81053180f2cbda831250d99ecb89cfa760217859aa78afbe9b3aefd" %} +{% set version = "3.0.4" %} +{% set sha256 = "6001a901e2e1ea5dbf19f34ee18b61ebd9afaf3a3c5107f937dd13e9b63ea870" %} package: name: {{ name|lower }} @@ -25,23 +25,24 @@ requirements: - make host: - perl - - zlib ==1.2.11 + - zlib run: - perl test: commands: - - spaln -h 2>&1 |grep 'SPALN version' >/dev/null - - makblk.pl 2>&1 |grep makblk.pl >/dev/null - - sortgrcd -h 2>&1 |grep sortgrcd >/dev/null - - makmdm -h 2>&1 |grep makmdm >/dev/null - - makdbs -h 2>&1 |grep makdbs >/dev/null - - makeidx.pl -h 2>&1 |grep makeidx.pl >/dev/null + - spaln -h 2>&1 | grep "version {{ version }}" >/dev/null + - makblk.pl 2>&1 | grep makblk.pl >/dev/null + - sortgrcd -h 2>&1 | grep sortgrcd >/dev/null + - makmdm -h 2>&1 | grep makmdm >/dev/null + - makdbs -h 2>&1 | grep makdbs >/dev/null + - makeidx.pl -h 2>&1 | grep makeidx.pl >/dev/null about: - home: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ + home: https://github.com/ogotoh/spaln + doc_url: "https://github.com/ogotoh/spaln/blob/master/README.md" dev_url: https://github.com/ogotoh/spaln - license: GPL-2.0 + license: "GPL-2.0-or-later" license_family: GPL license_file: COPYING summary: 'Map and align a set of cDNA/EST or protein sequences onto a genome' @@ -55,4 +56,5 @@ about: extra: identifiers: - doi:10.1093/nar/gks708 + - doi:10.1093/bioinformatics/btl067 - usegalaxy-eu:spaln From ff28dae94d100a642979e7b6ef68c0634135c711 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 05:12:28 -0400 Subject: [PATCH 1571/1813] Update sequali to 0.7.1 (#47280) --- recipes/sequali/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index e4dc25945e90c..6efff8664aeb6 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b1714f90fb62fa56524c9be5a1a96f92ac4b4739cbc5e85874b0890faf6eef8a + sha256: 4c77a54e986c8afbac80e3cc5511b0b1a53e6d8572db11ea691edd83fa58e08c build: number: 0 From 2309e0665133202bcb2915f2b9c421c8b860c411 Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Wed, 17 Apr 2024 15:38:33 +0200 Subject: [PATCH 1572/1813] Update bioconductor-tximeta to include rhdf5 dependency (#47286) * Add rhdf5 dependency to bioconductor-tximeta * Sort alphabetically * Increment build number --- recipes/bioconductor-tximeta/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-tximeta/meta.yaml b/recipes/bioconductor-tximeta/meta.yaml index f258f1c4275af..1195350a6e9cc 100644 --- a/recipes/bioconductor-tximeta/meta.yaml +++ b/recipes/bioconductor-tximeta/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 20a7fe1f7efc9be9ab420325932b8c0b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -31,6 +31,7 @@ requirements: - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.0.0,<2.46.1' - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-tximport >=1.30.0,<1.31.0' @@ -48,6 +49,7 @@ requirements: - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.0.0,<2.46.1' - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-tximport >=1.30.0,<1.31.0' From f7d0d72980b59da37071e1f8e688c85acccb9973 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Wed, 17 Apr 2024 18:42:23 +0200 Subject: [PATCH 1573/1813] [haddock_biobb] New package (#47283) * [haddock_biobb] update * adding runexports * add cpp compiler * Change env vars * change compiler input param for Makefile * Add C compiler * Fixed compiler naming error * Fix python command in build.sh * Fixed typo --------- Co-authored-by: Adam Hospital Gasch Co-authored-by: Adam Hospital Gasch --- recipes/haddock_biobb/build.sh | 23 +++++++++ recipes/haddock_biobb/meta.yaml | 76 ++++++++++++++++++++++++++++++ recipes/haddock_biobb/post-link.sh | 1 + 3 files changed, 100 insertions(+) create mode 100644 recipes/haddock_biobb/build.sh create mode 100644 recipes/haddock_biobb/meta.yaml create mode 100644 recipes/haddock_biobb/post-link.sh diff --git a/recipes/haddock_biobb/build.sh b/recipes/haddock_biobb/build.sh new file mode 100644 index 0000000000000..d6f14004f5408 --- /dev/null +++ b/recipes/haddock_biobb/build.sh @@ -0,0 +1,23 @@ +#!/usr/bin/env bash + +# Compile FCC +cd src/ +git clone https://github.com/haddocking/fcc.git +cd fcc/src +chmod u+x Makefile +make \ + CPP="${CXX}" +cd $SRC_DIR + +# Compile fast-rmsdmatrix +cd src/ +git clone https://github.com/mgiulini/fast-rmsdmatrix.git +cd fast-rmsdmatrix/src +chmod u+x Makefile +make \ + CC="${CC}" +cd $SRC_DIR + +${PYTHON} setup.py develop --no-deps + +mkdir -p $PREFIX/bin diff --git a/recipes/haddock_biobb/meta.yaml b/recipes/haddock_biobb/meta.yaml new file mode 100644 index 0000000000000..d2d5603309dd2 --- /dev/null +++ b/recipes/haddock_biobb/meta.yaml @@ -0,0 +1,76 @@ +{% set name = "haddock_biobb" %} +{% set version = "3.0.0" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://github.com/haddocking/haddock3/archive/refs/tags/v3.0.0-beta.5.tar.gz + sha256: e0651a4913fb659a57e897ac68c4f8e8f29b61e00abfcab3f3bbd623e1977f7b + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + - binutils + - pip + - python >=3.9 + - git + + host: + - python >=3.9 + - setuptools + - pip + - git + run: + - python >=3.9 + - pip + - git + - boost-cpp + - cxx-compiler + - c-compiler + # Pip dependencies + - biopython + - jsonpickle + - numpy + - pyyaml + - scipy + - toml + - tox + - pandas + - plotly + - kaleido-core + - freesasa + - pdb-tools + #- pdb-tools==2.5.0 + #- biopython==1.79 + #- jsonpickle==2.1.0 + #- numpy==1.22.2 + #- pyyaml==6.0 + #- scipy==1.10.0 + #- toml==0.10.2 + #- tox==3.24.5 + #- pandas==1.5.1 + #- plotly==5.11.0 + #- kaleido==0.2.1 + #- freesasa==2.2.1 + + + +test: + commands: + - echo "DONE!" + +about: + home: https://github.com/haddocking/haddock3 + license: Apache Software License + license_family: APACHE + summary: HADDOCK3 is the next generation integrative modelling software in the long-lasting HADDOCK project. + description: "HADDOCK3 is the next generation integrative modelling software in the long-lasting HADDOCK project. It represents a complete rethinking and rewriting of the HADDOCK2.X series, implementing a new way to interact with HADDOCK and offering new features to users who can now define custom workflows." diff --git a/recipes/haddock_biobb/post-link.sh b/recipes/haddock_biobb/post-link.sh new file mode 100644 index 0000000000000..20ec0915cce57 --- /dev/null +++ b/recipes/haddock_biobb/post-link.sh @@ -0,0 +1 @@ +echo "Create a softlink [ln -s] of the CNS executable to the ${PREFIX}/bin folder" > "${PREFIX}"/.messages.txt From 70e7718883983b92dec9620c6c8483f3a58a4e53 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Wed, 17 Apr 2024 11:35:03 -0700 Subject: [PATCH 1574/1813] Update ntroot build (#47291) --- recipes/ntroot/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ntroot/meta.yaml b/recipes/ntroot/meta.yaml index f61a5fa7999eb..f862511cee3a8 100644 --- a/recipes/ntroot/meta.yaml +++ b/recipes/ntroot/meta.yaml @@ -10,17 +10,17 @@ source: sha256: dd7a72cc0a2d92163a7ff7135e99e034d0831a6da16d3d8731039fff275502b5 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage("ntroot", max_pin="x") }} requirements: host: - - python + - python >=3.9 - perl run: - - python + - python >=3.9 - snakemake - samtools - ntedit >=2.0.1 From 9f4e438f685900abc02b20b5d9ac4d711005a78b Mon Sep 17 00:00:00 2001 From: Amine Ghozlane Date: Wed, 17 Apr 2024 20:43:13 +0200 Subject: [PATCH 1575/1813] Add Meteor (#47256) --- recipes/meteor/meta.yaml | 60 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 recipes/meteor/meta.yaml diff --git a/recipes/meteor/meta.yaml b/recipes/meteor/meta.yaml new file mode 100644 index 0000000000000..154327b4de91c --- /dev/null +++ b/recipes/meteor/meta.yaml @@ -0,0 +1,60 @@ +{% set name = "meteor" %} +{% set version = "2.0.9" %} + +package: + name: {{ name }} + version: {{ version }} + + +source: + url: https://github.com/metagenopolis/meteor/archive/{{ version }}.tar.gz + sha256: e828010c5dd52e04156f6f0263d9d2635831d1253df9a5e0dc47becbd8e45c43 + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . --no-deps -vv + run_exports: + - {{ pin_subpackage('meteor', max_pin="x.x") }} + +requirements: + host: + - python >=3.10 + - poetry + run: + - python >=3.10 + - bowtie2 >=2.3.5 + - pysam + - pyarrow + - pandas + - ete3 + - packaging + - cogent3 + - biom-format + - bcftools >=0.1.19 + - raxml-ng >=1.0.1 + - bedtools >=2.18.0 +test: + commands: + - meteor -h + - bowtie2 -h + - bedtools -h + - raxml-ng -h + - bcftools -h + imports: + - pysam + - pandas + - pyarrow + - ete3 + - packaging + - biom + - cogent3 + +about: + home: https://github.com/metagenopolis/meteor + license: GPL-3.0-or-later + license_file: COPYING + summary: 'Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems.' + description: | + Meteor relies on genes catalogue to perform specie level taxonomic assignments, functional and strain diffusion analysis. + license_family: GPL3 From 60597847846eadd7905d36b73865ac44e3e06c6c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 20:30:54 -0400 Subject: [PATCH 1576/1813] Update snakemake-interface-storage-plugins to 3.2.2 (#47250) * Update snakemake-interface-storage-plugins to 3.2.1 * Update snakemake-interface-storage-plugins to 3.2.2 --- recipes/snakemake-interface-storage-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-storage-plugins/meta.yaml b/recipes/snakemake-interface-storage-plugins/meta.yaml index 2203d95e3e6a7..f837051ef43ce 100644 --- a/recipes/snakemake-interface-storage-plugins/meta.yaml +++ b/recipes/snakemake-interface-storage-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-storage-plugins" %} -{% set version = "3.2.0" %} +{% set version = "3.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_storage_plugins-{{ version }}.tar.gz - sha256: 84f9a48d8a413f3d301a645379b79c2aeb1f453016389b140043ba046e37c4f8 + sha256: fc8a70ef5b1fd054bc64270925228e2054158da9bcf8fa8bd4be36d93a82678b build: noarch: python From cdceed628c44fe4e1fcc9e5c77895d29d27ed55f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 20:31:57 -0400 Subject: [PATCH 1577/1813] Update tissuumaps to 3.2.1.6 (#47279) --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index 0e538a5c241be..756c653c7c34b 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.1.5" %} +{% set version = "3.2.1.6" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 0166a573b70e65d8d77fe13d9caf5e804a924313f9e555568b2cc965ee00873e + sha256: e9e2a687e773a5d6c07014358cc6dfee951ef1400f5ec8c5e2387f3c0b6b4e8d build: number: 0 From dfe3d4fedb560728a4e2b887f0df8653b7e54131 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 20:32:04 -0400 Subject: [PATCH 1578/1813] Update pybiolib to 1.1.1988 (#47284) * Update pybiolib to 1.1.1984 * Update pybiolib to 1.1.1986 * Update pybiolib to 1.1.1988 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 4f947b7f8a974..6cece26eacbe0 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1979" %} +{% set version = "1.1.1988" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: f038b9dac4e5661ae22e96b17314fcf56b5625f59fce49c1e987f18453510888 + sha256: 465eeb3ecdc4f8df0fdb2ca1afddce403f412be3ed9fd937ef21eaff6c13ef3e build: noarch: python From e54b07fd37455e512bed4528129a2c32c069791d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 20:34:13 -0400 Subject: [PATCH 1579/1813] Update paraphase to 3.1.0 (#47292) --- recipes/paraphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/paraphase/meta.yaml b/recipes/paraphase/meta.yaml index df5ccd7268957..956ebc9f7a566 100644 --- a/recipes/paraphase/meta.yaml +++ b/recipes/paraphase/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.0.0" %} -{% set sha256 = "d26599b567e7e57003daedc5645cf19fc92789f1a4e88baff2e092723fbc3085" %} +{% set version = "3.1.0" %} +{% set sha256 = "fe01678e38a3856aeb82f3c52ca036d472b9eac9a4bb75f48bae39bd5fd66447" %} package: name: paraphase From ed83081747f13ae6405115056c7208f6512d044a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 20:44:34 -0400 Subject: [PATCH 1580/1813] Update segzoo to 1.0.13 (#47293) --- recipes/segzoo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/segzoo/meta.yaml b/recipes/segzoo/meta.yaml index 8c86f829f6e04..9d650119df3f1 100644 --- a/recipes/segzoo/meta.yaml +++ b/recipes/segzoo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "segzoo" %} -{% set version = "1.0.12" %} +{% set version = "1.0.13" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8e1001759aadd267ed2a92ca87089ce9725473a386d3713209f2a6d801d64e2a + sha256: 03903414891982e4d296f253119cf404a525844abdc84b02285923866926a708 build: noarch: python From 5ff8df995e5cd9d2da6d7d3aa053d031c59e4838 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 21:27:39 -0400 Subject: [PATCH 1581/1813] Update snakemake-executor-plugin-slurm to 0.4.5 (#47285) --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 9d831ade072b6..06ad75219b25e 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.4.4" %} +{% set version = "0.4.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 976367aa2c444ab169b263c7951294b25b54fcddba88e64210d52876ad132586 + sha256: 5b28371f17d81bb6287f35190fedd6cd50c78b62e21952cb30e4b4ba0b13d829 build: noarch: python From 27f8cc194a5bfb1906fdc995fcc519107875a194 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 21:50:53 -0400 Subject: [PATCH 1582/1813] Update snakemake-storage-plugin-fs to 1.0.3 (#47269) * Update snakemake-storage-plugin-fs to 1.0.2 * Update snakemake-storage-plugin-fs to 1.0.3 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake-storage-plugin-fs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-storage-plugin-fs/meta.yaml b/recipes/snakemake-storage-plugin-fs/meta.yaml index 1ee27eb1bf8c4..11ffa3559dade 100644 --- a/recipes/snakemake-storage-plugin-fs/meta.yaml +++ b/recipes/snakemake-storage-plugin-fs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-fs" %} -{% set version = "1.0.0" %} +{% set version = "1.0.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_fs-{{ version }}.tar.gz - sha256: de4ed37232173b604fadbf93cd84b05a8c28fa3e1d3167426bef181c7256e22c + sha256: 36086fc8a2970fd89218683655c345907a5834f07416f6c1ddf370489398f9c8 build: noarch: python From e9d4ef216ff296cf5564078c3878ec67425a1630 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 22:34:43 -0400 Subject: [PATCH 1583/1813] Update tcdemux to 0.0.25 (#47298) --- recipes/tcdemux/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tcdemux/meta.yaml b/recipes/tcdemux/meta.yaml index b424f8dcdc1fb..4da60218fbade 100644 --- a/recipes/tcdemux/meta.yaml +++ b/recipes/tcdemux/meta.yaml @@ -1,5 +1,5 @@ --- -{% set version = "0.0.24" %} +{% set version = "0.0.25" %} package: name: tcdemux @@ -7,7 +7,7 @@ package: source: url: https://github.com/TomHarrop/tcdemux/archive/refs/tags/{{ version }}.tar.gz - sha256: ab40fd9230e126e4691a9d7c0799cfe52baac0a7e86230f22aefa42206609fda + sha256: 03d8deea92762ad8ccc3fb3e2231cc00ec702efe52682c71fb8737f8317e819e build: number: 0 From 7fb523d9bf2aaca4e0630b13d4a0e4279e771d6c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Apr 2024 22:34:55 -0400 Subject: [PATCH 1584/1813] Update snakemake-storage-plugin-s3 to 0.2.11 (#47281) * Update snakemake-storage-plugin-s3 to 0.2.11 * edit dependencies --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian --- recipes/snakemake-storage-plugin-s3/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/snakemake-storage-plugin-s3/meta.yaml b/recipes/snakemake-storage-plugin-s3/meta.yaml index 55783267920c3..998e66cac163b 100644 --- a/recipes/snakemake-storage-plugin-s3/meta.yaml +++ b/recipes/snakemake-storage-plugin-s3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-s3" %} -{% set version = "0.2.10" %} +{% set version = "0.2.11" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_s3-{{ version }}.tar.gz - sha256: a4554d170b5621751aba20ee08e6357090471a0a68b173525b118580c287a12e + sha256: edbac21ca22d2e674eaadf05f21c611891df37366d4fbd6a712d79172d788895 build: noarch: python @@ -24,9 +24,10 @@ requirements: run: - python >=3.11.0,<4.0.0 - snakemake-interface-common >=1.14.0,<2.0.0 - - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 - - boto3 >=1.28.55,<2.0.0 - - botocore >=1.31.55,<2.0.0 + - snakemake-interface-storage-plugins >=3.2.2,<4.0.0 + - boto3 >=1.33.0,<2.0.0 + - botocore >=1.33.0,<2.0.0 + - urllib3 >=2.0,<2.2 test: # We do not test the import as the plugin needs snakemake for importing, but adding From 941a120ad6b9f881244faf7073f18af864db3fcc Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 18 Apr 2024 15:37:04 +1200 Subject: [PATCH 1585/1813] Added TIR-Learner (#46970) * Added TIR-Learner * Fixed package pin name * Updated source to lutianyu2001/TIR-Learner * Fixed linting issues * Fixed version lint issue * Rearranged dependencies * Updated to v3.0.1 --- recipes/tir-learner/build.sh | 15 +++++++++++ recipes/tir-learner/meta.yaml | 49 +++++++++++++++++++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 recipes/tir-learner/build.sh create mode 100644 recipes/tir-learner/meta.yaml diff --git a/recipes/tir-learner/build.sh b/recipes/tir-learner/build.sh new file mode 100644 index 0000000000000..0855b1275d676 --- /dev/null +++ b/recipes/tir-learner/build.sh @@ -0,0 +1,15 @@ +#!/bin/sh +set -x -e + +TIR_LEARNER_DIR=${PREFIX}/share/TIR-Learner3.0 + +mkdir -p ${PREFIX}/bin +mkdir -p ${TIR_LEARNER_DIR} +cp -r TIR-Learner3.0/* ${TIR_LEARNER_DIR} + +cat <>${PREFIX}/bin/TIR-Learner +#!/bin/bash +python3 ${TIR_LEARNER_DIR}/TIR-Learner3.0.py \$@ +END + +chmod a+x ${PREFIX}/bin/TIR-Learner diff --git a/recipes/tir-learner/meta.yaml b/recipes/tir-learner/meta.yaml new file mode 100644 index 0000000000000..f1e308ce75f47 --- /dev/null +++ b/recipes/tir-learner/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "TIR-Learner" %} +{% set version = "3.0.1" %} +{% set sha256 = "a5b8e41a0ff6cb18188e78722ade9dccab2b947cb9c23d21543ccbf2b05285f5" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/lutianyu2001/TIR-Learner/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('tir-learner', max_pin='x') }} + +requirements: + run: + - genericrepeatfinder + - genometools-genometools + - blast + - biopython + - scikit-learn + - pandas + - glob2 + - multiprocess + - regex + - tensorflow + - keras + - swifter + +test: + commands: + - TIR-Learner -v | grep 'TIR-Learner 3.0.1' + +about: + home: https://github.com/lutianyu2001/TIR-Learner + license: GPLv3 + license_family: GPL + license_file: LICENSE + summary: An ensemble method for TIR transposable element annotation + dev_url: https://github.com/lutianyu2001/TIR-Learner + doc_url: https://github.com/lutianyu2001/TIR-Learner/blob/main/docs/TIR-Learner%20v3%20flow%20chart_v2.drawio.png + +extra: + identifiers: + - doi:10.1016/j.molp.2019.02.008 From a1e09cb932e1a3324ef5290fca60fc6fcc90df2e Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 18 Apr 2024 06:40:58 +0300 Subject: [PATCH 1586/1813] libmaus2: add linux-aarch64 build (#47260) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/libmaus2/build.sh | 2 +- recipes/libmaus2/meta.yaml | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/libmaus2/build.sh b/recipes/libmaus2/build.sh index 7cead9ea7ceff..cdd58fb79e892 100644 --- a/recipes/libmaus2/build.sh +++ b/recipes/libmaus2/build.sh @@ -6,5 +6,5 @@ export LIBS="-lstdc++fs -lcurl" cat config.log -make +make -j${CPU_COUNT} make install diff --git a/recipes/libmaus2/meta.yaml b/recipes/libmaus2/meta.yaml index defd4a7cbe7c2..455532e4245a8 100644 --- a/recipes/libmaus2/meta.yaml +++ b/recipes/libmaus2/meta.yaml @@ -10,7 +10,7 @@ package: build: # There's some issue with clang skip: True # [osx] - number: 4 + number: 5 run_exports: - {{ pin_subpackage('libmaus2', max_pin='x.x') }} @@ -50,3 +50,7 @@ about: test: commands: - echo + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 66c6372b78203e9f42ed9530c34fc874f5ef2e18 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 18 Apr 2024 06:41:13 +0300 Subject: [PATCH 1587/1813] delly: add linux-aarch64 build (#47258) Always build from sources Signed-off-by: Martin Tzvetanov Grigorov --- recipes/delly/build.sh | 11 ++--------- recipes/delly/meta.yaml | 4 +++- 2 files changed, 5 insertions(+), 10 deletions(-) diff --git a/recipes/delly/build.sh b/recipes/delly/build.sh index 3da9d173f7a55..e70b4a265f219 100644 --- a/recipes/delly/build.sh +++ b/recipes/delly/build.sh @@ -1,12 +1,5 @@ #!/bin/sh mkdir -p "${PREFIX}/bin" -if [[ ${target_platform} == osx-64 ]] ; then - make all CXX=$CXX CXXFLAGS="-I${PREFIX}/include -L${PREFIX}/lib" - cp src/delly "${PREFIX}/bin" -else - wget "https://github.com/dellytools/delly/releases/download/v${PKG_VERSION}/delly_v${PKG_VERSION}_linux_x86_64bit" - mv delly_v${PKG_VERSION}_linux_x86_64bit delly - chmod +x delly - cp delly "${PREFIX}/bin" -fi +make all CXX=$CXX CXXFLAGS="-I${PREFIX}/include -L${PREFIX}/lib" +cp src/delly "${PREFIX}/bin" diff --git a/recipes/delly/meta.yaml b/recipes/delly/meta.yaml index ee0d6f0ea4c2d..1be26ed167cf9 100644 --- a/recipes/delly/meta.yaml +++ b/recipes/delly/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("delly", max_pin="x.x") }} @@ -42,6 +42,8 @@ about: summary: Structural variant discovery by integrated paired-end and split-read analysis extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1093/bioinformatics/bts378 - biotools:Delly2 From fd9e6a9ed90b0e4688a1d0fc00286015eae74348 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Thu, 18 Apr 2024 05:50:56 +0200 Subject: [PATCH 1588/1813] Update hictkpy to v0.0.5 (#47289) * Bump version * Update sha256 * Update checksum and URL --- recipes/hictkpy/conanfile.txt.patch | 8 ++++---- recipes/hictkpy/meta.yaml | 5 ++--- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/recipes/hictkpy/conanfile.txt.patch b/recipes/hictkpy/conanfile.txt.patch index 081aa3aa249c4..038babbd4c0df 100644 --- a/recipes/hictkpy/conanfile.txt.patch +++ b/recipes/hictkpy/conanfile.txt.patch @@ -1,12 +1,12 @@ diff --git a/conanfile.txt b/conanfile.txt -index af68e77..276b37f 100644 +index cffb547..66cf415 100644 --- a/conanfile.txt +++ b/conanfile.txt @@ -5,30 +5,12 @@ [requires] - bshoshany-thread-pool/4.0.1#b7ce99198b3a54e403393961480085c7 + bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502 --fast_float/6.1.0#85dc5bf9d3d6e605abf536818397baf3 +-fast_float/6.1.1#e29acaa3d0543dee343abe3f6815346e -fmt/10.2.1#9199a7a0611866dea5c8849a77467b25 -hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1 -highfive/2.9.0#c57477beed8b0110fadeb6da8f48bcc5 @@ -15,7 +15,7 @@ index af68e77..276b37f 100644 readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83 span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422 -spdlog/1.13.0#2775cc949e26b339029a852785b6b276 --zstd/1.5.5#b87dc3b185caa4b122979ac4ae8ef7e8 +-zstd/1.5.6#67383dae85d33f43823e7751a6745ea1 [generators] CMakeDeps diff --git a/recipes/hictkpy/meta.yaml b/recipes/hictkpy/meta.yaml index 552b88f866780..22be84e3abea8 100644 --- a/recipes/hictkpy/meta.yaml +++ b/recipes/hictkpy/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictkpy" %} -{% set version = "0.0.4" %} -{% set sha256 = "5fdbe2bb59643fcc084f1576a7557dbd949bfd5f14981e16dda50a8e8f49eb8f" %} +{% set version = "0.0.5" %} +{% set sha256 = "e9576a1a719ce378873da15b76e9f7e699748c0486901607e4d7e87c3f0c6556" %} package: name: {{ name|lower }} @@ -23,7 +23,6 @@ requirements: - cmake >=3.25 - conan >=2 - make - - eigen >=3.4 - fast_float >=5 - fmt >=10 - highfive >=2.7 From f0b481518df6110878df522c4c7e2c52e951c7cc Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Thu, 18 Apr 2024 05:52:00 +0200 Subject: [PATCH 1589/1813] Update hictk to v0.0.12 and enable linux-aarch64 builds (#47267) * Enable linux-aarch64 build * Ensure hictk builds on bioconda prior to tagging a release * Update conanfile.txt.patch * Update sha256 and patch file * Update URL and sha256 --- recipes/hictk/conanfile.txt.patch | 54 ++++--------------------------- recipes/hictk/meta.yaml | 8 ++--- 2 files changed, 10 insertions(+), 52 deletions(-) diff --git a/recipes/hictk/conanfile.txt.patch b/recipes/hictk/conanfile.txt.patch index b2752bd88fd25..294d8196b80d7 100644 --- a/recipes/hictk/conanfile.txt.patch +++ b/recipes/hictk/conanfile.txt.patch @@ -1,18 +1,16 @@ diff --git a/conanfile.txt b/conanfile.txt -index 06a2202..a6164f6 100644 +index c76a83a..434833d 100644 --- a/conanfile.txt +++ b/conanfile.txt -@@ -3,75 +3,13 @@ - # SPDX-License-Identifier: MIT +@@ -4,33 +4,12 @@ [requires] --boost/1.84.0#5cc9767cd47ba6b5e1b53ab4670f07fc - bshoshany-thread-pool/4.0.1#b7ce99198b3a54e403393961480085c7 --catch2/3.5.3#2178a424c7c53da1e7df5fef1a051f1f + bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c +-catch2/3.5.4#d346ca291f8f62040fd9c1a891654711 -cli11/2.4.1#afacffd31f631bbb8b7c7d6425fe7a66 concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502 -eigen/3.4.0#2e192482a8acff96fe34766adca2b24c --fast_float/6.1.0#d5ebf20d96102abc0f5d2d2269a317bc +-fast_float/6.1.1#e29acaa3d0543dee343abe3f6815346e -fmt/10.2.1#9199a7a0611866dea5c8849a77467b25 -hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1 -highfive/2.9.0#c57477beed8b0110fadeb6da8f48bcc5 @@ -21,52 +19,12 @@ index 06a2202..a6164f6 100644 readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83 span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422 -spdlog/1.13.0#8e88198fd5b9ee31d329431a6d0ccaa2 --zstd/1.5.5#b87dc3b185caa4b122979ac4ae8ef7e8 +-zstd/1.5.6#67383dae85d33f43823e7751a6745ea1 [generators] CMakeDeps [options] --boost*:system_no_deprecated=True --boost*:asio_no_deprecated=True --boost*:filesystem_no_deprecated=True --boost*:filesystem_version=4 --boost*:zlib=False --boost*:bzip2=False --boost*:lzma=False --boost*:zstd=False --boost*:without_atomic=False --boost*:without_chrono=True --boost*:without_container=True --boost*:without_context=True --boost*:without_contract=True --boost*:without_coroutine=True --boost*:without_date_time=True --boost*:without_exception=False --boost*:without_fiber=True --boost*:without_filesystem=False --boost*:without_graph=True --boost*:without_graph_parallel=True --boost*:without_iostreams=True --boost*:without_json=True --boost*:without_locale=True --boost*:without_log=True --boost*:without_math=True --boost*:without_mpi=True --boost*:without_nowide=True --boost*:without_program_options=True --boost*:without_python=True --boost*:without_random=True --boost*:without_regex=True --boost*:without_serialization=True --boost*:without_stacktrace=True --boost*:without_system=False --boost*:without_test=True --boost*:without_thread=True --boost*:without_timer=True --boost*:without_type_erasure=True --boost*:without_url=True --boost*:without_wave=True -fmt*:header_only=True -hdf5*:enable_cxx=False -hdf5*:hl=False diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index ebcfbb7c853f1..38ec7eed97116 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.11" %} -{% set sha256 = "a06b674de2301918188d1c890a95aaa4d6164377ebaa44cc07efb77fd9eb654c" %} +{% set version = "0.0.12" %} +{% set sha256 = "03e8f7c0076ea6209fdfee1580658e871895f6a59b895407c4a25512b9558fb7" %} package: name: {{ name|lower }} @@ -31,13 +31,11 @@ requirements: - spdlog >=1.12 host: - - boost-cpp >=1.80 - hdf5 >=1.12 - libdeflate - zstd >=1.5 run: - - libboost >=1.80 - hdf5 >=1.12 - libdeflate - zstd >=1.5 @@ -98,3 +96,5 @@ extra: identifiers: - biotools:hictk - doi:10.5281/zenodo.8214221 + additional-platforms: + - linux-aarch64 From c4b73c1d829069e6965efb41b3f7056d3597b3e5 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 18 Apr 2024 00:09:14 -0500 Subject: [PATCH 1590/1813] Try building gmap on OSX (#47299) * Try building gmap on OSX * edit build.sh * edit build.sh * edit build.sh --- recipes/gmap/build.sh | 9 +++++---- recipes/gmap/meta.yaml | 5 ++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/gmap/build.sh b/recipes/gmap/build.sh index 297d0e9a4c1d1..759a24c161362 100644 --- a/recipes/gmap/build.sh +++ b/recipes/gmap/build.sh @@ -6,16 +6,15 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3" export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" +export LC_ALL=en_US.UTF-8 + if [ "$(uname)" == "Darwin" ]; then # for Mac OSX export LDFLAGS="${LDFLAGS} -headerpad_max_install_names" export CFLAGS="${CFLAGS} -m64" + export LC_ALL=C fi -export LANGUAGE=en_US.UTF-8 -export LANG=en_US.UTF-8 -export LC_ALL=en_US.UTF-8 - case $(uname -m) in x86_64) SIMD_LEVEL="sse42" @@ -61,3 +60,5 @@ sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_introns sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_splicesites sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/snpindex sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/vcf_iit + +rm -rf ${PREFIX}/bin/*.bak diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index be517e1caa9e2..4c3580f4d8971 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -13,8 +13,7 @@ source: - single_quote_paths.patch build: - number: 1 - skip: True # [osx] + number: 2 run_exports: - {{ pin_subpackage('gmap', max_pin=None) }} @@ -25,8 +24,8 @@ requirements: - autoconf - automake - libtool - - perl host: + - perl - zlib - bzip2 run: From 3d9a850372f0c315c401e45576501720398ef7d2 Mon Sep 17 00:00:00 2001 From: Yuri Pirola Date: Thu, 18 Apr 2024 12:57:48 +0200 Subject: [PATCH 1591/1813] malva: pin kmc dependency and fix compilation issues (#47262) * Fix compilation issues * pin kmc (fix AlgoLab/malva#14) --- recipes/malva/build_failure.linux-64.yaml | 104 ---------------------- recipes/malva/malva.CMakeList.patch | 19 +++- recipes/malva/meta.yaml | 9 +- 3 files changed, 23 insertions(+), 109 deletions(-) delete mode 100644 recipes/malva/build_failure.linux-64.yaml diff --git a/recipes/malva/build_failure.linux-64.yaml b/recipes/malva/build_failure.linux-64.yaml deleted file mode 100644 index 414662d68c286..0000000000000 --- a/recipes/malva/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d1651f674064650225149083c22db4ade1849d8d8ac92fd1d03fd7168e972dce # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - export PREFIX=/opt/conda/conda-bld/malva_1685353511262/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - export BUILD_PREFIX=/opt/conda/conda-bld/malva_1685353511262/_build_env - export SRC_DIR=/opt/conda/conda-bld/malva_1685353511262/work - INFO: activate-binutils_linux-64.sh made the following environmental changes: - ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line - AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar - AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as - CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt - ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit - GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof - LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld - LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold - NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm - OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy - OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump - RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib - READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf - SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size - STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings - STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip - INFO: activate-gcc_linux-64.sh made the following environmental changes: - BUILD=x86_64-conda-linux-gnu - CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/malva-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr - CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot - CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu - CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu - CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp - CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include - DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/malva-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include - GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc - GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar - GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm - GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib - HOST=x86_64-conda-linux-gnu - LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu - build_alias=x86_64-conda-linux-gnu - host_alias=x86_64-conda-linux-gnu - -BUILD=x86_64-conda_cos6-linux-gnu - -CONDA_BUILD_SYSROOT= - INFO: activate-gxx_linux-64.sh made the following environmental changes: - CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/malva-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/malva-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g - -- The C compiler identification is GNU 12.2.0 - -- The CXX compiler identification is GNU 12.2.0 - -- Detecting C compiler ABI info - -- Detecting C compiler ABI info - done - -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped - -- Detecting C compile features - -- Detecting C compile features - done - -- Detecting CXX compiler ABI info - -- Detecting CXX compiler ABI info - done - -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped - -- Detecting CXX compile features - -- Detecting CXX compile features - done - -- SDSL found $BUILD_PREFIX/lib/libsdsl.a - -- KMC includes found $PREFIX/include - -- ZSTD found $BUILD_PREFIX/lib/libzstd.a - -- ZSTD includes found $PREFIX/include - -- Configuring done (0.4s) - -- Generating done (0.0s) - -- Build files have been written to: $SRC_DIR/build - [ 25%] Building CXX object CMakeFiles/malva-geno.dir/zstdstream.cpp.o - [ 50%] Building C object CMakeFiles/malva-geno.dir/xxhash.c.o - [ 75%] Building CXX object CMakeFiles/malva-geno.dir/main.cpp.o - In file included from /opt/conda/conda-bld/malva_1685353511262/work/main.cpp:44: - /opt/conda/conda-bld/malva_1685353511262/work/bloom_filter.hpp:28:10: fatal error: sdsl/bit_vectors.hpp: No such file or directory - 28 | #include - | ^~~~~~~~~~~~~~~~~~~~~~ - compilation terminated. - make[2]: *** [CMakeFiles/malva-geno.dir/build.make:104: CMakeFiles/malva-geno.dir/main.cpp.o] Error 1 - make[1]: *** [CMakeFiles/Makefile2:83: CMakeFiles/malva-geno.dir/all] Error 2 - make: *** [Makefile:91: all] Error 2 - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/malva_1685353511262/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/malva/malva.CMakeList.patch b/recipes/malva/malva.CMakeList.patch index 46fe9a0cedf2c..6f7bc733d2c36 100644 --- a/recipes/malva/malva.CMakeList.patch +++ b/recipes/malva/malva.CMakeList.patch @@ -1,8 +1,22 @@ diff --git a/CMakeLists.txt b/CMakeLists.txt -index 5796d8b..9030264 100644 +index 5796d8b..351fd24 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -32,9 +32,17 @@ else () +@@ -18,6 +18,13 @@ else () + message(STATUS "SDSL found ${SDSL}") + endif () + ++find_path(SDSL_INCLUDE_DIR NAMES sdsl/bit_vectors.hpp PATHS ${CMAKE_SYSTEM_PREFIX_PATH}) ++if (NOT SDSL_INCLUDE_DIR) ++ message(FATAL_ERROR "bit_vectors.hpp (part of sdsl-lite) required") ++else () ++ message(STATUS "SDSL includes found ${SDSL_INCLUDE_DIR}") ++endif () ++ + find_path(KMC_INCLUDE_DIR NAMES kmc_file.h PATHS ${CMAKE_SYSTEM_PREFIX_PATH} PATH_SUFFIXES "kmc") + if (NOT KMC_INCLUDE_DIR) + message(FATAL_ERROR "kmc_file.h (part of libkmc-dev) required") +@@ -32,9 +39,18 @@ else () message(STATUS "ZSTD found ${ZSTD}") endif () @@ -16,6 +30,7 @@ index 5796d8b..9030264 100644 target_include_directories(malva-geno PRIVATE ${PROJECT_SOURCE_DIR} PRIVATE ${KMC_INCLUDE_DIR} ++ PRIVATE ${SDSL_INCLUDE_DIR} + PRIVATE ${ZSTD_INCLUDE_DIR} ) diff --git a/recipes/malva/meta.yaml b/recipes/malva/meta.yaml index f82ac08b27bfd..72c392b21a442 100644 --- a/recipes/malva/meta.yaml +++ b/recipes/malva/meta.yaml @@ -13,8 +13,10 @@ source: - malva.CMakeList.patch build: - number: 3 + number: 4 skip: True # [osx] + run_exports: + - {{ pin_subpackage('malva', max_pin="x") }} requirements: build: @@ -27,10 +29,10 @@ requirements: host: - zlib - htslib - - kmc + - kmc =3.1 run: - htslib - - kmc + - kmc =3.1 test: commands: @@ -40,6 +42,7 @@ test: about: home: https://algolab.github.io/malva/ license: GPL-3.0-or-later + license_file: LICENSE summary: genotyping by Mapping-free ALternate-allele detection of known VAriants extra: From a5c19940685c312bffbe241b877df4e3ba2acdee Mon Sep 17 00:00:00 2001 From: Gerry Tonkin-Hill Date: Thu, 18 Apr 2024 21:33:26 +1000 Subject: [PATCH 1592/1813] Update shiver (#47248) * updated shiver version * update build number * remove shiver from blacklist * update noarch * add run exports --- build-fail-blacklist | 3 --- recipes/shiver/meta.yaml | 11 ++++++----- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index f1582c697e8fa..b9f2582e70255 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -419,9 +419,6 @@ recipes/intervalstats recipes/oligotyping recipes/oligotyping/2.0 -# missing file -recipes/shiver - # missing binary recipes/semeta diff --git a/recipes/shiver/meta.yaml b/recipes/shiver/meta.yaml index 267510208db68..c37a7b20052ee 100644 --- a/recipes/shiver/meta.yaml +++ b/recipes/shiver/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.5.7" %} # put in correct version here +{% set version = "1.7.0" %} # put in correct version here {% set name = "shiver" %} package: @@ -6,11 +6,12 @@ package: version: {{ version }} source: url: https://github.com/ChrisHIV/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 64973462bfc10c725ef5f21e85532ef8dd58d26795b2cee326a77f690d31ebf0 - patches: - - python2-python3.patch + sha256: 461752a23a284d6bf4fc186a4e263b5efd28e792b484813d237e3d749b3fbf2f build: - number: 1 + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('shiver', max_pin="x") }} requirements: From f7ae6652c12d7de3a2eec58df5a63fc2dc149a71 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Thu, 18 Apr 2024 21:19:53 +0900 Subject: [PATCH 1593/1813] Pin jax <0.4.26 in colabfold (#47277) --- recipes/colabfold/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/colabfold/meta.yaml b/recipes/colabfold/meta.yaml index 5b02beb3331bb..c69bc9d8395a3 100644 --- a/recipes/colabfold/meta.yaml +++ b/recipes/colabfold/meta.yaml @@ -14,7 +14,7 @@ build: python -m pip install --no-deps --ignore-installed alphafold/ run_exports: - {{ pin_subpackage('colabfold', max_pin="x") }} - number: 1 + number: 2 source: - url: https://github.com/sokrypton/ColabFold/archive/refs/tags/v{{ cf_version }}.tar.gz @@ -45,8 +45,8 @@ requirements: - importlib-metadata - dm-haiku >=0.0.12 - biopython <=1.82 - - jax >=0.4.23 - - jaxlib >=0.4.23 + - jax >=0.4.23,<0.4.26 + - jaxlib >=0.4.23,<0.4.26 - tensorflow-base >=2.12.1=cpu* - mmseqs2 >=15.6f452 - kalign2 >=2.04 From 1df053933cf672b4169c618aeef2e320a8b1ad42 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Thu, 18 Apr 2024 14:41:11 +0200 Subject: [PATCH 1594/1813] Haddock biobb (#47314) * [haddock_biobb] update * Change version num * Setup install * Setup install * Setup install * Setup install --- recipes/haddock_biobb/build.sh | 2 +- recipes/haddock_biobb/meta.yaml | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/haddock_biobb/build.sh b/recipes/haddock_biobb/build.sh index d6f14004f5408..7a64adb7ef0e4 100644 --- a/recipes/haddock_biobb/build.sh +++ b/recipes/haddock_biobb/build.sh @@ -18,6 +18,6 @@ make \ CC="${CC}" cd $SRC_DIR -${PYTHON} setup.py develop --no-deps +${PYTHON} setup.py install --single-version-externally-managed --record=record.txt mkdir -p $PREFIX/bin diff --git a/recipes/haddock_biobb/meta.yaml b/recipes/haddock_biobb/meta.yaml index d2d5603309dd2..35b33734ed52b 100644 --- a/recipes/haddock_biobb/meta.yaml +++ b/recipes/haddock_biobb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "haddock_biobb" %} -{% set version = "3.0.0" %} +{% set version = "3.0.1" %} package: name: '{{ name|lower }}' @@ -23,6 +23,7 @@ requirements: - pip - python >=3.9 - git + - setuptools host: - python >=3.9 From 144732c3a29848f34a6c51d333ac8d9dca95f7c6 Mon Sep 17 00:00:00 2001 From: lspindler2509 <83402447+lspindler2509@users.noreply.github.com> Date: Thu, 18 Apr 2024 15:31:35 +0200 Subject: [PATCH 1595/1813] new build number (#47309) --- recipes/robust-bias-aware/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/robust-bias-aware/meta.yaml b/recipes/robust-bias-aware/meta.yaml index dcfc453f25cb6..acc4799297c89 100644 --- a/recipes/robust-bias-aware/meta.yaml +++ b/recipes/robust-bias-aware/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 182c413b2f39b34d89fec657afdcf350a1c1a7b9f75b799746a3c0a18ce40744 build: - number: 0 + number: 1 script: - "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" - mkdir -p $PREFIX/site-packages From b59ba7b3732e324c1e8fc6f3e44d61c464900a36 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 18 Apr 2024 09:53:18 -0500 Subject: [PATCH 1596/1813] Update sra-tools recipe (#47122) * Update sra-tools recipe * add ossuuid * update dependencies * update build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh * edit build.sh --- recipes/sra-tools/build.sh | 42 +++++++++++++---------- recipes/sra-tools/conda_build_config.yaml | 4 +-- recipes/sra-tools/meta.yaml | 11 ++++-- 3 files changed, 33 insertions(+), 24 deletions(-) diff --git a/recipes/sra-tools/build.sh b/recipes/sra-tools/build.sh index 61adcee08e6b5..5b55bd0ccec80 100755 --- a/recipes/sra-tools/build.sh +++ b/recipes/sra-tools/build.sh @@ -1,17 +1,13 @@ #!/bin/bash -e -export INCLUDE_PATH="${PREFIX}/include" -export LIBRARY_PATH="${PREFIX}/lib" -export LDFLAGS="-L${PREFIX}/lib" -export CXX_FOR_BUILD=${CXX} - -export CFLAGS="-DH5_USE_110_API -I${PREFIX}/include ${LDFLAGS}" -export CXXFLAGS="-I${PREFIX}/include ${LDFLAGS}" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 -DH5_USE_110_API -D_FILE_OFFSET_BITS=64 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" echo "compiling sra-tools" if [[ ${OSTYPE} == "darwin"* ]]; then export CFLAGS="${CFLAGS} -DTARGET_OS_OSX" - export CXXFLAGS="${CXXFLAGS} -DTARGET_OS_OSX -D_LIBCPP_DISABLE_AVAILABILITY" + export CXXFLAGS="${CXXFLAGS} -DTARGET_OS_OSX" fi mkdir -p obj/ngs/ngs-java/javadoc/ngs-doc # prevent error on OSX @@ -20,16 +16,24 @@ mkdir -p obj/ngs/ngs-java/javadoc/ngs-doc # prevent error on OSX # Execute Make commands from a separate subdirectory. Else: # ERROR: In source builds are not allowed export SRA_BUILD_DIR=${SRC_DIR}/build_sratools -mkdir ${SRA_BUILD_DIR} -pushd ${SRA_BUILD_DIR} -cmake ../sra-tools/ -DVDB_BINDIR=${BUILD_PREFIX}/lib64 \ - -DVDB_LIBDIR=${BUILD_PREFIX}/lib64 \ - -DVDB_INCDIR=${BUILD_PREFIX}/include \ - -DCMAKE_INSTALL_PREFIX=${PREFIX} \ - -DCMAKE_BUILD_TYPE=Release -cmake --build . -j 4 -v -cmake --install . -popd +mkdir -p ${SRA_BUILD_DIR} + +if [[ "$(uname)" == "Darwin" ]]; then + export VDB_INC="${SRC_DIR}/ncbi-vdb/interfaces" +else + export VDB_INC="${PREFIX}/include" +fi + +cmake -S sra-tools/ -B build_sratools/ \ + -DVDB_BINDIR="${PREFIX}" \ + -DVDB_LIBDIR="${PREFIX}/lib64" \ + -DVDB_INCDIR="${VDB_INC}" \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" + +cmake --build build_sratools/ --target install -j ${CPU_COUNT} -v # Strip package version from binary names @@ -42,5 +46,5 @@ for exe in \ srapath-orig \ sra-pileup-orig do - ln -s "${exe}.${PKG_VERSION}" "${exe}" + ln -sf "${exe}.${PKG_VERSION}" "${exe}" done diff --git a/recipes/sra-tools/conda_build_config.yaml b/recipes/sra-tools/conda_build_config.yaml index 1271f9dfbd295..fc9d91e7aedb6 100644 --- a/recipes/sra-tools/conda_build_config.yaml +++ b/recipes/sra-tools/conda_build_config.yaml @@ -1,7 +1,7 @@ # current version does not build with newer compilers cxx_compiler_version: - - 10 # [linux] + - 11 # [linux] - 14 # [osx] c_compiler_version: - - 10 # [linux] + - 11 # [linux] - 14 # [osx] diff --git a/recipes/sra-tools/meta.yaml b/recipes/sra-tools/meta.yaml index 48524c74ccba4..bd3db099f622f 100644 --- a/recipes/sra-tools/meta.yaml +++ b/recipes/sra-tools/meta.yaml @@ -7,13 +7,15 @@ package: version: {{ version }} source: - url: https://github.com/ncbi/sra-tools/archive/refs/tags/{{version}}.tar.gz +- url: https://github.com/ncbi/sra-tools/archive/refs/tags/{{version}}.tar.gz sha256: {{ sha256 }} folder: sra-tools +- url: https://github.com/ncbi/ncbi-vdb/archive/refs/tags/{{version}}.tar.gz # [osx] + sha256: eec5a64b8353a201bd4cf2c58cfcbb3622327397c3b11696ae59d827fcfcea9d # [osx] + folder: ncbi-vdb # [osx] build: - number: 0 - skip: True # [osx] + number: 1 run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -24,6 +26,7 @@ requirements: - cmake - bison - flex + host: - ncbi-vdb >={{ version }} run: - ca-certificates @@ -57,6 +60,8 @@ about: description: | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. + dev_url: https://github.com/ncbi/sra-tools + doc_url: https://github.com/ncbi/sra-tools/wiki extra: notes: 'After installation, you should run the configuration tool: ./vdb-config From 0b4091ae6e3fb5fc67cb453ae1beeae637bffed1 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 18 Apr 2024 19:04:20 +0300 Subject: [PATCH 1597/1813] biobambam: add linux-aarch64 build (#47261) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/biobambam/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/biobambam/meta.yaml b/recipes/biobambam/meta.yaml index c7d758af69ab6..482c9c1b272d1 100644 --- a/recipes/biobambam/meta.yaml +++ b/recipes/biobambam/meta.yaml @@ -12,8 +12,10 @@ source: sha256: {{ sha256hash }} build: - number: 3 + number: 4 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} requirements: build: @@ -31,3 +33,7 @@ about: license: GPLv3 license_file: GPLv3 summary: Tools for early stage alignment file processing + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From fda1bb88d0eca43c76a9ad38a89fbfe6dcb7b773 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Apr 2024 16:47:02 -0400 Subject: [PATCH 1598/1813] Update paraphase to 3.1.1 (#47327) --- recipes/paraphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/paraphase/meta.yaml b/recipes/paraphase/meta.yaml index 956ebc9f7a566..1c59d226f457e 100644 --- a/recipes/paraphase/meta.yaml +++ b/recipes/paraphase/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.1.0" %} -{% set sha256 = "fe01678e38a3856aeb82f3c52ca036d472b9eac9a4bb75f48bae39bd5fd66447" %} +{% set version = "3.1.1" %} +{% set sha256 = "6f43404f35e158de787926811869eb5027e93e74e08c6c8a9db7993a50d89c3c" %} package: name: paraphase From 92f8fce02e9c49b62c9a4bd105e1cdaad5676e97 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Apr 2024 16:47:25 -0400 Subject: [PATCH 1599/1813] Update assemblycomparator2 to 2.6.2 (#47324) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index a42dba3fb3e72..cc2844dfddf15 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.6.1" %} +{% set version = "2.6.2" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 247d04a61c59b7849d79479f921f5d1ed4c112d5fa17e244add14321173aa74a + sha256: 52d1465c0da1955ee58848043309db81e551a87428e8b10fc55c02437addf6b8 build: From 31a959636231790036bbdabc1092ad7f736f3031 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Apr 2024 16:47:48 -0400 Subject: [PATCH 1600/1813] Update pybiolib to 1.1.1998 (#47315) * Update pybiolib to 1.1.1990 * Update pybiolib to 1.1.1995 * Update pybiolib to 1.1.1998 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 6cece26eacbe0..61bacb5386f21 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1988" %} +{% set version = "1.1.1998" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 465eeb3ecdc4f8df0fdb2ca1afddce403f412be3ed9fd937ef21eaff6c13ef3e + sha256: 1dfebf770dc36339939f1796f9936d61f24d0d2468fe6ab2aad20bf2c15c81e9 build: noarch: python From c9630b471b615a6126adcf417bc49ae5123ae86d Mon Sep 17 00:00:00 2001 From: mjohnpayne Date: Fri, 19 Apr 2024 10:19:25 +1000 Subject: [PATCH 1601/1813] Update salty to 1.0.6 (#47301) * Update salty to 1.0.6 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/salty/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/salty/meta.yaml b/recipes/salty/meta.yaml index baee1a01d7b94..1b9e8d2ffcbfa 100644 --- a/recipes/salty/meta.yaml +++ b/recipes/salty/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.5" %} +{% set version = "1.0.6" %} {% set name = "salty" %} package: @@ -7,12 +7,14 @@ package: source: url: https://github.com/LanLab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 85cc90e93fdce30685a9c0c2fecc0d3079c0d7903c02eba9096a1b73e2c4fbd6 + sha256: 85c7fd21665606e9e31807c36a6e6edf5dd77a41a3929eb10c94291cede6ff4b build: noarch: python - number: 1 + number: 0 script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: @@ -21,7 +23,7 @@ requirements: run: - python >=3.7 - kma >=1.4.9 - - pandas >=1.5.0 + - pandas >=2.0 - mlst >=2.23.0 test: From 138d8d1521b2d14d5a43f567740761060e271b8f Mon Sep 17 00:00:00 2001 From: farchaab <116543129+farchaab@users.noreply.github.com> Date: Fri, 19 Apr 2024 02:24:19 +0200 Subject: [PATCH 1602/1813] Update mess recipe (#47287) --- recipes/mess/meta.yaml | 56 +++++++++++++++++++++++++----------------- 1 file changed, 33 insertions(+), 23 deletions(-) diff --git a/recipes/mess/meta.yaml b/recipes/mess/meta.yaml index c442de1ebc1a2..a3cdfb5f6c92c 100644 --- a/recipes/mess/meta.yaml +++ b/recipes/mess/meta.yaml @@ -1,48 +1,58 @@ -{% set version = "0.2.2" %} -{% set sha256 = "84aca7989768a00d6ea0410645c3398d9a459a48b2fabf68552f9b68b0a711c1" %} +{% set name = "MeSS" %} +{% set version = "0.8.0" %} package: - name: mess + name: "{{ name|lower }}" version: {{ version }} source: - url: https://github.com/metagenlab/MeSS/archive/refs/tags/v{{ version }}.tar.gz - sha256: {{ sha256 }} + url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 3fc888a31f6c9acd71552b26f9e42f963a34382eeccb2215afcc872ba0f54c3e build: number: 0 - entry_points: - - mess=mess.mess:cli noarch: python - script: "python -m pip install --no-deps --ignore-installed ." + entry_points: + - mess=mess.__main__:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('mess', max_pin="x.x") }} + requirements: host: - - python>3.6,<3.9 + - python >=3.10 - pip run: - - python>3.6,<3.9 - - snakemake-minimal=6.2.1 - - pandas >1 - - click>=7 + - python >=3.10 + - snakemake-minimal >=7.32.4 + - pulp <2.8 + - snaketool-utils >=0.0.5 + - attrmap >=0.0.7 + - pyyaml >=6.0.1 + - pandas >=2.2.1 + - biopython >=1.83 + - rich-click >=1.7.4 test: - imports: - - mess - commands: - - mess run -h - - mess --version + commands: + - mess -h + - mess -v about: home: https://github.com/metagenlab/MeSS - license: GPL-3.0 + license: MIT + license_family: MIT license_file: LICENSE - summary: The Metagenomic Sequence Simulator (MeSS) is a snakemake workflow used for simulating metagenomic mock communities. + summary: "Snakemake pipeline for simulating shotgun metagenomic samples" + dev_url: https://github.com/metagenlab/MeSS + doc_url: https://metagenlab.github.io/MeSS extra: + container: + extended-base: true recipe-maintainers: - - idfarbanecha + - farchaab + - tpillone -container: - extended-base: true From 6412cc850668621f6f9af5e1bcbd809ffaf88ff1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Apr 2024 20:25:18 -0400 Subject: [PATCH 1603/1813] Update dxpy to 0.373.0 (#47321) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 0d5cbbcaf6e0a..3116782ae7bc7 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.372.0" %} +{% set version = "0.373.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 6be5cf0ecd03977c2ad09d863a7de17b6b866cc280ca85dc192612b4fb87da7b + sha256: 060fb6d03ea0b76ddf6f5c553a39bb1100bf3dbdcc2761881a8860a8f0cccddd build: number: 0 From 6b4ee55836b0786ce11ce5359dddddf8fd270e2b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Apr 2024 20:25:38 -0400 Subject: [PATCH 1604/1813] Update virusrecom to 1.1.5 (#47323) --- recipes/virusrecom/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/virusrecom/meta.yaml b/recipes/virusrecom/meta.yaml index 0eba5822dff3e..c6bd13b6864e9 100644 --- a/recipes/virusrecom/meta.yaml +++ b/recipes/virusrecom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virusrecom" %} -{% set version = "1.1.4" %} +{% set version = "1.1.5" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 904a7da6c681041063e20ab39424ec0dc73fbdfedbfe0d89cbac5e65966b420f + sha256: 88747b2590163526baa57115d649db6e0310ace792fab9e6b50275d71265f2ee build: number: 0 From 10f8c3894decff4207bfb6473204b9932dff9570 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Apr 2024 20:25:48 -0400 Subject: [PATCH 1605/1813] Update primerforge to 1.0.0 (#47325) * Update primerforge to 1.0.0 * Update primerforge to 1.0.0 * add maintainer --------- Co-authored-by: Robert A. Petit III --- recipes/primerforge/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 5c666d4ec97ee..1d12bb99781f3 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "0.7.4" %} +{% set version = "1.0.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 6409887f69d20d7ec86609997f55c9df0ae1e5f3e890b0f9d6f95be97d9fbdc6 + sha256: ac92e00f881d6c1817818bec88e5d7dc9232d7853e6ce1db8745ea809fd9d232 build: number: 0 @@ -37,3 +37,7 @@ about: license_family: Apache license_file: LICENSE summary: "primerForge: software to identify primers that can be used to distinguish genomes" + +extra: + recipe-maintainers: + - dr-joe-wirth From f0260a75a14204e2505dc0c7dc30c540c60e78d1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Apr 2024 20:26:11 -0400 Subject: [PATCH 1606/1813] Update phykit to 1.19.2 (#47328) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index c0cfae8640d07..1544d1303dc18 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.19.1" %} +{% set version = "1.19.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 09dcc2649d9a217d5afdefc151568d68beec3cfdc5789cfc3ec255610677cc5c + sha256: 90a21339828521aca055257a08846099134889f274b1584f0d989e891a921cd3 build: noarch: python From 5dbd53f1ce5da6158fe4b8bf0ea5cc290883ae5b Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 04:04:30 +0300 Subject: [PATCH 1607/1813] miniasm: add linux-aarch64 build (#47320) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/miniasm/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/miniasm/meta.yaml b/recipes/miniasm/meta.yaml index 2f319afb180cf..1d5f46060d2d0 100644 --- a/recipes/miniasm/meta.yaml +++ b/recipes/miniasm/meta.yaml @@ -5,7 +5,9 @@ package: version: {{ version }} build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage('miniasm', max_pin='x.x') }} source: url: https://github.com/lh3/miniasm/archive/refs/tags/v0.3.tar.gz @@ -29,3 +31,7 @@ about: license: MIT license_file: LICENSE.txt summary: Ultrafast de novo assembly for long noisy reads (though having no consensus step) + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 382f9ce6b9e6bef7f01a7f047ca3cb4d095f9e47 Mon Sep 17 00:00:00 2001 From: Jaebeom Kim <68528165+jaebeom-kim@users.noreply.github.com> Date: Fri, 19 Apr 2024 10:57:20 +0900 Subject: [PATCH 1608/1813] [Update] Metabuli 1.0.5 (#47268) * metabuli 1.0.4 * metabuli 1.0.4 * change to 1.0.5 * change to 1.0.5 --- recipes/metabuli/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/metabuli/meta.yaml b/recipes/metabuli/meta.yaml index 584f1202b94a8..0ff53ad0a4ce5 100644 --- a/recipes/metabuli/meta.yaml +++ b/recipes/metabuli/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "1.0.3" %} -{% set sha256 = "facfc3c411b4732e80ac4dfaccf1057cf8b86da4a8d4f05667b1f07dbb18077d" %} +{% set version = "1.0.5" %} +{% set sha256 = "c84a4e2436904f0cbea7126abf2a5f665a870735c8af786883e10f3f872bda28" %} package: name: metabuli version: {{ version|replace("-", ".") }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('metabuli', max_pin="x") }} @@ -49,4 +49,4 @@ extra: - milot-mirdita - jaebeom-kim additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 From 7744ab58fc6470dc654e15a3e7ee4a055287209b Mon Sep 17 00:00:00 2001 From: Jon Puritz Date: Thu, 18 Apr 2024 22:20:59 -0400 Subject: [PATCH 1609/1813] Update meta.yaml (#47326) --- recipes/ddocent/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ddocent/meta.yaml b/recipes/ddocent/meta.yaml index fd0da658b3618..d295e0eb03724 100644 --- a/recipes/ddocent/meta.yaml +++ b/recipes/ddocent/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage('ddocent', max_pin="x") }} @@ -30,7 +30,7 @@ requirements: - rainbow - cd-hit - bedtools >=2.26.0 - - vcflib >=0.1.11, <1.0.3 + - vcflib >=0.1.11, <1.0.4 - gnuplot - parallel - pear From 953a13bcea6af4748cd7491921ef09324a1803af Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:21:20 +0300 Subject: [PATCH 1610/1813] mummer: add linux-aarch64 build (#47303) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/mummer/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/mummer/meta.yaml b/recipes/mummer/meta.yaml index 2083f64a19486..3d57b44f09bfa 100644 --- a/recipes/mummer/meta.yaml +++ b/recipes/mummer/meta.yaml @@ -13,8 +13,10 @@ source: - patches/gnuplot_mouse_clipboardformat.patch build: - number: 16 + number: 17 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: build: @@ -48,5 +50,7 @@ about: summary: "MUMmer is a system for rapidly aligning entire genomes" extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:mummer From b681b7ccbf659b0cd0d56dadb09770804a5a1e35 Mon Sep 17 00:00:00 2001 From: pvanheus Date: Fri, 19 Apr 2024 04:38:17 +0200 Subject: [PATCH 1611/1813] Update JolyTree to version 2.1 (#47322) * Update JolyTree to version 2.1 * Add run_exports --- recipes/jolytree/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/jolytree/meta.yaml b/recipes/jolytree/meta.yaml index 5e7a9410d0d4a..ba38a2d116e19 100644 --- a/recipes/jolytree/meta.yaml +++ b/recipes/jolytree/meta.yaml @@ -1,7 +1,7 @@ {% set name = "JolyTree" %} -{% set version = "1.1b" %} +{% set version = "2.1" %} {% set owner = "GIPhy" %} -{% set sha256 = "e356c18d933f23bca900b6a620d6364bdbf0c39e7aeea2241f63f906fbc015ac" %} +{% set sha256 = "e3af4675c564e7d77bc104ae63f473dd1cdd7be6a82c883db70e7599acfb763b" %} package: name: {{ name|lower }} @@ -13,14 +13,16 @@ source: build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage("jolytree", max_pin="x") }} requirements: run: - mash >=1.0.2 - gawk >=4.1.3 - fastme >=2.1.5 - - req >=v1.3.190304ac + - req >=1.2 test: commands: From 1799300c22b0f19a033b2eb1829c1b81d5b88840 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Fri, 19 Apr 2024 12:38:53 +1000 Subject: [PATCH 1612/1813] Update tcdemux pinning (#47300) * fix pandas dependency * pin bbmap * Update meta.yaml --- recipes/tcdemux/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/tcdemux/meta.yaml b/recipes/tcdemux/meta.yaml index 4da60218fbade..68c8d6e811719 100644 --- a/recipes/tcdemux/meta.yaml +++ b/recipes/tcdemux/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 03d8deea92762ad8ccc3fb3e2231cc00ec702efe52682c71fb8737f8317e819e build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install --ignore-installed . run_exports: @@ -20,17 +20,17 @@ requirements: host: - python >=3.10 run: - - bbmap + - bbmap <=38.95 - biopython >=1.81 - - cutadapt >=4.4 - - pandas >=2.0.3 + - cutadapt >=4.5 + - pandas >=2.1.1 - pigz - python >=3.10 - r-bit64 >=4.0.5 - r-data.table >=1.14.8 - r-ggplot2 >=3.4.3 - r-viridis >=0.6.4 - - snakemake >=7.31.0 + - snakemake >=7.32.4 test: commands: From ec2c98c4ef0159c79c8023452dc2f066fa129fec Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:39:16 +0300 Subject: [PATCH 1613/1813] ucsc-bedtobigbed: add linux-aarch64 build (#47304) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-bedtobigbed/htmshell.patch | 11 +++++++++++ recipes/ucsc-bedtobigbed/meta.yaml | 9 ++++++++- 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 recipes/ucsc-bedtobigbed/htmshell.patch diff --git a/recipes/ucsc-bedtobigbed/htmshell.patch b/recipes/ucsc-bedtobigbed/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-bedtobigbed/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-bedtobigbed/meta.yaml b/recipes/ucsc-bedtobigbed/meta.yaml index 8006d0ba56728..dc6ece24ed64b 100644 --- a/recipes/ucsc-bedtobigbed/meta.yaml +++ b/recipes/ucsc-bedtobigbed/meta.yaml @@ -12,13 +12,16 @@ source: sha256: {{ sha256 }} patches: - include.patch + - htmshell.patch build: - number: 0 + number: 1 skip: True # [osx] ignore_run_exports: - libpng - libuuid + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -48,3 +51,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "Convert bed file to bigBed. (bbi version: 4)" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 7d223dd49ba24ad7f26c881a8c5536869d176c60 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:39:30 +0300 Subject: [PATCH 1614/1813] intarna: add linux-aarch64 build (#47305) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/intarna/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/intarna/meta.yaml b/recipes/intarna/meta.yaml index 8177abc6959ae..bb6a0cf472278 100644 --- a/recipes/intarna/meta.yaml +++ b/recipes/intarna/meta.yaml @@ -12,7 +12,7 @@ about: summary: Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('intarna', max_pin="x.x") }} @@ -43,6 +43,8 @@ test: - IntaRNA -t CCCCCCCCGGGGGGGGGGGGGG -q CCCCCCC extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:intarna - doi:10.1093/nar/gkx279 From 19cac3c4bb5faef6fbc2ae37757fc105a09544bb Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:39:57 +0300 Subject: [PATCH 1615/1813] ucsc-twobitinfo: add linux-aarch64 build (#47306) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-twobitinfo/htmshell.patch | 11 +++++++++++ recipes/ucsc-twobitinfo/meta.yaml | 7 ++++++- 2 files changed, 17 insertions(+), 1 deletion(-) create mode 100644 recipes/ucsc-twobitinfo/htmshell.patch diff --git a/recipes/ucsc-twobitinfo/htmshell.patch b/recipes/ucsc-twobitinfo/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-twobitinfo/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-twobitinfo/meta.yaml b/recipes/ucsc-twobitinfo/meta.yaml index 782f34538d8c9..32559085469d0 100644 --- a/recipes/ucsc-twobitinfo/meta.yaml +++ b/recipes/ucsc-twobitinfo/meta.yaml @@ -12,10 +12,11 @@ source: sha256: "{{ sha256 }}" patches: - "include.patch" + - htmshell.patch build: skip: True # [osx] - number: 0 + number: 1 ignore_run_exports: - libpng - libuuid @@ -50,3 +51,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "get information about sequences in a .2bit file" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 542d94a462aee23884ef783a2af099cc9a178cbe Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:40:15 +0300 Subject: [PATCH 1616/1813] pyfastx: add linux-aarch64 build (#47307) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/pyfastx/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/pyfastx/meta.yaml b/recipes/pyfastx/meta.yaml index e3e7a117d395f..0dfaf051f3fb7 100644 --- a/recipes/pyfastx/meta.yaml +++ b/recipes/pyfastx/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --no-deps -vvv skip: True # [py < 36] entry_points: @@ -44,3 +44,7 @@ about: pyfastx is a python module for fast random access to sequences from plain and gzipped FASTA/Q file + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 4843c876be3f485ab690ae78169d74cca142145b Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:40:55 +0300 Subject: [PATCH 1617/1813] umis: add linux-aarch64 build (#47308) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * umis: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Update the Git SHA Somehow the old one is no more valid ... ``` RuntimeError: SHA256 mismatch: '7d446da4cc31f075e539db6b6d7b31a3309e0c4c708875981d61780c2de7ed82' != 'a471522ccd2ad6d86cb9ae4cbb61f27ace8da80ca75d1f7f3faf980790424179'␛[0m 07:24:25 ␛[31mBIOCONDA ERROR␛[0m COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmp4xv7wn9n/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/circleci/project/recipes/umis:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7-aarch64 /bin/bash /opt/build_script.bash␛[0m ``` Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/umis/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/umis/meta.yaml b/recipes/umis/meta.yaml index daa5e038df0ce..3c7b4ddff3e27 100644 --- a/recipes/umis/meta.yaml +++ b/recipes/umis/meta.yaml @@ -6,11 +6,13 @@ package: version: "{{ version }}" build: - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage('umis', max_pin='x') }} source: url: "{{ github }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: a471522ccd2ad6d86cb9ae4cbb61f27ace8da80ca75d1f7f3faf980790424179 + sha256: 7d446da4cc31f075e539db6b6d7b31a3309e0c4c708875981d61780c2de7ed82 requirements: build: @@ -40,6 +42,8 @@ about: summary: Tools for processing UMI RNA-tag data extra: + additional-platforms: + - linux-aarch64 container: # click requires a unicode locale when used with Python 3 # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly From 421ec9f0fb8792fac25e874bba888ca14ad64e4b Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:41:14 +0300 Subject: [PATCH 1618/1813] atropos: add linux-aarch64 build (#47310) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/atropos/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/atropos/meta.yaml b/recipes/atropos/meta.yaml index 88e84a06fad27..8fd6958fa8d1b 100644 --- a/recipes/atropos/meta.yaml +++ b/recipes/atropos/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 # Ensure Cython is rerun by removing *.c output files and PKG-INFO (checked for by setup.py) script: find . "(" -name "*.c" -o -name PKG-INFO ")" -exec rm {} ";" && {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv run_exports: @@ -39,3 +39,7 @@ about: license: CC0 and partly MIT summary: 'trim adapters from high-throughput sequencing reads' doc_url: https://atropos.readthedocs.io + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 999d9b295873b369fe977676c107110dd5c2f77f Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:41:48 +0300 Subject: [PATCH 1619/1813] pytabix: add linux-aarch64 build (#47311) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/pytabix/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/pytabix/meta.yaml b/recipes/pytabix/meta.yaml index b1261eec08bf5..32f31a6178bde 100644 --- a/recipes/pytabix/meta.yaml +++ b/recipes/pytabix/meta.yaml @@ -6,8 +6,10 @@ package: version: {{ version }} build: - number: 4 + number: 5 script: '{{ PYTHON }} -m pip install . --no-deps -vv' + run_exports: + - {{ pin_subpackage('pytabix', max_pin='x.x') }} source: url: https://pypi.io/packages/source/p/pytabix/pytabix-{{ version }}.tar.gz @@ -35,3 +37,7 @@ about: license: MIT license_file: LICENSE summary: Fast random access to sorted files compressed with bgzip and indexed by tabix. + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 371fa14ee640a88bb7593a6abaec9cd9bed12ffa Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:42:01 +0300 Subject: [PATCH 1620/1813] vcfanno: add linux-aarch64 build (#47312) * vcfanno: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Fix YAML list for `sources` Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/vcfanno/meta.yaml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/recipes/vcfanno/meta.yaml b/recipes/vcfanno/meta.yaml index ab4d005b463ac..5432278f824fa 100644 --- a/recipes/vcfanno/meta.yaml +++ b/recipes/vcfanno/meta.yaml @@ -5,13 +5,15 @@ package: version: {{ version }} source: - url: https://github.com/brentp/vcfanno/releases/download/v{{ version }}/vcfanno_osx # [osx] - sha256: 2f51637c6358fec7e7fcb1dbbfc1b2cbbed6ff47a7c6b7ef386f1152ff74829f # [osx] - url: https://github.com/brentp/vcfanno/releases/download/v{{ version }}/vcfanno_linux64 # [linux] - sha256: a98a9be6dfec32b039b21563659c4ecf0ec884ad3cdfaf0732b44c3857520592 # [linux] + - url: https://github.com/brentp/vcfanno/releases/download/v{{ version }}/vcfanno_osx # [osx] + sha256: 2f51637c6358fec7e7fcb1dbbfc1b2cbbed6ff47a7c6b7ef386f1152ff74829f # [osx] + - url: https://github.com/brentp/vcfanno/releases/download/v{{ version }}/vcfanno_linux64 # [linux and x86_64] + sha256: a98a9be6dfec32b039b21563659c4ecf0ec884ad3cdfaf0732b44c3857520592 # [linux and x86_64] + - url: https://github.com/brentp/vcfanno/releases/download/v{{ version }}/vcfanno_linux_aarch64 # [linux and aarch64] + sha256: 732007523998f9a48071fa3dd75d4492c972dd786861b0a5d36cd0669f5d5288 # [linux and aarch64] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("vcfanno", max_pin="x") }} @@ -22,6 +24,8 @@ test: - "vcfanno 2>&1 | grep 'vcfanno'" extra: + additional-platforms: + - linux-aarch64 skip-lints: - should_be_noarch_generic # uses per platform binaries - should_not_be_noarch_source # uses binaries From 0a2b043bc005c7e23391a873b1e32c348eda8498 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:42:23 +0300 Subject: [PATCH 1621/1813] crispresso2: add linux-aarch64 build (#47316) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/crispresso2/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/crispresso2/meta.yaml b/recipes/crispresso2/meta.yaml index 877e9f4483714..106ea600a08eb 100644 --- a/recipes/crispresso2/meta.yaml +++ b/recipes/crispresso2/meta.yaml @@ -6,7 +6,7 @@ package: build: skip: True # [py2k] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('crispresso2', max_pin='x') }} @@ -48,3 +48,7 @@ about: license: Partners license_file: LICENSE.txt summary: "A software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 588ca3efde891b86e4df2464e24a7819c17e094a Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:42:36 +0300 Subject: [PATCH 1622/1813] pb-falcon & python-msgpack: add linux-aarch64 build (#47317) * pb-falcon: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * python-msgpack: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/pb-falcon/meta.yaml | 12 +++++++++--- recipes/python-msgpack/meta.yaml | 6 +++++- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/recipes/pb-falcon/meta.yaml b/recipes/pb-falcon/meta.yaml index 5ea3122f61ee8..dc4734f3db4f2 100644 --- a/recipes/pb-falcon/meta.yaml +++ b/recipes/pb-falcon/meta.yaml @@ -12,8 +12,10 @@ source: folder: pb-falcon build: - number: 4 + number: 5 skip: True # [py27 or py36 or osx] + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} requirements: build: @@ -31,9 +33,9 @@ requirements: - python - networkx >=1.9.1 - future >=0.16.0 - - python-edlib>=1.2.4 + - python-edlib >=1.2.4 - python-intervaltree - - python-msgpack>=0.6.1 + - python-msgpack >=0.6.1 - numpy - pysam @@ -55,3 +57,7 @@ about: - pb-cdunn - isovic - zkronenberg + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file diff --git a/recipes/python-msgpack/meta.yaml b/recipes/python-msgpack/meta.yaml index 7813176a17dcd..3df723ced1e0e 100644 --- a/recipes/python-msgpack/meta.yaml +++ b/recipes/python-msgpack/meta.yaml @@ -7,7 +7,9 @@ source: url: https://files.pythonhosted.org/packages/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-{{ version }}.tar.gz sha256: 4008c72f5ef2b7936447dcb83db41d97e9791c83221be13d5e19db0796df1972 build: - number: 8 + number: 9 + run_exports: + - {{ pin_subpackage('python-msgpack', max_pin='x.x') }} requirements: build: - {{ compiler('cxx') }} @@ -24,4 +26,6 @@ about: license: Apache 2.0 summary: "It's like JSON. But fast and small." extra: + additional-platforms: + - linux-aarch64 web: http://msgpack.org/ From 77641c436fdaf9b99bb19b71c9e08ae0e1e38e4b Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:43:08 +0300 Subject: [PATCH 1623/1813] taxonkit: add linux-aarch64 build (#47318) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/taxonkit/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/taxonkit/meta.yaml b/recipes/taxonkit/meta.yaml index 959579bd2784a..1027498def2d6 100644 --- a/recipes/taxonkit/meta.yaml +++ b/recipes/taxonkit/meta.yaml @@ -5,15 +5,17 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('taxonkit', max_pin='x.x') }} source: - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_amd64.tar.gz # [osx] md5: 0f36df3f255caf87004087b4f6a3c718 # [osx] - - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_amd64.tar.gz # [linux] - md5: dcf41d21493a29594b399cdafce16233 # [linux] + - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_amd64.tar.gz # [linux and x86_64] + md5: dcf41d21493a29594b399cdafce16233 # [linux and x86_64] + - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_arm64.tar.gz # [linux and aarch64] + md5: f07a5cff687752de4d03a0b1e6df9a9c # [linux and aarch64] test: commands: @@ -26,6 +28,8 @@ about: license_family: MIT extra: + additional-platforms: + - linux-aarch64 skip-lints: - should_be_noarch_generic - should_not_be_noarch_source From 230b51a90fccdaf75c21d96d354d342d7e60999e Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:43:20 +0300 Subject: [PATCH 1624/1813] pbgzip: add linux-aarch64 build (#47319) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/pbgzip/build.sh | 2 +- recipes/pbgzip/meta.yaml | 9 +++++++-- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/recipes/pbgzip/build.sh b/recipes/pbgzip/build.sh index 23e9ca4d9a87e..af8355c3b5830 100644 --- a/recipes/pbgzip/build.sh +++ b/recipes/pbgzip/build.sh @@ -4,5 +4,5 @@ sh autogen.sh ./configure --prefix ${PREFIX} --enable-igzip export C_INCLUDE_PATH=${PREFIX}/include export LIBRARY_PATH=${PREFIX}/lib -make +make -j${CPU_COUNT} make install diff --git a/recipes/pbgzip/meta.yaml b/recipes/pbgzip/meta.yaml index 9dd7a7132b0cf..dc3cfeeb5b6d3 100644 --- a/recipes/pbgzip/meta.yaml +++ b/recipes/pbgzip/meta.yaml @@ -7,8 +7,9 @@ source: sha256: 544820be0da38f6af7be18792d00d6d3dd2fe3f7f3b08a67c3aa35fb1bbeaeb1 build: - number: 4 - skip: False + number: 5 + run_exports: + - {{ pin_subpackage('pbgzip', max_pin=None) }} requirements: build: @@ -31,3 +32,7 @@ about: home: https://github.com/nh13/pbgzip summary: Parallel Block GZIP license: MIT/Expat + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 8723132b6c65522f6e1676d13709573047c271dd Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:44:14 +0300 Subject: [PATCH 1625/1813] deeptoolsintervals: add linux-aarch64 build (#47313) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/deeptoolsintervals/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/deeptoolsintervals/meta.yaml b/recipes/deeptoolsintervals/meta.yaml index c5b740e31279a..6611f446819f6 100644 --- a/recipes/deeptoolsintervals/meta.yaml +++ b/recipes/deeptoolsintervals/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6 build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage("deeptoolsintervals", max_pin="x.x") }} @@ -33,3 +33,7 @@ about: home: https://github.com/deeptools/deeptools_intervals license: MIT summary: A python module creating/accessing GTF-based interval trees with associated meta-data + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From b935e94852d7133ed181cd40ffe34f2fa8ff229b Mon Sep 17 00:00:00 2001 From: Shuai WANG <48624090+wshuai294@users.noreply.github.com> Date: Fri, 19 Apr 2024 10:46:13 +0800 Subject: [PATCH 1626/1813] Update description for localhgt in the same version (#47226) --- recipes/localhgt/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/localhgt/meta.yaml b/recipes/localhgt/meta.yaml index 1ed3dd5aa3c37..3b1dd482f1faf 100644 --- a/recipes/localhgt/meta.yaml +++ b/recipes/localhgt/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("localhgt", max_pin="x") }} entry_points: @@ -30,7 +30,7 @@ requirements: - biopython - scikit-learn - scipy - - numpy + - numpy <=1.24 - pandas - samtools >=1.11 - seqkit >=2.6.1 @@ -38,9 +38,9 @@ requirements: - fastp >=0.23.2 about: - home: https://github.com/samtools/samtools + home: https://github.com/deepomicslab/LocalHGT license: MIT - summary: Tools for dealing with SAM, BAM and CRAM files + summary: An ultrafast horizontal gene transfer detection method from large microbial communities test: commands: From 024b7e8526e57a2886d1954914bd5d43029c1c4a Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 05:47:35 +0300 Subject: [PATCH 1627/1813] rust-bio-tools & starcode: add linux-aarch64 build (#46802) * rust-bio-tools: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * starcode: add linux-aarch64 build Needed by rust-bio-tools Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/rust-bio-tools/meta.yaml | 4 +++- recipes/starcode/meta.yaml | 8 +++++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/recipes/rust-bio-tools/meta.yaml b/recipes/rust-bio-tools/meta.yaml index 169fcf16d2137..4df8383242ee8 100644 --- a/recipes/rust-bio-tools/meta.yaml +++ b/recipes/rust-bio-tools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('rust-bio-tools', max_pin="x.x") }} @@ -44,6 +44,8 @@ about: dev_url: https://github.com/rust-bio/rust-bio-tools extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - fxwiegand - felixmoelder diff --git a/recipes/starcode/meta.yaml b/recipes/starcode/meta.yaml index 7421d4d857ad0..2d1b57415ccf5 100644 --- a/recipes/starcode/meta.yaml +++ b/recipes/starcode/meta.yaml @@ -9,7 +9,9 @@ source: sha256: b4f0eae9498f2dcf9c8a7fa2fa88b141c6d5abcf6da44b03d5d85e5f1a8fd5b1 build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage('starcode', max_pin='x.x') }} requirements: build: @@ -25,3 +27,7 @@ about: home: https://github.com/gui11aume/starcode license: GPLv3 summary: 'Starcode: sequence clustering based on all-pairs search' + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 5982536accbb86c0017c7b948e4b9a99a30d8ee7 Mon Sep 17 00:00:00 2001 From: Lucas Freitas <114439901+lfreitasl@users.noreply.github.com> Date: Thu, 18 Apr 2024 23:48:44 -0300 Subject: [PATCH 1628/1813] Add recipe for rnamining package (#47215) * Add recipe for rnamining package * Correct recipe for linting * Fix recipe for testing --- recipes/rnamining/meta.yaml | 47 +++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/rnamining/meta.yaml diff --git a/recipes/rnamining/meta.yaml b/recipes/rnamining/meta.yaml new file mode 100644 index 0000000000000..75d6dbef536c0 --- /dev/null +++ b/recipes/rnamining/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "rnamining" %} +{% set version = "1.0.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/rnamining-{{ version }}.tar.gz + sha256: 03339dd81c1b163b966006559b50fbdca21481d3d82b14f52849b331d105012f + +build: + entry_points: + - rnamining = rnamining.rnamining:main + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + number: 0 + run_exports: + - {{ pin_subpackage('rnamining',max_pin="x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - scipy + - biopython >=1.78 + - scikit-learn >=0.21.3 + - pandas >=0.23.3 + - xgboost ==1.2.0 + +test: + imports: + - rnamining + commands: + - rnamining -h + +about: + home: https://github.com/lfreitasl/RNAmining/tree/pypackage + summary: Package to predict potential coding of RNA sequences provided in fasta format + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - lfreitasl From 78c7b1dd0dc8ea23a0e29ecc50e31d0fb911678b Mon Sep 17 00:00:00 2001 From: Gregg Thomas Date: Thu, 18 Apr 2024 22:52:23 -0400 Subject: [PATCH 1629/1813] adding a link to build (#47294) --- recipes/phyloacc/build.sh | 1 + recipes/phyloacc/meta.yaml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/phyloacc/build.sh b/recipes/phyloacc/build.sh index 449fa686bc283..b2034f66d9414 100644 --- a/recipes/phyloacc/build.sh +++ b/recipes/phyloacc/build.sh @@ -6,5 +6,6 @@ mkdir -p ${SP_DIR} make install CXX=${CXX} cp src/PhyloAcc-interface/phyloacc.py ${PREFIX}/bin/ +ln -s ${PREFIX}/bin/phyloacc.py ${PREFIX}/bin/phyloacc cp src/PhyloAcc-interface/phyloacc_post.py ${PREFIX}/bin/ cp -R src/PhyloAcc-interface/phyloacc_lib ${SP_DIR}/ diff --git a/recipes/phyloacc/meta.yaml b/recipes/phyloacc/meta.yaml index cd1702b9baf67..9468c7e2c2a16 100644 --- a/recipes/phyloacc/meta.yaml +++ b/recipes/phyloacc/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py < 38] run_exports: - {{ pin_subpackage('phyloacc', max_pin="x") }} From 0e3303a1bbb56837fa9510c8beee00a0306fb681 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Apr 2024 23:06:39 -0400 Subject: [PATCH 1630/1813] Update synapseclient to 4.2.0 (#47329) * Update synapseclient to 4.2.0 * edit dependencies --------- Co-authored-by: mencian --- recipes/synapseclient/meta.yaml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/recipes/synapseclient/meta.yaml b/recipes/synapseclient/meta.yaml index 9ecb6a51c0cd7..91cd8644638db 100644 --- a/recipes/synapseclient/meta.yaml +++ b/recipes/synapseclient/meta.yaml @@ -1,5 +1,5 @@ {% set name = "synapseclient" %} -{% set version = "4.1.1" %} +{% set version = "4.2.0" %} package: name: {{ name|lower }} @@ -7,14 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/synapseclient-{{ version }}.tar.gz - sha256: c5e0ac45faed1aa618cd66a0f50bf1a8149a2902a71d07487a0e470250955083 + sha256: 89222661125de1795b1a096cf8c58b8115c19d6b0fa5846ed2a41cdb394ef773 build: noarch: python entry_points: - synapse = synapseclient.__main__:main number: 0 - script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv run_exports: - {{ pin_subpackage('synapseclient', max_pin="x") }} @@ -26,18 +26,17 @@ requirements: - python >=3.8 - requests >=2.22 - urllib3 <2 - - six - - future - - backports.csv - deprecated >=1.2.4 - - keyring >=15.0.0 - opentelemetry-api - opentelemetry-sdk - - opentelemetry-exporter-otlp - run_constrained: - - pandas >=0.25.0 - - pysftp >=0.2.8 - - boto3 >=1.7.0 + - opentelemetry-exporter-otlp-proto-http + - nest-asyncio + - asyncio-atexit + - httpx + - tqdm + - loky + - async-lru + - psutil test: imports: @@ -55,3 +54,4 @@ about: scientists to share and analyze data together. license_file: LICENSE dev_url: https://github.com/Sage-Bionetworks/synapsePythonClient + doc_url: https://python-docs.synapse.org/ From 0f0f245db820997b436e8fbf5ad494bdee27d7cc Mon Sep 17 00:00:00 2001 From: Shuai WANG <48624090+wshuai294@users.noreply.github.com> Date: Fri, 19 Apr 2024 14:31:50 +0800 Subject: [PATCH 1631/1813] Update localhgt v1.0.1 (#47330) * update localhgt v1.0.1 * update localhgt v1.0.1 --- recipes/localhgt/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/localhgt/meta.yaml b/recipes/localhgt/meta.yaml index 3b1dd482f1faf..94f06028c03df 100644 --- a/recipes/localhgt/meta.yaml +++ b/recipes/localhgt/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage("localhgt", max_pin="x") }} entry_points: @@ -13,7 +13,7 @@ build: source: url: https://github.com/deepomicslab/LocalHGT/archive/refs/tags/v{{ version }}.tar.gz - sha256: f06c83372c8ffe9c220f0c4e8cdc1eaec82d52104fe5b32f178555b4a5babfbb + sha256: 4e1dca6c41f4f8519fd848d1d7fc3d290a62e4565bd12b27172846f1871ac4f8 requirements: build: From 74ef3b801202c4a1fc6b5f5a615fdd1a069355a1 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Fri, 19 Apr 2024 08:35:10 +0200 Subject: [PATCH 1632/1813] fix: Nextclade sha256sum for 3.3.1 osx_64 (#47271) * Update nextclade osx_64 sha to 3.3.1 --- recipes/nextclade/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index 2ceb70785f55a..a6321497f60ce 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -11,12 +11,12 @@ source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-unknown-linux-gnu # [aarch64] sha256: 63b38aac186b9b9776761bb1a321b87382044d01c17e6b4a2ba76ca614d04ed1 # [aarch64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: 330ad12cd1bb20429f49fd00bcd773c453b66662842913ec35bc9e288ab3db2a # [osx and x86_64] + sha256: d8e1604be6a32f34086616ebdf532ec1409d500b5fe72c239b6db2614d75e722 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [osx and arm64] sha256: b95e2ed966b08dbd481fe48d7aa1019a748d29ef330daad4773d1c98e6b007ba # [osx and arm64] build: - number: 1 + number: 2 binary_relocation: False run_exports: - {{ pin_compatible(name, max_pin='x') }} From 27b4ec18f7f9bd2165734c61299bd80ce25b4255 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 19 Apr 2024 11:08:58 +0200 Subject: [PATCH 1633/1813] [haddock_biobb] update (#47336) * [haddock_biobb] update * [haddock_biobb] update --- recipes/haddock_biobb/build.sh | 1 + recipes/haddock_biobb/meta.yaml | 2 +- recipes/haddock_biobb/post-link.sh | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/haddock_biobb/build.sh b/recipes/haddock_biobb/build.sh index 7a64adb7ef0e4..dc60e539c255e 100644 --- a/recipes/haddock_biobb/build.sh +++ b/recipes/haddock_biobb/build.sh @@ -21,3 +21,4 @@ cd $SRC_DIR ${PYTHON} setup.py install --single-version-externally-managed --record=record.txt mkdir -p $PREFIX/bin +mkdir -p $SRC_DIR/bin diff --git a/recipes/haddock_biobb/meta.yaml b/recipes/haddock_biobb/meta.yaml index 35b33734ed52b..90f5ca5d923fd 100644 --- a/recipes/haddock_biobb/meta.yaml +++ b/recipes/haddock_biobb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "haddock_biobb" %} -{% set version = "3.0.1" %} +{% set version = "3.0.2" %} package: name: '{{ name|lower }}' diff --git a/recipes/haddock_biobb/post-link.sh b/recipes/haddock_biobb/post-link.sh index 20ec0915cce57..e7047a4b3e016 100644 --- a/recipes/haddock_biobb/post-link.sh +++ b/recipes/haddock_biobb/post-link.sh @@ -1 +1 @@ -echo "Create a softlink [ln -s] of the CNS executable to the ${PREFIX}/bin folder" > "${PREFIX}"/.messages.txt +echo "Create a softlink [ln -s] of the CNS executable to the ${SRC_DIR}/bin folder" > "${PREFIX}"/.messages.txt From bd92adb4cc098d22e1084741a431ca321ebf0d6d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Apr 2024 06:41:43 -0400 Subject: [PATCH 1634/1813] Update oakvar to 2.9.97 (#47345) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 3db375fc44be0..bbf9564801906 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.96" %} -{% set sha256 = "7b5926b064c5b2f0bd354f2d294e7cd8ee6c64f95a976405e1aa8bed4dafc5a3" %} +{% set version = "2.9.97" %} +{% set sha256 = "c8cbd5f3c2f4c6c170b6527b2d911e3a5628ca7c0cb4d2f2a020949bcc18e27e" %} package: name: {{ name|lower }} From b262cbed88931c3ac47d9fc6b1c2dd5a30e85a12 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Apr 2024 06:41:55 -0400 Subject: [PATCH 1635/1813] Update peka to 1.0.2 (#47346) --- recipes/peka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/peka/meta.yaml b/recipes/peka/meta.yaml index 9a38b52189e86..7e59f23423422 100644 --- a/recipes/peka/meta.yaml +++ b/recipes/peka/meta.yaml @@ -1,5 +1,5 @@ {% set name = "PEKA" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/ulelab/peka/archive/refs/tags/v{{ version }}.tar.gz" - sha256: cddbe86774de3de6a7c4ed06b7187d812d736fdc30e19f384170c6bdd77b1174 + sha256: 1742af7941be04b960e5153ef1eccf40781f72bf9d2a9063a97b54f27b76b01f build: number: 0 From 69d45faa9e8cfe87b9c52f2575466fd2ba99730a Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 13:42:42 +0300 Subject: [PATCH 1636/1813] ivar: add linux-aarch64 build (#47331) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * ivar: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Add `host` requirement for zlib ``` /opt/conda/conda-bld/ivar_1713509296169/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory␛[0m 06:50:43 ␛[32mBIOCONDA INFO␛[0m (OUT) collect2: error: ld returned 1 exit status␛[0m ``` Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ivar/build.sh | 2 +- recipes/ivar/meta.yaml | 7 ++++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/ivar/build.sh b/recipes/ivar/build.sh index efb9691a31967..ae5ec4a1259df 100644 --- a/recipes/ivar/build.sh +++ b/recipes/ivar/build.sh @@ -4,7 +4,7 @@ export CPATH=${PREFIX}/include ./autogen.sh ./configure --prefix=$PREFIX --with-hts=$PREFIX -make +make -j${CPU_COUNT} # removing this for now as it triggers a build error from -Werror=maybe-uninitialized - pvanheus # make check make install diff --git a/recipes/ivar/meta.yaml b/recipes/ivar/meta.yaml index 9efba2fd8a3f7..fc9fd87e943eb 100644 --- a/recipes/ivar/meta.yaml +++ b/recipes/ivar/meta.yaml @@ -10,7 +10,9 @@ source: sha256: "{{ sha256 }}" build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage('ivar', max_pin='x') }} requirements: build: @@ -23,6 +25,7 @@ requirements: - pkg-config host: - htslib + - zlib run: - htslib - samtools @@ -39,6 +42,8 @@ about: dev_url: https://github.com/andersen-lab/ivar extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:ivar - usegalaxy-eu:ivar_variants From f9a6f6cac152bec30f7366b414e549c0a7f64764 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 13:43:06 +0300 Subject: [PATCH 1637/1813] ucsc-liftover: add linux-aarch64 build (#47343) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-liftover/build.sh | 12 ++++++------ recipes/ucsc-liftover/htmshell.patch | 11 +++++++++++ recipes/ucsc-liftover/meta.yaml | 9 ++++++++- 3 files changed, 25 insertions(+), 7 deletions(-) create mode 100644 recipes/ucsc-liftover/htmshell.patch diff --git a/recipes/ucsc-liftover/build.sh b/recipes/ucsc-liftover/build.sh index 49383fe092892..189c409009472 100644 --- a/recipes/ucsc-liftover/build.sh +++ b/recipes/ucsc-liftover/build.sh @@ -1,13 +1,13 @@ #!/bin/bash mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export L="${LDFLAGS}" mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/liftOver && make) +(cd kent/src/lib && make -j${CPU_COUNT}) +(cd kent/src/htslib && make -j${CPU_COUNT}) +(cd kent/src/jkOwnLib && make -j${CPU_COUNT}) +(cd kent/src/hg/lib && make -j${CPU_COUNT}) +(cd kent/src/hg/liftOver && make -j${CPU_COUNT}) cp bin/liftOver "$PREFIX/bin" chmod +x "$PREFIX/bin/liftOver" diff --git a/recipes/ucsc-liftover/htmshell.patch b/recipes/ucsc-liftover/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-liftover/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-liftover/meta.yaml b/recipes/ucsc-liftover/meta.yaml index e69762f7a6387..4d953bf48e005 100644 --- a/recipes/ucsc-liftover/meta.yaml +++ b/recipes/ucsc-liftover/meta.yaml @@ -12,13 +12,16 @@ source: sha256: {{ sha256 }} patches: - include.patch + - htmshell.patch build: - number: 0 + number: 1 skip: True # [osx] ignore_run_exports: - libpng - libuuid + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -48,3 +51,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "Move annotations from one assembly to another" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From cd766264d7014e063b147cf38a90cd8c6433bce1 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 13:43:19 +0300 Subject: [PATCH 1638/1813] primer3-py: add linux-aarch64 build (#47341) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/primer3-py/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/primer3-py/meta.yaml b/recipes/primer3-py/meta.yaml index 7eec666088e21..f9e5b1886a1c9 100644 --- a/recipes/primer3-py/meta.yaml +++ b/recipes/primer3-py/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1ec6ce99ea149b1c82361c654a0eab824e698ce32d5f9ed2dd8f8f37564b3f5f build: - number: 0 + number: 1 skip: True # [py < 38] run_exports: - {{ pin_subpackage('primer3-py', max_pin="x") }} @@ -40,5 +40,7 @@ about: doc_url: https://libnano.github.io/primer3-py/ extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - bgruening From 3cdd6b36f9605609f58023d0e07ff569ce42ef27 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Apr 2024 06:43:36 -0400 Subject: [PATCH 1639/1813] Update dodge to 1.0.0 (#47339) --- recipes/dodge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dodge/meta.yaml b/recipes/dodge/meta.yaml index 5e1278b3e5998..c346fc0fe1669 100644 --- a/recipes/dodge/meta.yaml +++ b/recipes/dodge/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.0" %} +{% set version = "1.0.0" %} {% set name = "dodge" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/LanLab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 6897fa29651f3ea9f404f73da8a8d0e2981e2f4e3b9a44a1252fb74a2b908a7a + sha256: 5b95858a6e317f0ecc7f46b369e052bd14734bc316ec38e360f2de3ae2f62116 build: noarch: python From b60f382747967bfaae67b37cf8c5e96eab644383 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 13:43:53 +0300 Subject: [PATCH 1640/1813] samblaster: add linux-aarch64 build (#47338) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/samblaster/build.sh | 2 +- recipes/samblaster/meta.yaml | 8 +++++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/samblaster/build.sh b/recipes/samblaster/build.sh index 6c134704ab89c..e583b50b8c314 100644 --- a/recipes/samblaster/build.sh +++ b/recipes/samblaster/build.sh @@ -3,5 +3,5 @@ BIN=$PREFIX/bin mkdir -p $BIN sed -i.bak 's/CPPFLAGS = /CPPFLAGS = $(CXXFLAGS) /' Makefile -make CPP=$CXX +make CPP=$CXX -j${CPU_COUNT} cp samblaster $BIN diff --git a/recipes/samblaster/meta.yaml b/recipes/samblaster/meta.yaml index 25b42d4cf8568..016234e899fb5 100644 --- a/recipes/samblaster/meta.yaml +++ b/recipes/samblaster/meta.yaml @@ -1,5 +1,7 @@ build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage('samblaster', max_pin='x.x') }} # Started based on: https://anaconda.org/Judowill/samblaster @@ -25,3 +27,7 @@ about: home: https://github.com/GregoryFaust/samblaster license: MIT summary: Mark duplicates in and extract discordant and split reads from SAM files. + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 6bce0c13c3c422d29ee4ea51ebd0f89ca5a95d5f Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 13:44:13 +0300 Subject: [PATCH 1641/1813] alfred: add linux-aarch64 build (#47333) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/alfred/build.sh | 2 +- recipes/alfred/meta.yaml | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/alfred/build.sh b/recipes/alfred/build.sh index dc2400afabae2..89d206cac27f5 100644 --- a/recipes/alfred/build.sh +++ b/recipes/alfred/build.sh @@ -1,3 +1,3 @@ #!/bin/sh -CXXFLAGS="${CXXFLAGS} -D__STDC_FORMAT_MACROS" make CXX="${CXX}" prefix="${PREFIX}" install +CXXFLAGS="${CXXFLAGS} -D__STDC_FORMAT_MACROS" make -j${CPU_COUNT} CXX="${CXX}" prefix="${PREFIX}" install diff --git a/recipes/alfred/meta.yaml b/recipes/alfred/meta.yaml index 6aa3e79ccff11..8316353573dbf 100644 --- a/recipes/alfred/meta.yaml +++ b/recipes/alfred/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('alfred', max_pin="x.x") }} @@ -41,3 +41,7 @@ about: license_family: BSD license_file: LICENSE summary: BAM alignment statistics, feature counting and feature annotation + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 6875951ec363b5e6510476f255707ef6d0508db2 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 19 Apr 2024 13:44:27 +0300 Subject: [PATCH 1642/1813] ucsc-genepredtobed: add linux-aarch64 build (#47337) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-genepredtobed/build.sh | 2 +- recipes/ucsc-genepredtobed/htmshell.patch | 11 +++++++++++ recipes/ucsc-genepredtobed/meta.yaml | 9 ++++++++- 3 files changed, 20 insertions(+), 2 deletions(-) create mode 100644 recipes/ucsc-genepredtobed/htmshell.patch diff --git a/recipes/ucsc-genepredtobed/build.sh b/recipes/ucsc-genepredtobed/build.sh index 106e6c404fcf1..73f68a12d7a6a 100644 --- a/recipes/ucsc-genepredtobed/build.sh +++ b/recipes/ucsc-genepredtobed/build.sh @@ -1,6 +1,6 @@ #!/bin/bash mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export L="${LDFLAGS}" mkdir -p "$BINDIR" diff --git a/recipes/ucsc-genepredtobed/htmshell.patch b/recipes/ucsc-genepredtobed/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-genepredtobed/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-genepredtobed/meta.yaml b/recipes/ucsc-genepredtobed/meta.yaml index 62b669805fbc6..ce54339cf9111 100644 --- a/recipes/ucsc-genepredtobed/meta.yaml +++ b/recipes/ucsc-genepredtobed/meta.yaml @@ -12,13 +12,16 @@ source: sha256: {{ sha256 }} patches: - include.patch + - htmshell.patch build: - number: 0 + number: 1 skip: True # [osx] ignore_run_exports: - libpng - libuuid + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -48,3 +51,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "Convert from genePred to bed format. Does not yet handle genePredExt" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From d1106217663ebdf067b15014bcf8f13220930abd Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 19 Apr 2024 11:45:04 +0100 Subject: [PATCH 1643/1813] Update meta.yaml for DESeq2 to include shrinkage methods (#47335) * Update meta.yaml for DESeq2 to include shrinkage methods * Update meta.yaml --- recipes/bioconductor-deseq2/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-deseq2/meta.yaml b/recipes/bioconductor-deseq2/meta.yaml index fbad8ff890c69..b8c6af265423b 100644 --- a/recipes/bioconductor-deseq2/meta.yaml +++ b/recipes/bioconductor-deseq2/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5eb89526ce9fd4da98b1a5e0b5ba0bf3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -21,6 +21,7 @@ build: # Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager requirements: host: + - bioconductor-apeglm - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-biocparallel >=1.36.0,<1.37.0' @@ -29,6 +30,7 @@ requirements: - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-ashr - r-base - 'r-ggplot2 >=3.4.0' - r-locfit @@ -38,6 +40,7 @@ requirements: - libblas - liblapack run: + - bioconductor-apeglm - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-biocparallel >=1.36.0,<1.37.0' @@ -46,6 +49,7 @@ requirements: - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-ashr - r-base - 'r-ggplot2 >=3.4.0' - r-locfit From 487d459f65dc172989f7fe0035d05b28bd1bd223 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 19 Apr 2024 12:45:32 +0200 Subject: [PATCH 1644/1813] mafft has been migrated to conda-forge (#47218) --- recipes/mafft/7.310/build.sh | 8 ----- recipes/mafft/7.310/linux-makefile.patch | 8 ----- recipes/mafft/7.310/meta.yaml | 33 ------------------- recipes/mafft/7.310/osx-makefile.patch | 17 ---------- recipes/mafft/build.sh | 7 ----- recipes/mafft/meta.yaml | 40 ------------------------ 6 files changed, 113 deletions(-) delete mode 100644 recipes/mafft/7.310/build.sh delete mode 100644 recipes/mafft/7.310/linux-makefile.patch delete mode 100644 recipes/mafft/7.310/meta.yaml delete mode 100644 recipes/mafft/7.310/osx-makefile.patch delete mode 100644 recipes/mafft/build.sh delete mode 100644 recipes/mafft/meta.yaml diff --git a/recipes/mafft/7.310/build.sh b/recipes/mafft/7.310/build.sh deleted file mode 100644 index 4b6aa5d8f2884..0000000000000 --- a/recipes/mafft/7.310/build.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -# cd to location of Makefile and source -cd $SRC_DIR/core - -export PRFX=$PREFIX -make CC="${CC} -fcommon" CXX="${CXX} -fcommon" -make install diff --git a/recipes/mafft/7.310/linux-makefile.patch b/recipes/mafft/7.310/linux-makefile.patch deleted file mode 100644 index 214b12eabf75d..0000000000000 --- a/recipes/mafft/7.310/linux-makefile.patch +++ /dev/null @@ -1,8 +0,0 @@ ---- core/Makefile 2015-10-19 11:46:17.000000000 -0400 -+++ core/linux-makefile 2015-10-19 12:06:49.000000000 -0400 -@@ -1,4 +1,4 @@ --PREFIX = /usr/local -+PREFIX = $(PRFX) - LIBDIR = $(PREFIX)/libexec/mafft - BINDIR = $(PREFIX)/bin - MANDIR = $(PREFIX)/share/man/man1 diff --git a/recipes/mafft/7.310/meta.yaml b/recipes/mafft/7.310/meta.yaml deleted file mode 100644 index 88bd286f36a22..0000000000000 --- a/recipes/mafft/7.310/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -package: - name: mafft - version: '7.310' - -source: - md5: fcb68a47d4506b93bb8463ff29b3cbc4 - url: http://mafft.cbrc.jp/alignment/software/mafft-7.310-without-extensions-src.tgz - patches: - - osx-makefile.patch # [osx] - - linux-makefile.patch # [linux] - -build: - number: 7 - skip: True # [osx] - -requirements: - build: - - make - - {{ compiler('c') }} - - {{ compiler('cxx') }} - -test: - commands: - - mafft --version - -about: - home: 'http://mafft.cbrc.jp/alignment/software/' - license: BSD - summary: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform - -extra: - skip-lints: - - should_not_be_noarch_source diff --git a/recipes/mafft/7.310/osx-makefile.patch b/recipes/mafft/7.310/osx-makefile.patch deleted file mode 100644 index 65ef81f93161d..0000000000000 --- a/recipes/mafft/7.310/osx-makefile.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- core/Makefile 2015-10-19 11:46:17.000000000 -0400 -+++ core/osx-makefile 2015-10-19 12:06:49.000000000 -0400 -@@ -1,4 +1,4 @@ --PREFIX = /usr/local -+PREFIX = $(PRFX) - LIBDIR = $(PREFIX)/libexec/mafft - BINDIR = $(PREFIX)/bin - MANDIR = $(PREFIX)/share/man/man1 -@@ -6,7 +6,7 @@ - - #MNO_CYGWIN = -mno-cygwin - --ENABLE_MULTITHREAD = -Denablemultithread -+#ENABLE_MULTITHREAD = -Denablemultithread - # Comment out the above line if your compiler - # does not support TLS (thread-local strage). - diff --git a/recipes/mafft/build.sh b/recipes/mafft/build.sh deleted file mode 100644 index 918d2ffe0c2db..0000000000000 --- a/recipes/mafft/build.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/bash - -# cd to location of Makefile and source -cd $SRC_DIR/core - -make CC="$CC" CFLAGS="$CFLAGS" PREFIX="$PREFIX" DASH_CLIENT="dash_client" -make install PREFIX="$PREFIX" DASH_CLIENT="dash_client" diff --git a/recipes/mafft/meta.yaml b/recipes/mafft/meta.yaml deleted file mode 100644 index c9d6d09e82b29..0000000000000 --- a/recipes/mafft/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set name = "mafft" %} -{% set version = "7.525" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: -# url: https://mafft.cbrc.jp/alignment/software/mafft-{{ version }}-without-extensions-src.tgz - url: https://gitlab.com/sysimm/mafft/-/archive/v{{ version }}/mafft-v{{ version }}.zip - sha256: "fbd94516539c3401243d80f0c33ee247362120b0efc92b31260b2d5db484b2a6" - -build: - number: 1 - run_exports: - - {{ pin_subpackage(name, max_pin="x") }} - -requirements: - build: - - make - - {{ compiler('c') }} - - {{ compiler('go-cgo') }} - run: - - gawk - -test: - commands: - - mafft --version - -about: - home: 'http://mafft.cbrc.jp/alignment/software/' - license: BSD - summary: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform - -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - doi:10.1093/nar/gkf436 - - usegalaxy-eu:rbc_mafft From 104b7451c73a87e3e00dcc697accfbe01c6b3103 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Fri, 19 Apr 2024 13:55:16 +0200 Subject: [PATCH 1645/1813] bump wisecondorx (#47348) * bump wisecondorx * copy paste fix * fix recipe --- recipes/wisecondorx/meta.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/wisecondorx/meta.yaml b/recipes/wisecondorx/meta.yaml index bcfd7b6e9b74d..8e371c1a090ad 100644 --- a/recipes/wisecondorx/meta.yaml +++ b/recipes/wisecondorx/meta.yaml @@ -1,25 +1,26 @@ -{% set version="1.2.5" %} +{% set version="1.2.6" %} package: name: wisecondorx version: {{ version }} source: url: https://github.com/CenterForMedicalGeneticsGhent/wisecondorX/archive/v{{ version }}.tar.gz - sha256: be60c95630cd89977f445b68f11560360ef10d6c994ea3028c0d0295fc7452c9 + sha256: 66c2373b05bd0e1a90ca781611642db0503b6d42d0eef4a2077bad7a81238405 build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps -vv" + run_exports: + - {{ pin_subpackage('wisecondorx', max_pin="x") }} requirements: host: - - python + - python >=3.6 - setuptools run: - - python + - python >=3.6 - pysam - - futures # [not py3k] - scipy - scikit-learn - numpy @@ -30,7 +31,7 @@ requirements: test: imports: - - wisecondorX + - wisecondorx commands: - WisecondorX --help - WisecondorX convert --help From d98e17ce1dea49b9460e0d3ef449ca759f7cd70a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Apr 2024 17:59:54 -0400 Subject: [PATCH 1646/1813] Update chopper to 0.8.0 (#47362) --- recipes/chopper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/chopper/meta.yaml b/recipes/chopper/meta.yaml index d48214ed8d874..d3d1d006ac7f4 100644 --- a/recipes/chopper/meta.yaml +++ b/recipes/chopper/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.0" %} +{% set version = "0.8.0" %} package: name: chopper @@ -11,7 +11,7 @@ build: source: url: https://github.com/wdecoster/chopper/archive/v{{ version }}.tar.gz - sha256: ff7e718084d16d4fa8ec40ede655d87dad5097e3e0f2d10cb278bcced02b586c + sha256: d79c3a3af8daf9e81f4a209061629e823a3cb0275ff13f9f7e800b9f62c19bab requirements: build: From bf169ad804fc7b9fdc8c37ffc3a1f979a558a58f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Apr 2024 19:21:05 -0400 Subject: [PATCH 1647/1813] Update pybiolib to 1.1.2004 (#47349) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 61bacb5386f21..b2b965aa43c9e 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1998" %} +{% set version = "1.1.2004" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 1dfebf770dc36339939f1796f9936d61f24d0d2468fe6ab2aad20bf2c15c81e9 + sha256: 95d6cdae9c6cae98542dc2a44bb197f8e1f1f1240d8a112a7289a8cf446a2135 build: noarch: python From 4c90d231493c4f244e196779071f09836d3e0ae4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 20 Apr 2024 04:46:27 -0400 Subject: [PATCH 1648/1813] Update pypgatk to 0.0.24 (#47364) * Update pypgatk to 0.0.24 * pin_subpackage added * dependencies added --------- Co-authored-by: Yasset Perez-Riverol --- recipes/pypgatk/meta.yaml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/pypgatk/meta.yaml b/recipes/pypgatk/meta.yaml index 870dcf9978182..d116777b91bb4 100644 --- a/recipes/pypgatk/meta.yaml +++ b/recipes/pypgatk/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypgatk" %} -{% set version = "0.0.23" %} +{% set version = "0.0.24" %} package: name: "{{ name|lower }}" @@ -7,11 +7,13 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "b99906a05cacb9c4bd5c58ba65b9ef71c4582bc788fd7684002d12832f280c2d" + sha256: "4505e80adf38fb27b80fa0c8ccdc956dcd72a58c839d7d93c42c1b73c9ca8b45" build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " requirements: @@ -35,6 +37,9 @@ requirements: - pandas # should be removed as soon as we patch the other packages - pysam >=0.16 + - pyahocorasick + - tqdm + - pathos test: imports: From a3b556a9b08c7f5ceeb8c08987f6240e4977bba0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 20 Apr 2024 09:45:57 -0400 Subject: [PATCH 1649/1813] Update tissuumaps to 3.2.1.7 (#47355) --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index 756c653c7c34b..91e0524d1ed51 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.1.6" %} +{% set version = "3.2.1.7" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: e9e2a687e773a5d6c07014358cc6dfee951ef1400f5ec8c5e2387f3c0b6b4e8d + sha256: d08b2e962f18bfd5fd0db32e85415a097c0655236c7f9b0f2d20dc5127ee3fc9 build: number: 0 From b9831c8c10a0a557a8d06345f146f1f55ccbce47 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Apr 2024 05:21:10 -0400 Subject: [PATCH 1650/1813] Update stringtie to 2.2.2 (#47369) --- recipes/stringtie/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/stringtie/meta.yaml b/recipes/stringtie/meta.yaml index bb60dcb570181..fe28cb6bc9bc5 100644 --- a/recipes/stringtie/meta.yaml +++ b/recipes/stringtie/meta.yaml @@ -1,6 +1,6 @@ {% set name = "StringTie" %} -{% set version = "2.2.1" %} -{% set sha256 = "ce4eec532bbbe39af462be844afa6395ab38fa3418ef5fc2431e2d6194129527" %} +{% set version = "2.2.2" %} +{% set sha256 = "f75f23b8466898d27984fb99cf6f828094fb3ed0307aed7af76e334acb997010" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ source: - patch build: - number: 6 + number: 0 run_exports: - {{ pin_subpackage("stringtie", max_pin="x.x") }} # TODO currently fails to build on osx. From f3d47c7fbf1835212fa6defda21df6012ffdc000 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Apr 2024 05:21:26 -0400 Subject: [PATCH 1651/1813] Update trackhub to 1.0 (#47368) * Update trackhub to 1.0 * modernize trackhub recipe * update dependencies * bs4 --------- Co-authored-by: Ryan Dale --- recipes/trackhub/meta.yaml | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/recipes/trackhub/meta.yaml b/recipes/trackhub/meta.yaml index 55e40d38900f7..0bdb126054bcf 100644 --- a/recipes/trackhub/meta.yaml +++ b/recipes/trackhub/meta.yaml @@ -1,14 +1,16 @@ package: name: trackhub - version: "0.2.4" + version: "1.0" source: - url: https://pypi.python.org/packages/25/db/cf42623bcb91f209469d7d28d9647b814af2b51e1bbf1dce0a2df006ca34/trackhub-0.2.4.tar.gz - md5: 6d80a98e48fbb62b27777f5e14e6159c + url: https://files.pythonhosted.org/packages/f1/76/42a10f8849a56de359fde3e34f495e60709fbb75a8048afac4fb239fb424/trackhub-1.0.tar.gz + sha256: b7d85fcb0b17834343a900bb713d2e7e01d06bb4bf1dd0e06680e270572bda22 build: noarch: python - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage("trackhub", max_pin="x.x") }} requirements: host: @@ -19,12 +21,18 @@ requirements: run: - python - docutils + - requests + - beautifulsoup4 + - html5lib + - openpyxl test: imports: - trackhub - trackhub.test - trackhub.test.data + commands: + - trackhub_from_excel -h about: home: http://github.com/daler/trackhub From ab9b0f6d42145428cd4c3e3f36a599c0028ac74b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Apr 2024 05:21:40 -0400 Subject: [PATCH 1652/1813] Update jvarkit to 2024.04.20 (#47366) --- recipes/jvarkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jvarkit/meta.yaml b/recipes/jvarkit/meta.yaml index edd61c75b9c09..2df572a94b08a 100644 --- a/recipes/jvarkit/meta.yaml +++ b/recipes/jvarkit/meta.yaml @@ -1,6 +1,6 @@ {% set name = "jvarkit" %} -{% set version = "2023.09.07" %} -{% set sha256 = "8cd3554d4614a323a6bb1d1b342d2d271f8b896769e595022c20198cf10bd254" %} +{% set version = "2024.04.20" %} +{% set sha256 = "e4bb5ad1d8743cccc2a94af2ea6f17e883c3ec5e6674d9dcd3162a84b7de9d45" %} package: name: {{ name|lower }} From 1b2a5e14cbe31abde35ad4416f81addb4b431fa5 Mon Sep 17 00:00:00 2001 From: mjohnpayne Date: Sun, 21 Apr 2024 19:23:38 +1000 Subject: [PATCH 1653/1813] Update dodge to v1.0.0 (#47334) * Update salty to 1.0.6 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update dodge to v1.0.0 From 94785666027dbd7616c142be6b064cd9500408c3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Apr 2024 05:24:34 -0400 Subject: [PATCH 1654/1813] Update oakvar to 2.9.106 (#47360) * Update oakvar to 2.9.98 * Update oakvar to 2.9.101 * Update oakvar to 2.9.102 * Update oakvar to 2.9.103 * Update oakvar to 2.9.104 * Update oakvar to 2.9.106 --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index bbf9564801906..7bad73ae05d36 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.97" %} -{% set sha256 = "c8cbd5f3c2f4c6c170b6527b2d911e3a5628ca7c0cb4d2f2a020949bcc18e27e" %} +{% set version = "2.9.106" %} +{% set sha256 = "f22f9451ba179989c8d226c04d6ef588d3f5863e8eac9ea839c183c180934ae2" %} package: name: {{ name|lower }} From e159c4703be3d24e54b3eb36920cc92fed3300ce Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Apr 2024 05:25:43 -0400 Subject: [PATCH 1655/1813] Update micom to 0.35.0 (#47353) --- recipes/micom/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/micom/meta.yaml b/recipes/micom/meta.yaml index 89346affc6dcd..13e69607e3381 100644 --- a/recipes/micom/meta.yaml +++ b/recipes/micom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "micom" %} -{% set version = "0.34.1" %} +{% set version = "0.35.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 9575949a6c93a32cead889b10f8c0f5ff5ffbee1acbe3ef0b3a521fd76fcb791 + sha256: 0df2fbb3282c10e1de6522bf104e39d9540c1b1a92c63cc6882bee9980e61ae3 build: number: 0 From 35c279cf537c95e1e9743c1db3df39c723d2c3e0 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Sun, 21 Apr 2024 12:26:04 +0300 Subject: [PATCH 1656/1813] exonerate: add linux-aarch64 build (#47342) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * exonerate: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Try with newer config.{guess,sub} files Trying to solve the following error: ``` Invalid configuration `aarch64-conda-linux-gnu': machine `aarch64-conda' not recognized␛[0m 08:46:18 ␛[32mBIOCONDA INFO␛[0m (OUT) configure: error: /bin/sh ./config.sub aarch64-conda-linux-gnu failed␛[0m ``` Signed-off-by: Martin Tzvetanov Grigorov * Try to build with GNU GCC 10 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/exonerate/build.sh | 7 +++++++ recipes/exonerate/conda_build_config.yaml | 5 +++++ recipes/exonerate/meta.yaml | 10 ++++++++-- 3 files changed, 20 insertions(+), 2 deletions(-) create mode 100644 recipes/exonerate/conda_build_config.yaml diff --git a/recipes/exonerate/build.sh b/recipes/exonerate/build.sh index 6b8ee4937a8a8..512cc3cc3a21f 100644 --- a/recipes/exonerate/build.sh +++ b/recipes/exonerate/build.sh @@ -1,4 +1,11 @@ #!/bin/sh + +set -xe + +# Download newer config.{sub,guess} files +wget "http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD" -O config.guess +wget "http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD" -O config.sub + mkdir -p ${PREFIX}/bin export CFLAGS="-I$PREFIX/include" diff --git a/recipes/exonerate/conda_build_config.yaml b/recipes/exonerate/conda_build_config.yaml new file mode 100644 index 0000000000000..8caf245450f76 --- /dev/null +++ b/recipes/exonerate/conda_build_config.yaml @@ -0,0 +1,5 @@ +c_compiler_version: + - 10 # [linux] + +cxx_compiler_version: + - 10 # [linux] diff --git a/recipes/exonerate/meta.yaml b/recipes/exonerate/meta.yaml index 3a6311a7d2c30..73b122af68549 100644 --- a/recipes/exonerate/meta.yaml +++ b/recipes/exonerate/meta.yaml @@ -9,7 +9,9 @@ source: sha256: f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042 build: - number: 7 + number: 8 + run_exports: + - {{ pin_subpackage('exonerate', max_pin='x') }} requirements: build: @@ -21,6 +23,7 @@ requirements: host: - glib - pcre + - wget run: - glib @@ -32,10 +35,13 @@ test: about: home: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate - license: GPL-3.0 + license: GPL-3.0-or-later + license_file: COPYING summary: Exonerate - A generic tool for pairwise sequence comparison / alignment extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:exonerate From 3510af812b8b93f180b78773d51f5da612ae4435 Mon Sep 17 00:00:00 2001 From: Khaled196 <56037954+khaled196@users.noreply.github.com> Date: Sun, 21 Apr 2024 10:27:02 +0100 Subject: [PATCH 1657/1813] Add beacon2-import and beacon2- search tools (#47282) * add recipy * add beacon2-import and beacon2-search * add home page and description * add run exp * fix * fix * fix python * rm --no-build-isolation from the build * try to fix python pypy api issue * try to fix python pypy api issue * try to fix python pypy api issue * try to fix python pypy api issue * try to fix python pypy api issue * fix argparse and typing packgins * fix argparse and typing packgins * fix argparse and typing packgins * fix argparse and typing packgins * fix argparse and typing packgins * fix argparse and typing packgins * fix argparse and typing packgins * change conda channels priority * remove areparse * remove typing --- recipes/beacon2-import/LICENSE | 21 ++++++++++++ recipes/beacon2-import/meta.yaml | 56 ++++++++++++++++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 recipes/beacon2-import/LICENSE create mode 100644 recipes/beacon2-import/meta.yaml diff --git a/recipes/beacon2-import/LICENSE b/recipes/beacon2-import/LICENSE new file mode 100644 index 0000000000000..08da4102474eb --- /dev/null +++ b/recipes/beacon2-import/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2023 European Galaxy Project + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/recipes/beacon2-import/meta.yaml b/recipes/beacon2-import/meta.yaml new file mode 100644 index 0000000000000..6764c6cd2219d --- /dev/null +++ b/recipes/beacon2-import/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "beacon2-import" %} +{% set version = "1.0.6" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/beacon2-import-{{ version }}.tar.gz + sha256: 5707364c9d5fdeb13e78709a727f93d00c6359f4673ceed42a29f52ae0a7d93f + +build: + entry_points: + - beacon2-import = beacon2_import.beacon2_import:beacon2_import + - beacon2-search = beacon2_search.beacon2_search:beacon_query + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('beacon2-import', max_pin="x") }} + +requirements: + host: + - python >=3.10 + - pip + run: + - python =3.6.15 + - jsonschema + - dataclasses + - bioblend =0.10.0 + - cyvcf2 + - pymongo + +test: + imports: + - beacon2_import + - beacon2_search + - utils + commands: + - pip check + - beacon2-import --help + - beacon2-search --help + requires: + - python >=3.6 + - pip + +about: + home: https://pypi.org/project/beacon2-import/ + summary: Seamlessly import and query genomic variant data from a beacon + description: "Effortlessly import genetic variants from targeted Galaxy histories or local repositories into your beacon instance with our utility. Simplify querying and analysis of genetic data, enabling comprehensive genetic inquiries with ease" + license: CC-BY-NC-4.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - khaled196 \ No newline at end of file From 680cdc5e2971d7ea372a03abc2f2241fc7e7cf91 Mon Sep 17 00:00:00 2001 From: Chris Wymant <15834752+ChrisHIV@users.noreply.github.com> Date: Sun, 21 Apr 2024 03:29:03 -0600 Subject: [PATCH 1658/1813] Update to version v1.7.1, added better tests (#47358) * Updated version to v1.7.1, added better tests * Add 'installation' of the config file to bring it back (it mysteriously disappeared between 1.3.5 and 1.7.0). Change where the tests look for what they need. * Continued trial & error searching for the config file for testing * Further continued trial & error searching for the config file for testing * Even more trial & error searching for the config file for testing * Bug fix in test * Update to 1.7.2 * More trial and error finding scripts inside tools/ * Added pandas requirement. Removed picard requirement (not needed with default config file) * Added bc to requirements, for docker --- recipes/shiver/build.sh | 1 + recipes/shiver/meta.yaml | 17 ++++++++++------- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/recipes/shiver/build.sh b/recipes/shiver/build.sh index 54b89dbf3429e..818082c74f256 100644 --- a/recipes/shiver/build.sh +++ b/recipes/shiver/build.sh @@ -6,6 +6,7 @@ install ${SRC_DIR}/shiver_full_auto.sh -t $PREFIX/bin install ${SRC_DIR}/shiver_funcs.sh -t $PREFIX/bin install ${SRC_DIR}/shiver_init.sh -t $PREFIX/bin install ${SRC_DIR}/shiver_map_reads.sh -t $PREFIX/bin +install ${SRC_DIR}/config.sh -t $PREFIX/bin install ${SRC_DIR}/tools/*.py -t $PREFIX/bin/tools/ install ${SRC_DIR}/tools/*.R -t $PREFIX/bin/tools/ diff --git a/recipes/shiver/meta.yaml b/recipes/shiver/meta.yaml index c37a7b20052ee..6bbf2969773c3 100644 --- a/recipes/shiver/meta.yaml +++ b/recipes/shiver/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.7.0" %} # put in correct version here +{% set version = "1.7.2" %} # put in correct version here {% set name = "shiver" %} package: @@ -6,7 +6,7 @@ package: version: {{ version }} source: url: https://github.com/ChrisHIV/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 461752a23a284d6bf4fc186a4e263b5efd28e792b484813d237e3d749b3fbf2f + sha256: a94c91aae1abed423ec46238b27eed718f1365084dcfdff274df1ef6da6a4969 build: number: 0 noarch: generic @@ -22,16 +22,18 @@ requirements: - samtools - biopython - mafft - - picard - blast >=2.2.28 - pyfastaq + - six + - pandas + - bc test: commands: - - shiver_init.sh 2>&1 | grep "Arguments" - - shiver_full_auto.sh 2>&1 | grep "Arguments" - - shiver_align_contigs.sh 2>&1 | grep "Arguments" - - shiver_map_reads.sh 2>&1 | grep "Arguments" + - shiver_init.sh --test $PREFIX/bin/config.sh + - shiver_align_contigs.sh --test $PREFIX/bin/config.sh + - shiver_map_reads.sh --test $PREFIX/bin/config.sh paired + - $PREFIX/bin/tools/TestPythonModulesInstalled.py about: home: https://github.com/ChrisHIV/shiver @@ -44,3 +46,4 @@ extra: recipe-maintainers: - notestaff - gtonkinhill + - chrishiv From 2448739fda6826d72212aea604d4592b75afb1a4 Mon Sep 17 00:00:00 2001 From: Ningshan Li <50506882+az7jh2@users.noreply.github.com> Date: Sun, 21 Apr 2024 21:34:51 +0800 Subject: [PATCH 1659/1813] Update sdeper to version 1.1.0 (#47367) * update sdeper * update sdeper 2 --- recipes/sdeper/LICENSE | 21 --------------------- recipes/sdeper/meta.yaml | 18 ++++++++++++------ 2 files changed, 12 insertions(+), 27 deletions(-) delete mode 100755 recipes/sdeper/LICENSE diff --git a/recipes/sdeper/LICENSE b/recipes/sdeper/LICENSE deleted file mode 100755 index 5a026b2d7d3bb..0000000000000 --- a/recipes/sdeper/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2023 az7jh2 - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/recipes/sdeper/meta.yaml b/recipes/sdeper/meta.yaml index 4c96919459ae1..bd72e1eace202 100755 --- a/recipes/sdeper/meta.yaml +++ b/recipes/sdeper/meta.yaml @@ -1,7 +1,7 @@ # This is the recipe file to publish SDePER to Bioconda {% set name = "sdeper" %} -{% set version = "1.0.0" %} +{% set version = "1.1.0" %} package: name: "{{ name|lower }}" @@ -9,7 +9,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 9790a1d6e9534f2354e6257cfc9e82fd5fe3b4ee88ee07296308289dcabcb964 + sha256: 9b02688715cf283521102f7a48e260b92b6fb8baf63295158a23d5e91ad96215 build: number: 0 @@ -18,10 +18,12 @@ build: - runImputation = imputation:main script: "{{ PYTHON }} -m pip install . -vv" noarch: python + run_exports: + - {{ pin_subpackage('sdeper', max_pin="x.x") }} requirements: host: - - python >=3.9.12 + - python >=3.9.12,<=3.11 - pip run: - distinctipy ==1.2.2 @@ -31,15 +33,18 @@ requirements: - numpy ==1.22.4 - openpyxl ==3.0.10 - pandas ==1.4.3 - - python >=3.9.12 - - reportlab ==3.6.12 + - python >=3.9.12,<=3.11 + - reportlab ==4.1.0 - scanpy ==1.9.1 - scikit-learn ==1.1.1 - scikit-misc ==0.1.4 - scipy ==1.8.1 - seaborn ==0.11.2 - - tensorflow ==2.9.1 + - tensorflow-base 2.9.1 cpu_* # explicitly specify to use cpu version out from cpu_, cuda, eigen_, gpu_, or mkl_ in conda packages - umap-learn ==0.5.3 + - libopencv ==4.6.0 # install opencv in conda requires installing these 3 packages, headless version is used + - opencv ==4.6.0 + - py-opencv ==4.6.0 test: commands: @@ -54,6 +59,7 @@ about: summary: "Spatial Deconvolution method with Platform Effect Removal" doc_url: "https://sdeper.readthedocs.io/en/latest/" dev_url: "https://github.com/az7jh2/SDePER" + description: "SDePER (Spatial Deconvolution method with Platform Effect Removal) is a hybrid machine learning and regression method to deconvolve Spatial barcoding-based transcriptomic data using reference single-cell RNA sequencing data, considering platform effects removal, sparsity of cell types per capture spot and across-spots spatial correlation in cell type compositions. SDePER is also able to impute cell type compositions and gene expression at unmeasured locations in a tissue map with enhanced resolution." extra: recipe-maintainers: From 4d8bc0aeeff856fc20387d95beced8c9db00bb4a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Apr 2024 03:16:43 -0400 Subject: [PATCH 1660/1813] Update minigraph to 0.21 (#47370) * Update minigraph to 0.21 * add run_exports --------- Co-authored-by: mencian --- recipes/minigraph/build.sh | 5 +++-- recipes/minigraph/meta.yaml | 14 ++++++++++---- 2 files changed, 13 insertions(+), 6 deletions(-) diff --git a/recipes/minigraph/build.sh b/recipes/minigraph/build.sh index 5f145077a6afa..36a34c892d737 100644 --- a/recipes/minigraph/build.sh +++ b/recipes/minigraph/build.sh @@ -2,7 +2,8 @@ mkdir -p $PREFIX/bin -export CPATH=${PREFIX}/include +export C_INCLUDE_PATH="${PREFIX}/include" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -make CC="${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" +make CC="${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" cp minigraph $PREFIX/bin diff --git a/recipes/minigraph/meta.yaml b/recipes/minigraph/meta.yaml index 22b50fddd42fd..6a1a93b243c54 100644 --- a/recipes/minigraph/meta.yaml +++ b/recipes/minigraph/meta.yaml @@ -1,15 +1,18 @@ -{% set version = "0.20" %} +{% set name = "minigraph" %} +{% set version = "0.21" %} package: - name: minigraph + name: {{ name }} version: {{ version }} source: url: https://github.com/lh3/minigraph/archive/refs/tags/v{{ version }}.tar.gz - sha256: ef695e69d57bbc34478d7d3007e4153422ee2e3534e4f3fcbb8930cfaa5e1dc0 + sha256: 4272447393f0ae1e656376abe144de96cbafc777414d4c496f735dd4a6d3c06a build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('minigraph', max_pin="x.x") }} requirements: build: @@ -25,8 +28,11 @@ test: about: home: https://github.com/lh3/minigraph license: MIT + license_family: MIT license_file: LICENSE.txt summary: Proof-of-concept seq-to-graph mapper and graph generator + doc_url: https://lh3.github.io/minigraph/minigraph.html + dev_url: https://github.com/lh3/minigraph extra: identifiers: From f5503eb60d274166a50500b0da24480bdad25e97 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Apr 2024 03:18:00 -0400 Subject: [PATCH 1661/1813] Update wfa2-lib to 2.3.5 (#47365) * Update wfa2-lib to 2.3.5 * remove patch --------- Co-authored-by: mencian --- recipes/wfa2-lib/build.sh | 4 ++-- recipes/wfa2-lib/meta.yaml | 12 ++++++------ recipes/wfa2-lib/patches/1-macOS_endian.patch | 16 ---------------- 3 files changed, 8 insertions(+), 24 deletions(-) delete mode 100644 recipes/wfa2-lib/patches/1-macOS_endian.patch diff --git a/recipes/wfa2-lib/build.sh b/recipes/wfa2-lib/build.sh index c8b9552cd5b41..1c1d621252dc4 100644 --- a/recipes/wfa2-lib/build.sh +++ b/recipes/wfa2-lib/build.sh @@ -16,10 +16,10 @@ fi cmake -S . -B build \ -DCMAKE_CXX_COMPILER="${CXX}" \ -DCMAKE_C_COMPILER="${CC}" \ - -DCMAKE_CXX_FLAGS="-O3 -D_FILE_OFFSET_BITS=64 -I${PREFIX}/include ${LDFLAGS}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS} -O3 -D_FILE_OFFSET_BITS=64 -I${PREFIX}/include ${LDFLAGS}" \ -DEXTRA_FLAGS="${EXTRA_FLAGS}" \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ -DOPENMP=TRUE -cmake --build build/ --target install -v +cmake --build build/ --target install -j ${CPU_COUNT} -v diff --git a/recipes/wfa2-lib/meta.yaml b/recipes/wfa2-lib/meta.yaml index 82dd47e20f99c..dc5ce51a913f7 100644 --- a/recipes/wfa2-lib/meta.yaml +++ b/recipes/wfa2-lib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "wfa2-lib" %} -{% set version = "2.3.4" %} -{% set sha256 = "3a02d19b45c7efcdcabdd956421b1e449e771fca0b0f072e02d7aa65ebb29f23" %} +{% set version = "2.3.5" %} +{% set sha256 = "2609d5f267f4dd91dce1776385b5a24a2f1aa625ac844ce0c3571c69178afe6e" %} package: name: {{ name|lower }} @@ -9,11 +9,9 @@ package: source: url: https://github.com/smarco/WFA2-lib/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} - patches: - - patches/1-macOS_endian.patch # [osx] build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -25,7 +23,7 @@ requirements: host: - pkg-config - rhash # [osx] - - libgomp # [linux or aarch64] + - libgomp # [linux] - llvm-openmp # [osx] test: @@ -39,6 +37,8 @@ about: license_family: MIT license_file: LICENSE summary: "Wavefront alignment algorithm library v2" + dev_url: "https://github.com/smarco/WFA2-lib" + doc_url: "https://github.com/smarco/WFA2-lib/blob/main/README.md" extra: identifiers: diff --git a/recipes/wfa2-lib/patches/1-macOS_endian.patch b/recipes/wfa2-lib/patches/1-macOS_endian.patch deleted file mode 100644 index 309ffb4a13a45..0000000000000 --- a/recipes/wfa2-lib/patches/1-macOS_endian.patch +++ /dev/null @@ -1,16 +0,0 @@ -index 7600442..a1fab79 100644 ---- a/wavefront/wavefront_extend_kernels.c -+++ b/wavefront/wavefront_extend_kernels.c -@@ -29,7 +29,11 @@ - * DESCRIPTION: WFA module for the "extension" of exact matches - */ - --#include -+#if defined(__APPLE__) || defined(__FreeBSD__) -+#include // __BYTE_ORDER -+#else -+#include // __BYTE_ORDER -+#endif - - #include "wavefront_extend_kernels.h" - #include "wavefront_termination.h" From 3cc3d994c40b9255764f04b40e032135e3b44ee5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Apr 2024 03:19:52 -0400 Subject: [PATCH 1662/1813] Update civicpy to 3.1.0 (#47357) * Update civicpy to 3.1.0 * add run_exports --------- Co-authored-by: mencian --- recipes/civicpy/meta.yaml | 23 ++++++++--------------- 1 file changed, 8 insertions(+), 15 deletions(-) diff --git a/recipes/civicpy/meta.yaml b/recipes/civicpy/meta.yaml index e757499136520..d4efb9149751d 100644 --- a/recipes/civicpy/meta.yaml +++ b/recipes/civicpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "civicpy" %} -{% set version = "3.0.0" %} +{% set version = "3.1.0" %} package: name: "{{ name|lower }}" @@ -7,29 +7,23 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 6aa80d2e37718b6a646a2adee5d2432f1a8fa87d6d13fd6e3de11a6834a0ba77 + sha256: 1e9d5a36dff490c5a806cfc152c5f998ba13a54e409cb72eff392dc2ada14537 build: number: 0 - noarch: generic + noarch: python entry_points: - civicpy=civicpy.cli:cli - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('civicpy', max_pin="x") }} requirements: - host: - - backports-datetime-fromisoformat =2.0.0 - - click - - deprecation - - networkx - - obonet =0.2.3 - - pandas + host: - pip - - pysam - python >=3.5 - - requests - - vcfpy run: + - python >=3.5 - backports-datetime-fromisoformat =2.0.0 - click - deprecation @@ -37,7 +31,6 @@ requirements: - obonet =0.2.3 - pandas - pysam - - python >=3.5 - requests - vcfpy From da94bc5783555f4c4ef627620830f89fe224a6d2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Apr 2024 04:18:43 -0400 Subject: [PATCH 1663/1813] Update snakemake to 8.10.8 (#47340) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake to 8.10.8 * fix smart_open pinning Following PR #47371. --------- Co-authored-by: Johannes Köster --- recipes/snakemake/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index b41496df85412..6e4d7dec6c04d 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.10.7" %} +{% set version = "8.10.8" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: c64e0ddfe2af6c06f0c50f5451b8cffad0775a829364754e40da418b4c1118d6 + sha256: 75711faa668324f9e6c44a860f2f9645be358763a97ee411bb32f7a8f6dca6b7 build: number: 0 @@ -102,7 +102,7 @@ outputs: - pyyaml - requests >=2.8.1 - reretry - - smart_open >=3.0,<4.0 + - smart_open >=3.0,<8.0 - snakemake-interface-executor-plugins >=9.1.0,<10.0.0 - snakemake-interface-common >=1.17.0,<2.0 - snakemake-interface-storage-plugins >=3.1.0,<4.0 From fb387d6d5242687e308def52f1c255d203434ae7 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 22 Apr 2024 14:32:56 +0300 Subject: [PATCH 1664/1813] goleft: add linux-aarch64 build (#47354) --- recipes/goleft/build.sh | 2 +- recipes/goleft/meta.yaml | 16 +++++++++++----- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/recipes/goleft/build.sh b/recipes/goleft/build.sh index 49d4ada78fb2a..5b317e41721de 100644 --- a/recipes/goleft/build.sh +++ b/recipes/goleft/build.sh @@ -1,4 +1,4 @@ #!/bin/bash -chmod a+x golef* +chmod a+x goleft* mkdir -p $PREFIX/bin cp goleft* $PREFIX/bin/goleft diff --git a/recipes/goleft/meta.yaml b/recipes/goleft/meta.yaml index 48a4be6f328e7..0b170fe53ab2d 100644 --- a/recipes/goleft/meta.yaml +++ b/recipes/goleft/meta.yaml @@ -1,18 +1,22 @@ -{% set version = "0.2.4" %} +{% set version = "0.2.6" %} package: name: goleft version: '{{ version }}' source: - - url: https://github.com/brentp/goleft/releases/download/v{{ version }}/goleft_linux64 # [linux] - sha256: 5f8df703f7a369213961b4fc583aa625012548fb213dd906eaaeaaed89a319ab # [linux] + - url: https://github.com/brentp/goleft/releases/download/v{{ version }}/goleft_linux64 # [linux and x86_64] + sha256: 3fbb8076c1b2da4a1d7bcb5edd0cc879fe608066c0ca58221db155e7edd5bcb3 # [linux and x86_64] + - url: https://github.com/brentp/goleft/releases/download/v{{ version }}/goleft_linux_aarch64 # [linux and aarch64] + sha256: bf3179de66297b916e720f72a4afd57fef937b098d869926d5ac967f9634b8b8 # [linux and aarch64] - url: https://github.com/brentp/goleft/releases/download/v{{ version }}/goleft_osx # [osx] - sha256: eab89fe80063095f9d01d02bac6770ea9ef102abab900ce01477ebb6fd9bdebc # [osx] + sha256: 1aebf606658b1007669d96a76de9a1a3106b5caa4c4d5b786a75339d35d0e54e # [osx] build: - number: 1 + number: 0 binary_relocation: false + run_exports: + - {{ pin_subpackage('goleft', max_pin='x.x') }} requirements: run: @@ -29,6 +33,8 @@ about: summary: goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary extra: + additional-platforms: + - linux-aarch64 skip-lints: - should_be_noarch_generic - should_not_be_noarch_source From 64c37779404c2f6b9b775da63230a2e769df6de6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Apr 2024 17:23:02 -0400 Subject: [PATCH 1665/1813] Update primerforge to 1.0.2 (#47387) * Update primerforge to 1.0.1 * added a `--check_install` step * edit dependencies * fixed typo in biopython version * Update primerforge to 1.0.2 --------- Co-authored-by: Joe Wirth <71667025+dr-joe-wirth@users.noreply.github.com> Co-authored-by: mencian --- recipes/primerforge/meta.yaml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml index 1d12bb99781f3..404d73f1ffd56 100644 --- a/recipes/primerforge/meta.yaml +++ b/recipes/primerforge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primerForge" %} -{% set version = "1.0.0" %} +{% set version = "1.0.2" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: ac92e00f881d6c1817818bec88e5d7dc9232d7853e6ce1db8745ea809fd9d232 + sha256: b834ad463b39eb68634ef7869881a8aec57181d4e372963f933bf52ddc40b501 build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + entry_points: + - primerForge=bin.main:main run_exports: - {{ pin_subpackage('primerforge', max_pin="x.x") }} @@ -21,7 +23,8 @@ requirements: - python >=3.11 - pip run: - - biopython + - python >=3.11 + - biopython ==1.81 - matplotlib-base >=3.7 - numpy - primer3-py >=2.0 @@ -30,6 +33,7 @@ requirements: test: commands: - primerForge --help + - primerForge --check_install about: home: https://github.com/dr-joe-wirth/{{ name }} From fb1675c6a08bb59a879586e787bf04699e75bb97 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Apr 2024 18:14:07 -0400 Subject: [PATCH 1666/1813] Update hmftools-mark-dups to 1.1.5 (#47388) --- recipes/hmftools-mark-dups/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-mark-dups/meta.yaml b/recipes/hmftools-mark-dups/meta.yaml index 0946d070a6942..b3a5ae8fd6f73 100644 --- a/recipes/hmftools-mark-dups/meta.yaml +++ b/recipes/hmftools-mark-dups/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.4" %} -{% set sha256 = "0cf4bf1113321fb821b041b8be77d6d4948fda13998ad3d4e72c36bea41379b1" %} +{% set version = "1.1.5" %} +{% set sha256 = "59cc87f1e7923b11d5c1b59c3c8fb531ace6d5d39dac61a165d76b4d1c472c10" %} package: name: hmftools-mark-dups From 217a257e0d8db3392583f2e55e95647fd1b75f7f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Apr 2024 20:59:33 -0400 Subject: [PATCH 1667/1813] Update prophyle to 0.3.3.2 (#47372) --- recipes/prophyle/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/prophyle/meta.yaml b/recipes/prophyle/meta.yaml index 982f843ee47bc..1765b8cd3a11e 100644 --- a/recipes/prophyle/meta.yaml +++ b/recipes/prophyle/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.3.1" %} -{% set sha256 = "7007f4858020f4ee2926b8ebe6089a886119d07358f645adfc869b444c52d32c" %} +{% set version = "0.3.3.2" %} +{% set sha256 = "b9476c617bcbc3eea229a1becd7f70133d3d3c59869e90284dfaf4b915757366" %} package: name: prophyle From 923a3ef24cf85f0dd1436dd4d0269b5ac84be8e5 Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Mon, 22 Apr 2024 22:30:15 -0700 Subject: [PATCH 1668/1813] Update nextclade to 3.4.0 (#47391) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index a6321497f60ce..f5a4d4ad86804 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.3.1" %} +{% set version = "3.4.0" %} package: name: "{{ name|lower }}" @@ -7,16 +7,16 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 9eecdb2e56362d24cfedb510b236f2054c3d02264f3ca7e8c586fe234d25e2f2 # [linux64] + sha256: 5c9925fc94281fd83fcaa9a24246ae5bb0a1eee85f07cb506cde7e4fd71a6140 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-unknown-linux-gnu # [aarch64] - sha256: 63b38aac186b9b9776761bb1a321b87382044d01c17e6b4a2ba76ca614d04ed1 # [aarch64] + sha256: 3f8dcfcda22d9c7c99f357bcdec962cb884b6ecdd29889ee45699f5a04d14995 # [aarch64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: d8e1604be6a32f34086616ebdf532ec1409d500b5fe72c239b6db2614d75e722 # [osx and x86_64] + sha256: 8554c739b892ca39c87794155ae70189a2bf0445982e3f1034f6f0ebe6e14b44 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [osx and arm64] - sha256: b95e2ed966b08dbd481fe48d7aa1019a748d29ef330daad4773d1c98e6b007ba # [osx and arm64] + sha256: e45861111ee1adb3e4239b889ae7b206be8ea0f839a2edb277fc6d3aa8a2359f # [osx and arm64] build: - number: 2 + number: 0 binary_relocation: False run_exports: - {{ pin_compatible(name, max_pin='x') }} From ccb1e0acbade9baaa783a01399d05d364cf32e9e Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 23 Apr 2024 08:50:52 +0200 Subject: [PATCH 1669/1813] update hicexplorer scikit-learn requirement (#47390) --- recipes/hicexplorer/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/hicexplorer/meta.yaml b/recipes/hicexplorer/meta.yaml index 4ee9927c54e42..913f95bb1835f 100644 --- a/recipes/hicexplorer/meta.yaml +++ b/recipes/hicexplorer/meta.yaml @@ -9,7 +9,7 @@ source: sha256: db80bb90772795e603136b781f7dc81659509977e1e86dea7b298490cab73444 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps -vv" noarch: python run_exports: @@ -46,7 +46,7 @@ requirements: - tqdm >=4.66 - hyperopt >=0.2.7 - python-graphviz >=0.20 - - scikit-learn >=1.3.1 + - scikit-learn <=1.3 - imbalanced-learn >=0.11 - cleanlab >=2.5 @@ -95,8 +95,8 @@ test: - hicInterIntraTAD --version - hicTADClassifier --version - hicTrainTADClassifier --version - - + + about: home: https://github.com/deeptools/HiCExplorer license: GPL3 From 8e44d2c66ccc5194a748ef5b2b792c799c021365 Mon Sep 17 00:00:00 2001 From: Leonid Kostrykin Date: Tue, 23 Apr 2024 09:19:06 +0200 Subject: [PATCH 1670/1813] Add giatools recipe (#47378) --- recipes/giatools/meta.yaml | 43 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/giatools/meta.yaml diff --git a/recipes/giatools/meta.yaml b/recipes/giatools/meta.yaml new file mode 100644 index 0000000000000..7d1451b600566 --- /dev/null +++ b/recipes/giatools/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "giatools" %} +{% set version = "0.1" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: "https://github.com/BMCV/giatools/archive/refs/tags/{{ version }}.zip" + sha256: 99e4b126a62178247b889d6f71c138457f86954d9a773be8d0003408e86fb4cf + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv " + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.8,<3.12 + - pip + - setuptools + - numpy >=1.18 + - scikit-image >=0.18 + run: + - python >=3.8,<3.12 + - numpy >=1.18 + - scikit-image >=0.18 + +test: + commands: + - python -c "import giatools; print(giatools.VERSION)" + +about: + home: "https://github.com/BMCV/giatools" + license: MIT + summary: "Tools required for Galaxy Image Analysis" + dev_url: "https://github.com/BMCV/giatools" + +extra: + recipe-maintainers: + - kostrykin From f4a7343ecfcd3d11b28138d1b9277c959a3daebb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Salom=C3=A9=20Brunon?= <91611978+Salome-Brunon@users.noreply.github.com> Date: Tue, 23 Apr 2024 09:20:21 +0200 Subject: [PATCH 1671/1813] Updated ToulligQc to v2.5.5 (#47377) * Updated ToulligQc to v2.5.4 * UPDATE: updated ToulligQC to v2.5.5 --- recipes/toulligqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/toulligqc/meta.yaml b/recipes/toulligqc/meta.yaml index c47895becce79..cf09283366e10 100644 --- a/recipes/toulligqc/meta.yaml +++ b/recipes/toulligqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "toulligqc" %} -{% set version = "2.5.4" %} +{% set version = "2.5.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 27524706a9483b9fd38b1122b8622214126b02fa13cb2c198c6686346bd7c880 + sha256: aa614700d670218500c436004e1ec7f895f8d95ebf3f95fdbfc7e718be96710b build: number: 0 From 9a809c3d490b50a0e94fa0005a4ba0d7e76fa8a9 Mon Sep 17 00:00:00 2001 From: Morten Enemark Lund Date: Tue, 23 Apr 2024 15:29:15 +0200 Subject: [PATCH 1672/1813] Update snakemake minimum version for smart-open (#47374) * Update minimum version for smart-open * Trigger new CI run --- recipes/snakemake/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 6e4d7dec6c04d..53a7d88eb8bb7 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 75711faa668324f9e6c44a860f2f9645be358763a97ee411bb32f7a8f6dca6b7 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage("snakemake", max_pin="x") }} @@ -83,7 +83,7 @@ outputs: - pip - setuptools run: - # Keep in sync with snakemake/setup.cfg + # Keep in sync with snakemake/setup.cfg - python >=3.11,<3.13 - appdirs - immutables @@ -102,7 +102,7 @@ outputs: - pyyaml - requests >=2.8.1 - reretry - - smart_open >=3.0,<8.0 + - smart_open >=4.0,<8.0 - snakemake-interface-executor-plugins >=9.1.0,<10.0.0 - snakemake-interface-common >=1.17.0,<2.0 - snakemake-interface-storage-plugins >=3.1.0,<4.0 From 43f17da731608b40a040a0af467e72d23d1b0d9c Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 23 Apr 2024 17:16:10 +0300 Subject: [PATCH 1673/1813] infernal: add linux-aarch64 build (#46956) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * infernal: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * edit ARCH_OPTS * Use newer versions of config.{guess,sub} for Linux ARM64 Solves the following error: ``` ./configure --prefix=/opt/conda/conda-bld/infernal_1712151558751/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac ''�[0m 13:41:21 �[32mBIOCONDA INFO�[0m (OUT) configure: WARNING: you should use --build, --host, --target�[0m 13:41:21 �[32mBIOCONDA INFO�[0m (OUT) configure: Configuring Infernal for your system.�[0m 13:41:21 �[32mBIOCONDA INFO�[0m (OUT) Invalid configuration `aarch64-conda-linux-gnu': machine `aarch64-conda' not recognized�[0m 13:41:21 �[32mBIOCONDA INFO�[0m (OUT) configure: error: /bin/sh ./config.sub aarch64-conda-linux-gnu failed�[0 ``` Signed-off-by: Martin Tzvetanov Grigorov * Build without MPI Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov Co-authored-by: mencian --- recipes/infernal/build.sh | 18 ++++++++++++++++-- recipes/infernal/meta.yaml | 9 +++++++-- 2 files changed, 23 insertions(+), 4 deletions(-) diff --git a/recipes/infernal/build.sh b/recipes/infernal/build.sh index cf8e77142882d..96e0f326ebabc 100644 --- a/recipes/infernal/build.sh +++ b/recipes/infernal/build.sh @@ -5,6 +5,20 @@ set -ex grep -l -r "/usr/bin/perl" . | xargs sed -i.bak -e 's/usr\/bin\/perl/usr\/bin\/env perl/g' autoreconf -i -./configure --prefix="${PREFIX}" --enable-sse -make -j 2 + +case $(uname -m) in + "x86_64") + ARCH_OPTS="--enable-sse" + ;; + "aarch64") + # Download newer config.{sub,guess} files that support aarch64-conda-linux-gnu + wget "http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD" -O config.guess + wget "http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD" -O config.sub + ;; + *) + ;; +esac + +./configure --prefix="${PREFIX}" "${ARCH_OPTS}" +make -j${CPU_COUNT} make install diff --git a/recipes/infernal/meta.yaml b/recipes/infernal/meta.yaml index 33fd6e2aa733d..e98e342633c4d 100644 --- a/recipes/infernal/meta.yaml +++ b/recipes/infernal/meta.yaml @@ -10,9 +10,9 @@ source: sha256: ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f build: - number: 0 + number: 1 run_exports: - - {{ pin_subpackage('infernal', max_pin="x") }} + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: @@ -23,6 +23,9 @@ requirements: - libtool host: - perl + - libgomp # [linux] + - llvm-openmp # [osx] + - wget test: commands: @@ -48,6 +51,8 @@ about: dev_url: https://github.com/EddyRivasLab/infernal extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1093/bioinformatics/btt509 - biotools:infernal From 7ed3e61ac7c3c419d9ad5df5123c7804f2c2c470 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Tue, 23 Apr 2024 17:25:35 +0300 Subject: [PATCH 1674/1813] kmc: add linux-aarch64 build (#47409) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * kmc: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Update the sha256 for Linux ARM64 Signed-off-by: Martin Tzvetanov Grigorov * Disable the test for Linux ARM64. It requires GLIBC 2.29+ ``` + kmc --help␛[0m 12:19:06 ␛[32mBIOCONDA INFO␛[0m (OUT) kmc: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by kmc)␛[0m 12:19:06 ␛[32mBIOCONDA INFO␛[0m (OUT) kmc: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by kmc)␛[0m 12:19:06 ␛[32mBIOCONDA INFO␛[0m (OUT) kmc: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by kmc)␛[0m 12:19:06 ␛[32mBIOCONDA INFO␛[0m (OUT) kmc: /lib64/libc.so.6: version `GLIBC_2.35' not found (required by kmc)␛[0m 12:19:06 ␛[32mBIOCONDA INFO␛[0m (OUT) kmc: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by kmc)␛[0m 12:19:06 ␛[32mBIOCONDA INFO␛[0m (OUT) kmc: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by kmc)␛[0m 12:19:06 ␛[32mBIOCONDA INFO␛[0m (OUT) kmc: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by kmc)␛[0m 12:19:08 ␛[32mBIOCONDA INFO␛[0m (OUT) Tests failed for kmc-3.2.4-hf9a8d21_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken␛[0m ``` Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/kmc/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/kmc/meta.yaml b/recipes/kmc/meta.yaml index d96d701a183c5..bde88e12d619b 100644 --- a/recipes/kmc/meta.yaml +++ b/recipes/kmc/meta.yaml @@ -2,6 +2,8 @@ {% set version = "3.2.4" %} {% set url = "https://github.com/refresh-bio/KMC/releases/download/v3.2.4/KMC3.2.4.linux.x64.tar.gz" %} # [linux and x86_64] {% set sha256 = "158f2084f8d928b3f33b8aaf7d1220fee4183bf46837787e5e6b16bbdf54d31d" %} # [linux and x86_64] +{% set url = "https://github.com/refresh-bio/KMC/releases/download/v3.2.4/KMC3.2.4.linux.arm64.tar.gz" %} # [linux and aarch64] +{% set sha256 = "3049745a71c4219fb05cf003a53b03a9f434e8afacb79c710488f1aefae0a9c8" %} # [linux and aarch64] {% set url = "https://github.com/refresh-bio/KMC/releases/download/v3.2.4/KMC3.2.4.mac.x64.tar.gz" %} # [osx] {% set sha256 = "70d66545d5802cf116469e41acb2a04631271feac81ff5c4d1c299e9407ca326" %} # [osx] @@ -14,7 +16,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("kmc", max_pin="x") }} @@ -31,7 +33,7 @@ requirements: test: commands: - - kmc --help + - kmc --help # [not aarch64] about: home: https://github.com/refresh-bio/kmc @@ -45,6 +47,8 @@ about: dev_url: https://github.com/refresh-bio/kmc extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:kmc - doi:10.1093/bioinformatics/btx304 From 1e3de9f00442ccb16b52c4d039f07beab57ef5b7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:49:18 -0400 Subject: [PATCH 1675/1813] Update r-ldweaver to 1.5 (#47396) --- recipes/r-ldweaver/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-ldweaver/meta.yaml b/recipes/r-ldweaver/meta.yaml index 26d05b5b7316e..9d1ef8ded260c 100644 --- a/recipes/r-ldweaver/meta.yaml +++ b/recipes/r-ldweaver/meta.yaml @@ -1,6 +1,6 @@ {% set name = "r-ldweaver" %} -{% set version = "1.4" %} -{% set sha256 = "8fca169dbf073a280cb47d1352fbb1a49b7f0b4daeba146928705def61650608" %} +{% set version = "1.5" %} +{% set sha256 = "4952b30c4e50850d6ed119469b377ecd49047f4802c5c1b84564cad60d972676" %} package: name: {{ name }} From 258abea24ed768b7a6278967b0a2fa1dc551baae Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 24 Apr 2024 03:49:27 +0300 Subject: [PATCH 1676/1813] cdbtools: add linux-aarch64 build (#47395) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/cdbtools/build.sh | 2 +- recipes/cdbtools/meta.yaml | 8 +++++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/cdbtools/build.sh b/recipes/cdbtools/build.sh index 3298b9ab314d0..facdc9734cb9e 100644 --- a/recipes/cdbtools/build.sh +++ b/recipes/cdbtools/build.sh @@ -1,4 +1,4 @@ mkdir -pv $PREFIX/bin -make CC="${CXX}" LINKER="${CXX}" +make CC="${CXX}" LINKER="${CXX}" -j ${CPU_COUNT} cp cdbfasta $PREFIX/bin cp cdbyank $PREFIX/bin diff --git a/recipes/cdbtools/meta.yaml b/recipes/cdbtools/meta.yaml index a95d6334963bb..fd3037deed543 100644 --- a/recipes/cdbtools/meta.yaml +++ b/recipes/cdbtools/meta.yaml @@ -10,7 +10,9 @@ source: - zlib.patch build: - number: 9 + number: 10 + run_exports: + - {{ pin_subpackage('cdbtools', max_pin='x.x') }} requirements: build: @@ -31,4 +33,8 @@ about: license: Public Domain summary: CDB (Constant DataBase) indexing and retrieval tools for FASTA files +extra: + additional-platforms: + - linux-aarch64 + # vim:set ts=8 sw=2 From e7b23e3e4230b5b434535715474049ba89dfa82c Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 24 Apr 2024 03:49:37 +0300 Subject: [PATCH 1677/1813] trimal: add linux-aarch64 build (#47398) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/trimal/build.sh | 2 +- recipes/trimal/meta.yaml | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/trimal/build.sh b/recipes/trimal/build.sh index 27923c51cacab..3b76620205a47 100644 --- a/recipes/trimal/build.sh +++ b/recipes/trimal/build.sh @@ -1,7 +1,7 @@ #!/bin/sh cd source -make CC="${CXX}" FLAGS="${CPPFLAGS} ${CXXFLAGS}" +make CC="${CXX}" FLAGS="${CPPFLAGS} ${CXXFLAGS}" -j ${CPU_COUNT} mkdir -p $PREFIX/bin diff --git a/recipes/trimal/meta.yaml b/recipes/trimal/meta.yaml index 27bf643b5e1ef..c9a3dea2d9fab 100644 --- a/recipes/trimal/meta.yaml +++ b/recipes/trimal/meta.yaml @@ -7,7 +7,9 @@ source: md5: cb193397635da45be350e9ac96dafe45 build: - number: 8 + number: 9 + run_exports: + - {{ pin_subpackage('trimal', max_pin='x') }} requirements: build: @@ -27,5 +29,7 @@ about: license: GNU General Public License v3 or later (GPLv3+) extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:trimAl From bc6ff73a79e42dd527b45de388f726b00655baf3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:50:04 -0400 Subject: [PATCH 1678/1813] Update dnarrange to 1.6.2 (#47393) --- recipes/dnarrange/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnarrange/meta.yaml b/recipes/dnarrange/meta.yaml index 5bf8821eb06a2..71980172cffb7 100644 --- a/recipes/dnarrange/meta.yaml +++ b/recipes/dnarrange/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.6.1" %} +{% set version = "1.6.2" %} package: name: dnarrange @@ -6,7 +6,7 @@ package: source: url: https://github.com/mcfrith/dnarrange/archive/{{ version }}.tar.gz - sha256: e5046acb96e561b3dc12c4685eb0acf3170b812577a32655c08c21b8eb5a957d + sha256: 1f6b82b51160855455cc2c8ce198dffca7bdfe635806a3c0adc0e58669f8dbe3 build: number: 0 From d8991e23e101f80a27bcad74b08c5784b225ec10 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:50:11 -0400 Subject: [PATCH 1679/1813] Update seqnado to 0.5.1 (#47415) --- recipes/seqnado/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqnado/meta.yaml b/recipes/seqnado/meta.yaml index 762463faf64bf..0d5423f036b96 100644 --- a/recipes/seqnado/meta.yaml +++ b/recipes/seqnado/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqnado" %} -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqnado-{{ version }}.tar.gz - sha256: e5f226b590006b043c37cb1e4308950032cbd192b69d530f49682425e0efd677 + sha256: 3202446e4b1fdb046b5b79c30e5558e84fb05b7b7a507d0c9bfaf279fba5effa build: From 79a5a2f8307f01e588656cf4bcf0aafd8e729217 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:50:18 -0400 Subject: [PATCH 1680/1813] Update giatools to 0.1.1 (#47416) --- recipes/giatools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/giatools/meta.yaml b/recipes/giatools/meta.yaml index 7d1451b600566..f63d780aa5808 100644 --- a/recipes/giatools/meta.yaml +++ b/recipes/giatools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "giatools" %} -{% set version = "0.1" %} +{% set version = "0.1.1" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/BMCV/giatools/archive/refs/tags/{{ version }}.zip" - sha256: 99e4b126a62178247b889d6f71c138457f86954d9a773be8d0003408e86fb4cf + sha256: 7b4aeb897382d493dd55f5440a3d2a81e70a096ddf88155faebfb38f0ec774f7 build: number: 0 From 0615af1a6157f4b444bdac2a0b2e241a1c5dc2fe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:50:28 -0400 Subject: [PATCH 1681/1813] Update oakvar to 2.9.109 (#47418) * Update oakvar to 2.9.108 * Update oakvar to 2.9.109 --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 7bad73ae05d36..ef365d3fb2a96 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.106" %} -{% set sha256 = "f22f9451ba179989c8d226c04d6ef588d3f5863e8eac9ea839c183c180934ae2" %} +{% set version = "2.9.109" %} +{% set sha256 = "e314a119d1b435df9cb917b23c1be8be9be4593094e73a6bbe3ad37544733d0b" %} package: name: {{ name|lower }} From 4d20a57e0bf9eaa133176b0c311941ae6d5027f7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:51:09 -0400 Subject: [PATCH 1682/1813] Update pairtools to 1.1.0 (#47419) --- recipes/pairtools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pairtools/meta.yaml b/recipes/pairtools/meta.yaml index 43d9a7bf44b70..62746b7ac48ad 100644 --- a/recipes/pairtools/meta.yaml +++ b/recipes/pairtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pairtools" %} -{% set version = "1.0.3" %} +{% set version = "1.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 12b482f04d66a01b80ababfb4b6d37959f7995c29f4bb1640f1102d8566d478f + sha256: 3f265ebcd50fb07a36199a99c58f6b17810b48bacf2d5f3096453319c89bd522 build: number: 0 From d73ec63eeb655fca69846a73740f233580392322 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:51:24 -0400 Subject: [PATCH 1683/1813] Update snakemake-executor-plugin-lsf to 0.2.4 (#47420) --- recipes/snakemake-executor-plugin-lsf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-lsf/meta.yaml b/recipes/snakemake-executor-plugin-lsf/meta.yaml index 1c8ea46a2f0c2..c894203d80e0d 100644 --- a/recipes/snakemake-executor-plugin-lsf/meta.yaml +++ b/recipes/snakemake-executor-plugin-lsf/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-lsf" %} -{% set version = "0.2.3" %} +{% set version = "0.2.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_lsf-{{ version }}.tar.gz - sha256: da628c4388d7d37c45190184e02c972acfa398bcd18d571d1ad3ca41ca8bb834 + sha256: b4a7e59d0aacdfb48dc152169602ec0a3ff1b5a4b3c3a26bd52eb597539a63a0 build: noarch: python From 581054b121dff43c8ea93afce4cfcbf76f3e8b8b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:51:49 -0400 Subject: [PATCH 1684/1813] Update wgd to 2.0.32 (#47381) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index b38be15c19f8b..759a972943853 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.31" %} +{% set version = "2.0.32" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: 451db487d5584417623b49d8807919173af94c984112cd0812a80484c6719775 + sha256: 5c599eb509cab810aaa11815464e8522edc3583e8a429f28695656213c7db0ca build: number: 0 From 6e4ffbedc12bb1201c8d4eff352ba2c29dbc81a8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:52:11 -0400 Subject: [PATCH 1685/1813] Update nanocaller to 3.6.0 (#47383) --- recipes/nanocaller/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanocaller/meta.yaml b/recipes/nanocaller/meta.yaml index 9b41a43016d16..46a4efde3bf6e 100644 --- a/recipes/nanocaller/meta.yaml +++ b/recipes/nanocaller/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanocaller" %} -{% set version = "3.5.0" %} +{% set version = "3.6.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/WGLab/NanoCaller/archive/refs/tags/v{{ version }}.zip - sha256: fcdcec8a64d75db376ce4671eaee353b6356547c6a7f43f6e13b058a2803337e + sha256: 63acb2fd97bef760f9fd8a06021dd1a0865e6b9d22b461d3bd58acc4028d9c31 build: number: 0 From 32b3878aaf1f360bfc11c54b46de8aac4569131f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:58:52 -0400 Subject: [PATCH 1686/1813] Update tracknado to 0.2.4 (#47376) --- recipes/tracknado/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tracknado/meta.yaml b/recipes/tracknado/meta.yaml index a54f302c9211c..9d5e8997a66e1 100644 --- a/recipes/tracknado/meta.yaml +++ b/recipes/tracknado/meta.yaml @@ -1,6 +1,6 @@ {% set name = "tracknado" %} -{% set version = "0.2.3" %} -{% set sha256 = "a7a1e25b54f41c1b5b18fbe1a2fab626e00cd4da4f747f901b58b4f78d4c2651" %} +{% set version = "0.2.4" %} +{% set sha256 = "5d03efa896c0c61e0d5072dd2e6474e308d9014a0ef387cf11d4148ac376f64b" %} package: name: {{ name|lower }} From 6f1bd205fd838db3e1d58c1c71c4f982aaa1ec4c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 20:58:59 -0400 Subject: [PATCH 1687/1813] Update sneep to 1.1 (#47375) --- recipes/sneep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sneep/meta.yaml b/recipes/sneep/meta.yaml index 3d68af7b52d46..3b772e54672ed 100644 --- a/recipes/sneep/meta.yaml +++ b/recipes/sneep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SNEEP" %} -{% set version = "1.0" %} +{% set version = "1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/SchulzLab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 6b6ebfa90db3ea4c5c75a0c2cb6ce4fd12ba62aa0d6a1d524f4269f2e58298d0 + sha256: 663a327abb928770c3252630a2ba3a0f69888f81e803567e32a2e5df09d94de9 build: skip: True # [py2k] From b198e8b4e0c8961a63a439e728cdc4ad031e1776 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 24 Apr 2024 03:59:32 +0300 Subject: [PATCH 1688/1813] nextalign: add linux-aarch64 build (#47394) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * nextalign: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Require sysroot_linux 2.18+ for Linux aarch64 The tests needs it. Signed-off-by: Martin Tzvetanov Grigorov * Export LD_LIBRARY_PATH for the tests Trying to solve: ``` nextalign run test-data/sequences.fasta --reference test-data/reference.fasta --genemap test-data/genemap.gff --output-all output/ --output-basename nextalign␛[0m 07:42:14 ␛[32mBIOCONDA INFO␛[0m (OUT) nextalign: relocation error: nextalign: symbol __cxa_thread_atexit_impl, version GLIBC_2.18 not defined in file libc.so.6 with link time reference ``` Signed-off-by: Martin Tzvetanov Grigorov * More debug. Disable the tests on Linux aarch64 Signed-off-by: Martin Tzvetanov Grigorov * Export LD_LIBRARY_PATH and PATH pointing to the installed sysroot for Linux Signed-off-by: Martin Tzvetanov Grigorov * Use glibc 2.18+ as a build dependency for Linux ARM64 Signed-off-by: Martin Tzvetanov Grigorov * Do not run tests on Linux ARM64 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/nextalign/meta.yaml | 18 ++++++++++++------ recipes/nextalign/run_test.sh | 15 ++++++++++----- 2 files changed, 22 insertions(+), 11 deletions(-) diff --git a/recipes/nextalign/meta.yaml b/recipes/nextalign/meta.yaml index f2d7a6d6dc9bf..249e23a402905 100644 --- a/recipes/nextalign/meta.yaml +++ b/recipes/nextalign/meta.yaml @@ -6,16 +6,20 @@ package: version: "{{ version }}" source: - - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 90602c64c89c6921f6713d60f726b890d8892b4c1f4f0334fbd6e4b10fd8db69 # [linux64] + - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux and x86_64] + sha256: 90602c64c89c6921f6713d60f726b890d8892b4c1f4f0334fbd6e4b10fd8db69 # [linux and x86_64] + - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-unknown-linux-gnu # [linux and aarch64] + sha256: b6fddd12cc4767c0316b13ce5f6fe8d6e26097bfb52f5c957615ffc884ce2448 # [linux and aarch64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] sha256: 0585a0c4af33ac28a2cb2dd63eb5d5c9b749bf6a1af319b999b8440da9dd35d8 # [osx and x86_64] - - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: 2d8ec8f379b150c2ac271f3c08ca79ee372b1fb14da3dc8e1b3033a1b65cfc58 # [arm64] + - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [osx and arm64] + sha256: 2d8ec8f379b150c2ac271f3c08ca79ee372b1fb14da3dc8e1b3033a1b65cfc58 # [osx and arm64] build: - number: 0 + number: 1 binary_relocation: False + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: @@ -23,7 +27,7 @@ test: files: - test-data commands: - - nextalign --help + - nextalign --help # [not aarch64] about: home: https://github.com/nextstrain/nextclade @@ -34,6 +38,8 @@ about: dev_url: https://github.com/nextstrain/nextclade extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - cjw85 - thanhleviet diff --git a/recipes/nextalign/run_test.sh b/recipes/nextalign/run_test.sh index ca4e450ff02c5..d7affe3faa46c 100644 --- a/recipes/nextalign/run_test.sh +++ b/recipes/nextalign/run_test.sh @@ -2,9 +2,14 @@ set -euxo pipefail +# the binary needs GLIBC 2.18+ on Linux ARM64 while 2.17 is available +if [ $(uname -m) != "aarch64" ]; then + nextalign run \ -test-data/sequences.fasta \ ---reference test-data/reference.fasta \ ---genemap test-data/genemap.gff \ ---output-all output/ \ ---output-basename nextalign + test-data/sequences.fasta \ + --reference test-data/reference.fasta \ + --genemap test-data/genemap.gff \ + --output-all output/ \ + --output-basename nextalign + +fi \ No newline at end of file From 9ec759a3a826e01f3395da158bbafb1ecdc2c27e Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 24 Apr 2024 03:59:40 +0300 Subject: [PATCH 1689/1813] illumina-interop: add linux-aarch64 build (#47399) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/illumina-interop/build.sh | 4 +++- recipes/illumina-interop/meta.yaml | 6 +++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/illumina-interop/build.sh b/recipes/illumina-interop/build.sh index faaf3519bce3b..37efdca568dbf 100644 --- a/recipes/illumina-interop/build.sh +++ b/recipes/illumina-interop/build.sh @@ -1,12 +1,14 @@ #!/bin/bash +set -ex + mkdir -p $PREFIX/interop/bin mkdir -p $PREFIX/bin mkdir -p build cd build cmake -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX/interop .. -make +make -j ${CPU_COUNT} make install for FPATH in $(find $PREFIX/interop/bin -maxdepth 1 -mindepth 1 -type f -or -type l); do ln -sfvn $FPATH $PREFIX/bin/interop_$(basename $FPATH) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 6417abb1d19e2..4d1c368792cfd 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -6,7 +6,7 @@ package: version: '{{version}}' build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage('illumina-interop', max_pin="x.x") }} @@ -47,3 +47,7 @@ about: faster display of a subset of the original data (collapsed quality scores). dev_url: https://github.com/Illumina/interop license_family: GPL + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 477436334afdcc6df830e76aa1bf5589ea69c51f Mon Sep 17 00:00:00 2001 From: Chris Wymant <15834752+ChrisHIV@users.noreply.github.com> Date: Tue, 23 Apr 2024 19:00:54 -0600 Subject: [PATCH 1690/1813] Update shiver: fix non-fatal absence of HXB2 sequence file (#47384) * Testing we can find a file whose absence currently gives a non-fatal error * Update 1.7.2 to 1.7.3, in which files moved * Bug fix in file location --- recipes/shiver/build.sh | 25 ++++++++++++------------- recipes/shiver/meta.yaml | 4 ++-- 2 files changed, 14 insertions(+), 15 deletions(-) diff --git a/recipes/shiver/build.sh b/recipes/shiver/build.sh index 818082c74f256..9ec97bacf120e 100644 --- a/recipes/shiver/build.sh +++ b/recipes/shiver/build.sh @@ -1,17 +1,16 @@ #!/bin/bash mkdir $PREFIX/bin -mkdir $PREFIX/bin/tools -install ${SRC_DIR}/shiver_align_contigs.sh -t $PREFIX/bin -install ${SRC_DIR}/shiver_full_auto.sh -t $PREFIX/bin -install ${SRC_DIR}/shiver_funcs.sh -t $PREFIX/bin -install ${SRC_DIR}/shiver_init.sh -t $PREFIX/bin -install ${SRC_DIR}/shiver_map_reads.sh -t $PREFIX/bin -install ${SRC_DIR}/config.sh -t $PREFIX/bin - -install ${SRC_DIR}/tools/*.py -t $PREFIX/bin/tools/ -install ${SRC_DIR}/tools/*.R -t $PREFIX/bin/tools/ -install ${SRC_DIR}/tools/*.sh -t $PREFIX/bin/tools/ - - +mkdir $PREFIX/bin/tools +mkdir $PREFIX/data +mkdir $PREFIX/data/external +install ${SRC_DIR}/bin/shiver_align_contigs.sh -t $PREFIX/bin +install ${SRC_DIR}/bin/shiver_funcs.sh -t $PREFIX/bin +install ${SRC_DIR}/bin/shiver_init.sh -t $PREFIX/bin +install ${SRC_DIR}/bin/shiver_map_reads.sh -t $PREFIX/bin +install ${SRC_DIR}/bin/config.sh -t $PREFIX/bin +install ${SRC_DIR}/bin/tools/*.py -t $PREFIX/bin/tools/ +install ${SRC_DIR}/bin/tools/*.R -t $PREFIX/bin/tools/ +install ${SRC_DIR}/bin/tools/*.sh -t $PREFIX/bin/tools/ +install ${SRC_DIR}/data/external/B.FR.83.HXB2_LAI_IIIB_BRU.K03455.fasta -t $PREFIX/data/external diff --git a/recipes/shiver/meta.yaml b/recipes/shiver/meta.yaml index 6bbf2969773c3..0838950193b3e 100644 --- a/recipes/shiver/meta.yaml +++ b/recipes/shiver/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.7.2" %} # put in correct version here +{% set version = "1.7.3" %} # put in correct version here {% set name = "shiver" %} package: @@ -6,7 +6,7 @@ package: version: {{ version }} source: url: https://github.com/ChrisHIV/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: a94c91aae1abed423ec46238b27eed718f1365084dcfdff274df1ef6da6a4969 + sha256: 4d373bf4d257e52ea1cc548c492bfe654dc677c65df1d07402f898f73c9f1c65 build: number: 0 noarch: generic From b996c327b784116cc38efa9720af093315184535 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 24 Apr 2024 04:07:13 +0300 Subject: [PATCH 1691/1813] vt: add linux-aarch64 build (#47405) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/vt/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/vt/meta.yaml b/recipes/vt/meta.yaml index b2f9584f8b7f0..d4d1cefbc1bdc 100644 --- a/recipes/vt/meta.yaml +++ b/recipes/vt/meta.yaml @@ -10,7 +10,9 @@ source: sha256: 8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17 build: - number: 9 + number: 10 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: build: @@ -38,3 +40,7 @@ about: home: https://genome.sph.umich.edu/wiki/Vt license: MIT summary: A tool set for manipulating and generating VCF files + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From cb25d8a2df9a9e0dccf524aa448d180ee1be9d51 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 24 Apr 2024 04:07:22 +0300 Subject: [PATCH 1692/1813] cmappy: add linux-aarch64 build (#47406) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/cmappy/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/cmappy/meta.yaml b/recipes/cmappy/meta.yaml index 196a2880e7b0d..69d6ac37d40e1 100644 --- a/recipes/cmappy/meta.yaml +++ b/recipes/cmappy/meta.yaml @@ -15,9 +15,11 @@ build: - gct2gctx=cmapPy.pandasGEXpress.gct2gctx:main - concat=cmapPy.pandasGEXpress.concat:main - subset=cmapPy.pandasGEXpress.subset:main - number: 5 + number: 6 skip: True # [py<30] script: {{ PYTHON }} -m pip install . --no-deps -vv + run_exports: + - {{ pin_subpackage('cmappy', max_pin='x') }} requirements: build: @@ -50,3 +52,7 @@ about: license_family: BSD summary: Assorted tools for interacting with .gct, .gctx, .grp, and .gmt files as well as other Connectivity Map (Broad Institute) data/tools + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 72d27b4a5fb2449c1df2e10ee453fe32850a7437 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 24 Apr 2024 04:07:41 +0300 Subject: [PATCH 1693/1813] bindash: add linux-aarch64 build (#47408) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bindash/build.sh | 2 +- recipes/bindash/meta.yaml | 8 +++++--- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/bindash/build.sh b/recipes/bindash/build.sh index 82b50c2465b8b..26b05df755bd5 100644 --- a/recipes/bindash/build.sh +++ b/recipes/bindash/build.sh @@ -1,7 +1,7 @@ #!/bin/bash mkdir release && pushd release cmake -DCMAKE_BUILD_TYPE=Release .. -make VERBOSE=1 +make VERBOSE=1 -j ${CPU_COUNT} install -d $PREFIX/bin install bindash $PREFIX/bin popd diff --git a/recipes/bindash/meta.yaml b/recipes/bindash/meta.yaml index 7c0643e62aca4..8e211caaf2494 100644 --- a/recipes/bindash/meta.yaml +++ b/recipes/bindash/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('bindash', max_pin="x.x") }} @@ -40,5 +40,7 @@ about: summary: Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop extra: - identifiers: - - doi:10.1371/journal.pgen.1007758 + additional-platforms: + - linux-aarch64 + identifiers: + - doi:10.1371/journal.pgen.1007758 From d27b97c48cbe8173c9dd5fc7c2953503a98b5a24 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 24 Apr 2024 04:07:48 +0300 Subject: [PATCH 1694/1813] popdel: add linux-aarch64 build (#47410) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/popdel/build.sh | 2 +- recipes/popdel/meta.yaml | 8 +++++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/popdel/build.sh b/recipes/popdel/build.sh index 883edc14d8a69..64407b7894404 100644 --- a/recipes/popdel/build.sh +++ b/recipes/popdel/build.sh @@ -1,4 +1,4 @@ #!/bin/sh -make CXX=${CXX} +make CXX=${CXX} -j ${CPU_COUNT} mkdir -p ${PREFIX}/bin cp popdel ${PREFIX}/bin diff --git a/recipes/popdel/meta.yaml b/recipes/popdel/meta.yaml index 31750f441b621..b73c3594094cf 100644 --- a/recipes/popdel/meta.yaml +++ b/recipes/popdel/meta.yaml @@ -7,7 +7,9 @@ source: sha256: c4f9dd1838379a9bcb3545da3a8d2d779f85212528a523215df9d2dc505fe515 build: - number: 6 + number: 7 + run_exports: + - {{ pin_subpackage('popdel', max_pin='x') }} requirements: build: @@ -28,3 +30,7 @@ about: license: GPL-3.0 license_file: LICENSE summary: Fast structural deletion calling on population-scale short read paired-end germline WGS data. + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From d985290a5f74f4e2d0fb35b404f06edf7976a625 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 24 Apr 2024 04:08:02 +0300 Subject: [PATCH 1695/1813] kaiju: add linux-aarch64 build (#47411) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/kaiju/build.sh | 2 +- recipes/kaiju/meta.yaml | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/kaiju/build.sh b/recipes/kaiju/build.sh index 18d6b28918644..8ce3705bf9885 100755 --- a/recipes/kaiju/build.sh +++ b/recipes/kaiju/build.sh @@ -11,7 +11,7 @@ mkdir -p $PREFIX/bin cd $SRC_DIR/src/ -make CC=${CC} CXX=${CXX} +make CC=${CC} CXX=${CXX} -j ${CPU_COUNT} cd $SRC_DIR/bin/ cp kaiju* $PREFIX/bin diff --git a/recipes/kaiju/meta.yaml b/recipes/kaiju/meta.yaml index f93353ab203e3..db305614f3c6f 100644 --- a/recipes/kaiju/meta.yaml +++ b/recipes/kaiju/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 3cc05533bf6007ffeff2d755c935354952b09a6b903c5e538dff14285b3c86e8 build: - number: 0 + number: 1 no_link: - bin/kaiju-makedb.sh run_exports: @@ -42,6 +42,8 @@ about: dev_url: https://github.com/bioinformatics-centre/kaiju extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:kaiju - doi:10.1038/ncomms11257 From 6622b84bbe765f9e181a4e66774c05d8dfcb2706 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Apr 2024 22:15:57 -0400 Subject: [PATCH 1696/1813] Update oakvar to 2.9.110 (#47421) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index ef365d3fb2a96..79b7a5cf5bee1 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.109" %} -{% set sha256 = "e314a119d1b435df9cb917b23c1be8be9be4593094e73a6bbe3ad37544733d0b" %} +{% set version = "2.9.110" %} +{% set sha256 = "32e96a2fad564a117ea9adc6bf5458a2f98baa6b89a01fded50d84ea716a89ff" %} package: name: {{ name|lower }} From ebac57a36cf25aec3ee659bbada8ca1b9baa8624 Mon Sep 17 00:00:00 2001 From: Susie Grigson <54240311+susiegriggo@users.noreply.github.com> Date: Wed, 24 Apr 2024 12:48:06 +0930 Subject: [PATCH 1697/1813] update phynteny v0.1.13 (#47403) * add phynteny v0.1.13 * Update meta.yaml add run_exports * Update meta.yaml used same hash as pypi * Update meta.yaml can't determine why url won't find package. Trying URL pasted from pypi downloads. * Update meta.yaml * Update meta.yaml remove ref to pickle5 * Update meta.yaml * Update meta.yaml * Update meta.yaml change URL from pypi to gihub so that updates happen automatically * Update meta.yaml removed v in version --- recipes/phynteny/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/phynteny/meta.yaml b/recipes/phynteny/meta.yaml index c5e06d161d10e..695e5ad48931a 100644 --- a/recipes/phynteny/meta.yaml +++ b/recipes/phynteny/meta.yaml @@ -1,13 +1,13 @@ {% set name = "Phynteny" %} -{% set version = "0.1.11" %} +{% set version = "0.1.13" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 750c7a8dc1be5032beec0524d6312b893513d62dbc4cd51a96affb598e461f16 + url: "https://github.com/susiegriggo/Phynteny/archive/refs/tags/{{ version }}.tar.gz" + sha256: b613950a00ebf60714cf053cf846c5bc84da668b2e87dd2fd83361c7856a8e04 build: number: 0 @@ -18,6 +18,8 @@ build: - compute_confidence=train_phynteny.compute_confidence:main - install_models=phynteny_utils.install_models:main script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('phynteny', max_pin='x') }} requirements: host: @@ -27,10 +29,10 @@ requirements: - biopython >=1.79 - click - joblib + - alive-progress - loguru - numpy - pandas - - pickle5 >=0.0.10 - python <3.11 - scikit-learn <=1.2.2 - tensorflow-cpu ==2.9.1 From 7a8314178317e0a69b4a66822410f368ad7df4dd Mon Sep 17 00:00:00 2001 From: Akihiro Kuno Date: Wed, 24 Apr 2024 13:08:38 +0900 Subject: [PATCH 1698/1813] Update DAJIN2 (#47425) Co-authored-by: Akihiro Kuno --- recipes/dajin2/meta.yaml | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index 23fad00eb9725..263b0d54587fd 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,13 +1,13 @@ {% set name = "DAJIN2" %} -{% set version = "0.4.3" %} +{% set version = "0.4.5" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: 1a5334a6639f8958e2a8b0254e73066991ff849f00a1194d236a324b3507fbb3 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dajin2-{{ version }}.zip + sha256: f20fa8d86a17aa3b13c74da959fae02ff57acd5bf7bdd1a852a3cebb6ee1efb3 build: entry_points: @@ -24,23 +24,22 @@ requirements: - pip run: - python - - numpy >=1.20.0 - - scipy >=1.6.0 + - numpy >=1.24.0 + - scipy >=1.10.0 - pandas >=1.0.0 - - openpyxl >=3.0.0 - - rapidfuzz >=3.0.0 - - statsmodels >=0.13.5 - - scikit-learn >=1.0.0 + - openpyxl >=3.1.0 + - rapidfuzz >=3.6.0 + - scikit-learn >=1.3.0 - mappy >=2.24 - - pysam >=0.19.0 + - pysam >=0.21.0 - flask >=2.2.0 - waitress >=2.1.0 - jinja2 >=3.1.0 - - plotly >=5.0.0 + - plotly >=5.19.0 - python-kaleido >=0.2.0 - cstag >=1.0.0 - - midsv >=0.10.1 - - wslpath >=0.3.0 + - midsv >=0.11.0 + - wslpath >=0.4.1 test: imports: From c84a20c81ace0867995870cd18924caed0a9805f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 00:55:57 -0400 Subject: [PATCH 1699/1813] Update gtdbtk to 2.4.0 (#47423) * Update gtdbtk to 2.4.0 * update gtdbtk --------- Co-authored-by: Aaron Mussig --- recipes/gtdbtk/download-db.sh | 6 +++--- recipes/gtdbtk/meta.yaml | 7 +++++-- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/gtdbtk/download-db.sh b/recipes/gtdbtk/download-db.sh index c3c77b25d433c..236e3f44671c1 100755 --- a/recipes/gtdbtk/download-db.sh +++ b/recipes/gtdbtk/download-db.sh @@ -1,9 +1,9 @@ set -e # Configuration -N_FILES_IN_TAR=181718 -DB_URL="https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/gtdbtk_r214_data.tar.gz" -TARGET_TAR_NAME="gtdbtk_r214_data.tar.gz" +N_FILES_IN_TAR=241860 +DB_URL="https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz" +TARGET_TAR_NAME="gtdbtk_r220_data.tar.gz" # Script variables (no need to configure) TARGET_DIR=${1:-$GTDBTK_DATA_PATH} diff --git a/recipes/gtdbtk/meta.yaml b/recipes/gtdbtk/meta.yaml index 611e22a30947f..8818a51c4193e 100644 --- a/recipes/gtdbtk/meta.yaml +++ b/recipes/gtdbtk/meta.yaml @@ -1,16 +1,18 @@ {% set name = "gtdbtk" %} -{% set version = "2.3.2" %} +{% set version = "2.4.0" %} package: name: {{ name|lower }} version: {{ version }} source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 80efd31e10007d835f56a3d6fdf039a59db3b6ba4be26b234692da5e688aa99f + sha256: e67bab2c8f3e47c7242c70236c78e85bb9dc4721636bbf5044b171f18f22b1f7 build: number: 0 noarch: python entry_points: - gtdbtk = gtdbtk.__main__:main + run_exports: + - {{ pin_subpackage('gtdbtk', max_pin="x") }} requirements: host: - pip @@ -27,6 +29,7 @@ requirements: - mash >=2.0 - tqdm >=4.35.0 - pydantic >=1.9.2, <2 + - skani >=0.2.0 test: imports: - gtdbtk From 70f9debd5e79de82a0da1d472c73a2926f365e89 Mon Sep 17 00:00:00 2001 From: Pierre Chaumeil Date: Wed, 24 Apr 2024 16:08:20 +1000 Subject: [PATCH 1700/1813] Update post-link.sh (#47427) * Update post-link.sh * Update meta.yaml --- recipes/gtdbtk/meta.yaml | 2 +- recipes/gtdbtk/post-link.sh | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/gtdbtk/meta.yaml b/recipes/gtdbtk/meta.yaml index 8818a51c4193e..3023022470731 100644 --- a/recipes/gtdbtk/meta.yaml +++ b/recipes/gtdbtk/meta.yaml @@ -7,7 +7,7 @@ source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz sha256: e67bab2c8f3e47c7242c70236c78e85bb9dc4721636bbf5044b171f18f22b1f7 build: - number: 0 + number: 1 noarch: python entry_points: - gtdbtk = gtdbtk.__main__:main diff --git a/recipes/gtdbtk/post-link.sh b/recipes/gtdbtk/post-link.sh index 4ac76d7c003f8..ee340a4676c67 100644 --- a/recipes/gtdbtk/post-link.sh +++ b/recipes/gtdbtk/post-link.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash echo " - GTDB-Tk v${PKG_VERSION} requires ~78G of external data which needs to be downloaded + GTDB-Tk v${PKG_VERSION} requires ~110G of external data which needs to be downloaded and extracted. This can be done automatically, or manually. Automatic: @@ -12,11 +12,11 @@ echo " Manual: 1. Manually download the latest reference data: - wget https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/gtdbtk_r214_data.tar.gz + wget https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz 2. Extract the archive to a target directory: - tar -xvzf gtdbtk_r214_data.tar.gz -C \"/path/to/target/db\" --strip 1 > /dev/null - rm gtdbtk_r214_data.tar.gz + tar -xvzf gtdbtk_r220_data.tar.gz -C \"/path/to/target/db\" --strip 1 > /dev/null + rm gtdbtk_r220_data.tar.gz 3. Set the GTDBTK_DATA_PATH environment variable by running: conda env config vars set GTDBTK_DATA_PATH=\"/path/to/target/db\" From f9fb2e60c84e5769a505b14c7812c54a5f60a37f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 03:16:02 -0400 Subject: [PATCH 1701/1813] Update pysam to 0.22.1 (#47426) --- recipes/pysam/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pysam/meta.yaml b/recipes/pysam/meta.yaml index ae7239552b75a..ac9c338d92f61 100644 --- a/recipes/pysam/meta.yaml +++ b/recipes/pysam/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.22.0" %} +{% set version = "0.22.1" %} package: name: pysam @@ -6,12 +6,12 @@ package: source: url: https://github.com/pysam-developers/pysam/archive/v{{ version }}.tar.gz - sha256: 61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f + sha256: e4981524d7627c53fa0d3f8cbec2bd65c2ea7520092f25e1029af12cb7b82ff6 patches: - arm_hwcap.patch build: - number: 1 + number: 0 skip: True # [py2k] binary_relocation: False # [linux] run_exports: From 9739462d5767204e55132c3587f7b9771ecfd8d9 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 24 Apr 2024 12:32:03 +0200 Subject: [PATCH 1702/1813] bump wisecondorx (#47429) --- recipes/wisecondorx/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wisecondorx/meta.yaml b/recipes/wisecondorx/meta.yaml index 8e371c1a090ad..c32c17e5562fa 100644 --- a/recipes/wisecondorx/meta.yaml +++ b/recipes/wisecondorx/meta.yaml @@ -1,11 +1,11 @@ -{% set version="1.2.6" %} +{% set version="1.2.7" %} package: name: wisecondorx version: {{ version }} source: url: https://github.com/CenterForMedicalGeneticsGhent/wisecondorX/archive/v{{ version }}.tar.gz - sha256: 66c2373b05bd0e1a90ca781611642db0503b6d42d0eef4a2077bad7a81238405 + sha256: 4597377e664afd5b4d78f92061d854186bbaba92ba9951f034e9e7ce4c2d1c29 build: number: 0 From 7d2ba07107e36014f4ab2e9d68475a109a995078 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Wed, 24 Apr 2024 14:35:59 +0200 Subject: [PATCH 1703/1813] [haddock_biobb] update: Add post-link.sh install instructions (#47431) --- recipes/haddock_biobb/meta.yaml | 17 +---------------- recipes/haddock_biobb/post-link.sh | 3 ++- 2 files changed, 3 insertions(+), 17 deletions(-) diff --git a/recipes/haddock_biobb/meta.yaml b/recipes/haddock_biobb/meta.yaml index 90f5ca5d923fd..e5511fb188a2c 100644 --- a/recipes/haddock_biobb/meta.yaml +++ b/recipes/haddock_biobb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "haddock_biobb" %} -{% set version = "3.0.2" %} +{% set version = "3.0.3" %} package: name: '{{ name|lower }}' @@ -37,7 +37,6 @@ requirements: - boost-cpp - cxx-compiler - c-compiler - # Pip dependencies - biopython - jsonpickle - numpy @@ -50,20 +49,6 @@ requirements: - kaleido-core - freesasa - pdb-tools - #- pdb-tools==2.5.0 - #- biopython==1.79 - #- jsonpickle==2.1.0 - #- numpy==1.22.2 - #- pyyaml==6.0 - #- scipy==1.10.0 - #- toml==0.10.2 - #- tox==3.24.5 - #- pandas==1.5.1 - #- plotly==5.11.0 - #- kaleido==0.2.1 - #- freesasa==2.2.1 - - test: commands: diff --git a/recipes/haddock_biobb/post-link.sh b/recipes/haddock_biobb/post-link.sh index e7047a4b3e016..b634ad9fd28ed 100644 --- a/recipes/haddock_biobb/post-link.sh +++ b/recipes/haddock_biobb/post-link.sh @@ -1 +1,2 @@ -echo "Create a softlink [ln -s] of the CNS executable to the ${SRC_DIR}/bin folder" > "${PREFIX}"/.messages.txt +echo "Before using HADDOCK please install CNS. Instructions: https://github.com/haddocking/haddock3/blob/main/docs/CNS.md" +echo "And create a softlink [ln -s] of the CNS executable to the ${PREFIX}lib/pythonX.XX/bin/ folder (Replace the X by your env python version)" > "${PREFIX}"/.messages.txt From 627e2cd30be07f2a4d6a7b675ba570d45a17ec03 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 10:25:04 -0400 Subject: [PATCH 1704/1813] Update cooltools to 0.7.0 (#47386) * Update cooltools to 0.7.0 * edit dependencies --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cooltools/meta.yaml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/recipes/cooltools/meta.yaml b/recipes/cooltools/meta.yaml index 13642309de7a2..b85e63fb65783 100644 --- a/recipes/cooltools/meta.yaml +++ b/recipes/cooltools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cooltools" %} -{% set version = "0.6.1" %} +{% set version = "0.7.0" %} package: name: "{{ name|lower }}" @@ -7,14 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1082186215c1215b1f1192b1c5dd2d103e0db6df3dca3a9e49ec15676f5c0adb + sha256: 8b26d4857cc76b2dd3d1097b85f828cf6d5f1cf85b0cfd4b67a310e33e7ece1c build: number: 0 - skip: True # [py <= 37] + skip: True # [py < 37] entry_points: - cooltools = cooltools.cli:cli - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" run_exports: - {{ pin_subpackage('cooltools', max_pin="x.x") }} @@ -25,16 +25,17 @@ requirements: - cython - pip - python - - numpy <1.24 + - numpy run: - bioframe >=0.4.1 - click >=7 - cooler >=0.9.1 - joblib - matplotlib-base + - multiprocess - numba - - numpy <1.24 # remove constraint once https://github.com/numba/numba/issues/8615 has been resolved - - pandas >=1.5.1,<2 #Temporary upper ceiling + - {{ pin_compatible('numpy') }} + - pandas >=1.5.1 - python - scikit-learn >=1.1.2 - scipy From c08ae6917d965cef540f216780930e0286343e7f Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Wed, 24 Apr 2024 19:09:48 +0200 Subject: [PATCH 1705/1813] Updating Sentieon to 202308.02 (#47433) * Updating sentieon to 202308.02 * Trying to fix sentieon_symlinks.patch --- recipes/sentieon/meta.yaml | 4 ++-- recipes/sentieon/sentieon_symlinks.patch | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/sentieon/meta.yaml b/recipes/sentieon/meta.yaml index 2660842aebff9..cb9b80ca081b4 100644 --- a/recipes/sentieon/meta.yaml +++ b/recipes/sentieon/meta.yaml @@ -1,11 +1,11 @@ -{% set version="202308.01" %} +{% set version="202308.02" %} package: name: sentieon version: {{ version }} source: - url: https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-{{ version }}.tar.gz # [linux64] - sha256: 047899a2b4247adaace82032a6fe269a57f70b1c9ecbc84d77914f902a714d50 # [linux64] + sha256: a04b98c1b7c4e8916fdc45f15685d5fd83db56386ec2478eb5ea594170405bd5 # [linux64] patches: # [linux64] # Fix driver scripts so they resolves location including symlinks - sentieon_symlinks.patch # [linux64] diff --git a/recipes/sentieon/sentieon_symlinks.patch b/recipes/sentieon/sentieon_symlinks.patch index 41c95cc0c9b16..7278200c99ff8 100644 --- a/recipes/sentieon/sentieon_symlinks.patch +++ b/recipes/sentieon/sentieon_symlinks.patch @@ -4,7 +4,7 @@ index 52f51aaefd..e27fea8c2b 100755 +++ b/bin/sentieon @@ -1,13 +1,17 @@ #!/bin/sh - # Copyright (c) 2014-2023 Sentieon Inc. All rights reserved + # Copyright (c) 2014-2024 Sentieon Inc. All rights reserved -case "$0" in -/*) bin_dir=$(dirname "$0");; -*) bin_dir=$(dirname "$(pwd)/$0");; From 192500d4e159abc34e094ed7da6114527941e4d6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 19:43:47 -0400 Subject: [PATCH 1706/1813] Update pronto to 2.5.7 (#47442) --- recipes/pronto/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pronto/meta.yaml b/recipes/pronto/meta.yaml index 4651abcbc0bd9..d6d9f73830252 100644 --- a/recipes/pronto/meta.yaml +++ b/recipes/pronto/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pronto" %} -{% set version = "2.5.6" %} +{% set version = "2.5.7" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: eacdaa9b629042d1a07c59470241576c111751229ac052a05bfce8180df33bf8 + sha256: 014a5b02064781d6edd7ca5b4f63b13342dd9b5322248f5a4740f48a98464629 build: noarch: python From 383a0be2750897811f0ee3cbb724bb3d5bb4f388 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 19:54:55 -0400 Subject: [PATCH 1707/1813] Update peaks2utr to 1.2.6 (#47440) --- recipes/peaks2utr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/peaks2utr/meta.yaml b/recipes/peaks2utr/meta.yaml index 03cb588cdd03b..3d0de3bfbe81d 100644 --- a/recipes/peaks2utr/meta.yaml +++ b/recipes/peaks2utr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "peaks2utr" %} -{% set version = "1.2.5" %} +{% set version = "1.2.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/peaks2utr-{{ version }}.tar.gz - sha256: d24ed841692059e237800cceca00adb4f17638c6751b214d4146ca0fe26cf97e + sha256: ba17dd81b942e6b846804b03154358e331c489d7bc12573711c551faece11fed build: number: 0 From 307e46bf56eb180519ab12da852108f8bd8f0336 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 19:56:00 -0400 Subject: [PATCH 1708/1813] Update snakedeploy to 0.10.0 (#47439) --- recipes/snakedeploy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakedeploy/meta.yaml b/recipes/snakedeploy/meta.yaml index 4a3d9f0e594f6..ee301e9d00857 100644 --- a/recipes/snakedeploy/meta.yaml +++ b/recipes/snakedeploy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9.1" %} +{% set version = "0.10.0" %} package: name: snakedeploy @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakedeploy/snakedeploy-{{ version }}.tar.gz - sha256: 3ce399ae67f991647f62ff67a73649cbf786842d888c17a93b1f98b34bfb98e5 + sha256: 85922677897e90e3d179e74ba41f28e174084ed184d4e2712a4c0be3890c6279 build: number: 0 From ab62d6f1c5f76c87519978bcb912f3a036486f4a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 19:56:21 -0400 Subject: [PATCH 1709/1813] Update primers to 0.5.10 (#47430) --- recipes/primers/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primers/meta.yaml b/recipes/primers/meta.yaml index da109904de0c9..1eec7202a9635 100644 --- a/recipes/primers/meta.yaml +++ b/recipes/primers/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primers" %} -{% set version = "0.5.4" %} +{% set version = "0.5.10" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 6ad13316985a59bba3763a803dbddfbf67a2336a7a51cdaef86d61eabaf434ba + sha256: 3ff2cd4c27a47326faeb8e54f36649752e6905109fdd3b22b90c2c167233f060 patches: - 0001-directly-write-requirements-in-setup.py.patch From f4fbba74ab123e2189ec540daf0a254c7d6cad8f Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 25 Apr 2024 03:05:51 +0300 Subject: [PATCH 1710/1813] groot: add linux-aarch64 build (#47412) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * groot: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Remove groot from the blacklist Signed-off-by: Martin Tzvetanov Grigorov * Try with Go 1.20.x. The tests pass fine with 1.20.2 on my dev machine Signed-off-by: Martin Tzvetanov Grigorov * Do not run the tests on Linux ARM64 Signed-off-by: Martin Tzvetanov Grigorov * Try with older version of Go - 1.16 Signed-off-by: Martin Tzvetanov Grigorov * Disable the tests due to a problem with an old test dependnecy ``` gopath/pkg/mod/github.com/dgryski/go-minhash@v0.0.0-20190315135803-ad340ca03076/minwise_test.go:6:2: no required module provides package github.com/dgryski/go-metro; to add it:␛[0m ``` Signed-off-by: Martin Tzvetanov Grigorov * Try with GO111MODULE=on for the tests Signed-off-by: Martin Tzvetanov Grigorov * Try with GO111MODULE=off Signed-off-by: Martin Tzvetanov Grigorov * Explicitly get go-metro before running the tests Signed-off-by: Martin Tzvetanov Grigorov * Explicitly go get go-minhash Signed-off-by: Martin Tzvetanov Grigorov * Explicitly go get github.com/dgryski/go-spooky Signed-off-by: Martin Tzvetanov Grigorov * Try without getting go-minhash Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- build-fail-blacklist | 1 - recipes/groot/build.sh | 7 ++++++- recipes/groot/meta.yaml | 6 +++++- 3 files changed, 11 insertions(+), 3 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index b9f2582e70255..e8e163736a075 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -763,7 +763,6 @@ recipes/cesm recipes/minnow recipes/quip recipes/conterminator -recipes/groot recipes/mantis recipes/apoc recipes/quorum diff --git a/recipes/groot/build.sh b/recipes/groot/build.sh index e318969a521b2..1bd6e5d9aaee4 100644 --- a/recipes/groot/build.sh +++ b/recipes/groot/build.sh @@ -1,7 +1,12 @@ -#!/bin/bash +#!/usr/bin/env bash + +set -xe + mkdir -p $PREFIX/bin go get -d -v ./... +go get github.com/dgryski/go-metro +go get github.com/dgryski/go-spooky go test -v ./... go build -o groot diff --git a/recipes/groot/meta.yaml b/recipes/groot/meta.yaml index 20d9c2ec28ccd..b824757d8e733 100644 --- a/recipes/groot/meta.yaml +++ b/recipes/groot/meta.yaml @@ -9,7 +9,9 @@ source: sha256: 46c6f67990397c2230f580be40697e4fdc284fbe7f0a38999a05d81cd6da5928 build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage('groot', max_pin='x') }} requirements: build: @@ -27,5 +29,7 @@ about: summary: A tool for resistome profiling of metagenomic samples. extra: + additional-platforms: + - linux-aarch64 skip-lints: - should_be_noarch_generic From 9d16febab4d8655958f330499a7d892ae8185655 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 25 Apr 2024 03:07:32 +0300 Subject: [PATCH 1711/1813] epic2: add linux-aarch64 build (#47401) * epic2: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Add run dependency to zlib Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/epic2/meta.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/epic2/meta.yaml b/recipes/epic2/meta.yaml index bf674d7045e4c..278c65055a381 100644 --- a/recipes/epic2/meta.yaml +++ b/recipes/epic2/meta.yaml @@ -11,9 +11,11 @@ source: sha256: '{{ hash_value }}' build: - number: 6 + number: 7 # Compilation errors on OSX skip: True # [osx or py27] + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: build: @@ -25,6 +27,7 @@ requirements: - setuptools - pysam - htslib + - zlib run: - python - scipy @@ -47,6 +50,8 @@ about: summary: 'Ultraperformant Chip-Seq broad domain finder based on SICER.' extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1093/bioinformatics/btz232 recipe-maintainers: From 1e3694cf1eb95e056c3574582c9ad304c367d672 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 25 Apr 2024 03:07:56 +0300 Subject: [PATCH 1712/1813] lofreq: add linux-aarch64 build (#47436) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/lofreq/build.sh | 2 +- recipes/lofreq/meta.yaml | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/lofreq/build.sh b/recipes/lofreq/build.sh index 14aa9cefba636..d349a75b80adb 100644 --- a/recipes/lofreq/build.sh +++ b/recipes/lofreq/build.sh @@ -2,5 +2,5 @@ set -eu -o pipefail ./configure --with-htslib=system --prefix=${PREFIX} -make +make -j ${CPU_COUNT} make install diff --git a/recipes/lofreq/meta.yaml b/recipes/lofreq/meta.yaml index 8599a1283fd08..0f18251ee95d3 100644 --- a/recipes/lofreq/meta.yaml +++ b/recipes/lofreq/meta.yaml @@ -9,7 +9,9 @@ source: sha256: 43028af07faa23c7ec0e167855492ae7bd31c4e7f8158114e51ec12aba5fd184 build: - number: 10 + number: 11 + run_exports: + - {{ pin_subpackage('lofreq', max_pin='x') }} requirements: build: @@ -34,5 +36,7 @@ about: summary: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data extra: + additional-platforms: + - linux-aarch64 identifiers: - usegalaxy-eu:lofreq_call From da43d91d20b5774a2671a9cc90c6813d877991d5 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 25 Apr 2024 03:10:05 +0300 Subject: [PATCH 1713/1813] megalodon: add linux-aarch64 build (#47432) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/megalodon/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/megalodon/meta.yaml b/recipes/megalodon/meta.yaml index 9056a14a6a404..c619becf36135 100644 --- a/recipes/megalodon/meta.yaml +++ b/recipes/megalodon/meta.yaml @@ -16,7 +16,7 @@ build: - megalodon = megalodon.__main__:_main - megalodon_extras = megalodon_extras.__main__:_main script: {{ PYTHON }} -m pip install . --no-deps -vv - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -60,6 +60,8 @@ about: dev_url: https://github.com/nanoporetech/megalodon extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - marcus1487 - npavlovikj From 4e7ce2bb24e3e04e61b6fbb274bba7cb00e33cde Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 20:27:06 -0400 Subject: [PATCH 1714/1813] Update metacoag to 1.2.0 (#47428) * Update metacoag to 1.2.0 * add run_exports --------- Co-authored-by: mencian --- recipes/metacoag/meta.yaml | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/recipes/metacoag/meta.yaml b/recipes/metacoag/meta.yaml index 1f17d44b66cce..495e6305e02c9 100644 --- a/recipes/metacoag/meta.yaml +++ b/recipes/metacoag/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MetaCoAG" %} -{% set version = "1.1.4" %} +{% set version = "1.2.0" %} package: name: "{{ name|lower }}" @@ -7,22 +7,26 @@ package: source: url: "https://github.com/metagentools/{{ name }}/archive/v{{ version }}.tar.gz" - sha256: de300e1abfe38b2595e5d7253da26dc29fcd1fd9f7d17ab958d1f75d7582a6ef + sha256: 994917716c50beb748730bada2d9e76901635fa52e4b64e1f2e5b73c88059587 build: number: 0 noarch: python entry_points: - - combine_cov=metacoag_utils.support.combine_cov:main + - metacoag = metacoag.cli:main + - combine_cov = metacoag.metacoag_utils.support.combine_cov:main script: - - "{{ PYTHON }} -m pip install . -vv" + - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('metacoag', max_pin="x") }} requirements: host: - pip - - python + - python >=3.9,<3.13 + - flit-core >=3.2 run: - - python + - python >=3.9,<3.13 - click - biopython - cairocffi @@ -42,8 +46,8 @@ test: about: home: "https://github.com/metagentools/MetaCoAG" - license: GPL-3.0 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: "MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs" description: | From a9b8d96377b4f0069a4189667d77c9c2a9b087e0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 20:34:32 -0400 Subject: [PATCH 1715/1813] Update open-cravat to 2.6.0 (#47441) * Update open-cravat to 2.6.0 * edit dependencies --------- Co-authored-by: mencian --- recipes/open-cravat/meta.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/open-cravat/meta.yaml b/recipes/open-cravat/meta.yaml index b02c7491e9f12..334f0068efb07 100644 --- a/recipes/open-cravat/meta.yaml +++ b/recipes/open-cravat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "open-cravat" %} -{% set version = "2.5.0" %} +{% set version = "2.6.0" %} package: name: "{{ name|lower }}" @@ -7,24 +7,25 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 683ac5248f4bb6694cff8958f3da1289efc51637ede26412ef353e0b15aa42ec + sha256: c0dee114a1805bc366a2242af8594dd5f2840b77243db9fb36a5ff5a7546ecfa build: number: 0 entry_points: - oc=cravat.oc:main noarch: python - script: {{PYTHON}} -m pip install . -vvv --no-build-isolation --no-deps + script: {{PYTHON}} -m pip install . -vvv --no-build-isolation --no-deps --no-cache-dir run_exports: - {{ pin_subpackage('open-cravat', max_pin="x") }} requirements: host: - pip - - python >=3.8,<3.12 + - python >=3.8 run: - - aiohttp + - aiohttp <4.0.0 - aiosqlite + - biopython - chardet >=3.0.4 - intervaltree - markdown @@ -34,7 +35,7 @@ requirements: - oyaml - psutil - pyliftover - - python >=3.8,<3.12 + - python >=3.8 - pyyaml - requests - requests-toolbelt From b8bba09bd808545e85f8ab2e7fbab1f38546d81b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 22:57:22 -0400 Subject: [PATCH 1716/1813] Update pango-designation to 1.27 (#47452) --- recipes/pango-designation/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pango-designation/meta.yaml b/recipes/pango-designation/meta.yaml index f19439657e130..5be34f04fd20a 100644 --- a/recipes/pango-designation/meta.yaml +++ b/recipes/pango-designation/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.26" %} +{% set version = "1.27" %} package: name: pango-designation @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pango-designation/archive/refs/tags/v{{ version }}.tar.gz - sha256: 15e2b6c22f4022385b67acf58638d89b9aa39e5c17f0f6f44beefc2f4bec10ff + sha256: da3e697eabb73fc835490b737a8c88558a8b92fc81601f9363baef50c70b350e build: number: 0 From 47945fcb43c7f6a7fbce7facf3aa644aa41f2ef2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 23:38:38 -0400 Subject: [PATCH 1717/1813] Update hicexplorer to 3.7.4 (#47449) * Update hicexplorer to 3.7.4 * edit dependencies --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/hicexplorer/meta.yaml | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/recipes/hicexplorer/meta.yaml b/recipes/hicexplorer/meta.yaml index 913f95bb1835f..02e1d69a4de4a 100644 --- a/recipes/hicexplorer/meta.yaml +++ b/recipes/hicexplorer/meta.yaml @@ -1,19 +1,20 @@ -{% set version = "3.7.3" %} +{% set name = "hicexplorer" %} +{% set version = "3.7.4" %} package: - name: hicexplorer - version: '{{ version }}' + name: {{ name }} + version: {{ version }} source: url: https://github.com/deeptools/HiCExplorer/archive/{{ version }}.tar.gz - sha256: db80bb90772795e603136b781f7dc81659509977e1e86dea7b298490cab73444 + sha256: 4c19c0bbb74417a87096ec0c9238bb7e59874020c6c82fadf114efb96d3be0d8 build: - number: 1 - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" noarch: python run_exports: - - {{ pin_subpackage('hicexplorer', max_pin="x.x") }} + - {{ pin_subpackage('hicexplorer', max_pin="x") }} requirements: host: @@ -36,7 +37,6 @@ requirements: - future - unidecode - hicmatrix >=17 - - cooler >=0.9.3 - pygenometracks >=3.8 - hic2cool >=0.8.3 - fit_nbinom >=1.2 @@ -46,7 +46,7 @@ requirements: - tqdm >=4.66 - hyperopt >=0.2.7 - python-graphviz >=0.20 - - scikit-learn <=1.3 + - scikit-learn >=1.3,<1.4 - imbalanced-learn >=0.11 - cleanlab >=2.5 @@ -98,9 +98,13 @@ test: about: - home: https://github.com/deeptools/HiCExplorer - license: GPL3 + home: "https://github.com/deeptools/HiCExplorer" + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE summary: Set of programs to process, analyze and visualize Hi-C and capture Hi-C data + dev_url: "https://github.com/deeptools/HiCExplorer" + doc_url: "https://hicexplorer.readthedocs.org/" extra: identifiers: @@ -108,3 +112,4 @@ extra: - doi:10.1093/nar/gkaa220 - doi:10.1093/gigascience/giac061 - usegalaxy-eu:hicexplorer_hicplotviewpoint + - biotools:hicexplorer From c54639a3fd5009ddf2323133d6e61c3c2bf11c71 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 23:38:49 -0400 Subject: [PATCH 1718/1813] Update wgd to 2.0.33 (#47445) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index 759a972943853..5b062a4fafe5c 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.32" %} +{% set version = "2.0.33" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: 5c599eb509cab810aaa11815464e8522edc3583e8a429f28695656213c7db0ca + sha256: d5158f42f536412bdb034dca99d79377a53c45f6450aca0e294bbed7a6a99b07 build: number: 0 From 374f3578e2a53ceb433923f1c93a00d9ca4d7011 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 24 Apr 2024 22:45:31 -0500 Subject: [PATCH 1719/1813] Update nextdenovo recipe (#47424) * Update nextdenovo recipe * edit build.sh * edit build.sh --- recipes/nextdenovo/build.sh | 12 +++++----- recipes/nextdenovo/meta.yaml | 45 ++++++++++++++++++++---------------- 2 files changed, 31 insertions(+), 26 deletions(-) diff --git a/recipes/nextdenovo/build.sh b/recipes/nextdenovo/build.sh index adf1e0d4cba9b..2bbd1256310bb 100644 --- a/recipes/nextdenovo/build.sh +++ b/recipes/nextdenovo/build.sh @@ -1,10 +1,10 @@ #!/bin/bash -set -x +set -ex + +OUTDIR="${SP_DIR}/nextdenovo" -PYVER=`python -c 'import sys; print(str(sys.version_info[0])+"."+str(sys.version_info[1]))'` -OUTDIR=${PREFIX}/lib/python${PYVER}/site-packages/nextdenovo mkdir -p ${PREFIX}/bin ${OUTDIR} -cp -r ./* ${OUTDIR} -chmod a+x ${OUTDIR}/nextDenovo -ln -s ${OUTDIR}/nextDenovo ${PREFIX}/bin/nextDenovo +cp -rf ${SRC_DIR}/* ${OUTDIR} +chmod 755 ${OUTDIR}/nextDenovo +ln -sf ${OUTDIR}/nextDenovo ${PREFIX}/bin/nextDenovo diff --git a/recipes/nextdenovo/meta.yaml b/recipes/nextdenovo/meta.yaml index 41813d4ac069a..6ce4c5e6440d4 100644 --- a/recipes/nextdenovo/meta.yaml +++ b/recipes/nextdenovo/meta.yaml @@ -1,8 +1,9 @@ +{% set name = "nextdenovo" %} {% set version = "2.5.2" %} {% set sha256 = "5c7ca4aa3de234f4e0efd8aaf9eaf60ebd79b5e545ad2878a76162b29d815fe0" %} package: - name: nextdenovo + name: {{ name }} version: {{ version }} source: @@ -11,25 +12,22 @@ source: sha256: {{ sha256 }} build: - number: 3 - # repackages binaries - skip: True # [osx or py < 36] + number: 4 + binary_has_prefix_files: + - nextDenovo + run_exports: + - {{ pin_subpackage('nextdenovo', max_pin="x") }} requirements: + build: + - {{ compiler('c') }} + - make host: - python + - pip + - paralleltask - bzip2 - - ca-certificates - zlib - - ncurses - - openssl - - pip - - readline - - setuptools - - tk - - tzdata - - wheel - - xz run: - python - paralleltask @@ -39,13 +37,20 @@ test: - test_data commands: - 'nextDenovo --help' - #- 'nextDenovo test_data/run.cfg' # Partly success: some jobs are submitted, but others are killed before completion + #- 'nextDenovo test_data/run.cfg + # Partly success: some jobs are submitted, but others are killed before completion about: - home: https://github.com/Nextomics/NextDenovo - license: GNU General Public License v3.0 - summary: String graph-based de novo assembler for long reads (CLR, HiFi and ONT) + home: "https://github.com/Nextomics/NextDenovo" + license: "GPL-3.0-or-later" + license_family: GPL3 + license_file: LICENSE + summary: "String graph-based de novo assembler for long reads (CLR, HiFi and ONT)" + dev_url: "https://github.com/Nextomics/NextDenovo" + doc_url: "https://nextdenovo.readthedocs.io/en/latest" extra: - skip-lints: - - should_be_noarch_generic + identifiers: + - doi:10.1101/2023.03.09.531669 + - biotools:nextdenovo + - usegalaxy-eu:nextdenovo From 16b13f389dbcd4b380a8434ce44b3860613b2216 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Apr 2024 23:46:04 -0400 Subject: [PATCH 1720/1813] Update hapcut2 to 1.3.4 (#47448) * Update hapcut2 to 1.3.4 * add run_exports --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/hapcut2/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/hapcut2/meta.yaml b/recipes/hapcut2/meta.yaml index 471c87eb7587e..e27214ae0c444 100644 --- a/recipes/hapcut2/meta.yaml +++ b/recipes/hapcut2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "HapCUT2" %} -{% set version = "1.3.3" %} +{% set version = "1.3.4" %} package: name: {{ name|lower }} @@ -7,10 +7,12 @@ package: source: - url: https://github.com/vibansal/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 95b832e667638aff1de51721e54c906dfe8b46793b1ca8ecf1b6790d4f84aade + sha256: 33d0a047c4d9b7ef4287be979cc580183acbd09a3ab518b9f5ebc5f41c2bf34e build: - number: 5 + number: 0 + run_exports: + - {{ pin_subpackage('hapcut2', max_pin="x") }} requirements: build: @@ -37,4 +39,6 @@ about: summary: Tools for haplotype assembly from sequence data home: https://github.com/vibansal/HapCUT2/ license: BSD-2-Clause + license_family: BSD license_file: LICENSE + dev_url: https://github.com/vibansal/HapCUT2/ From 9697790f890fc89fd372f5a1aeddbef7ffe18f75 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 24 Apr 2024 22:49:16 -0500 Subject: [PATCH 1721/1813] Update nextpolish recipe (#47450) * Update nextpolish recipe * edit build.sh --- recipes/nextpolish/build.sh | 20 ++++++++++++-------- recipes/nextpolish/meta.yaml | 30 +++++++++++++++++------------- 2 files changed, 29 insertions(+), 21 deletions(-) diff --git a/recipes/nextpolish/build.sh b/recipes/nextpolish/build.sh index a4aee7c2a3417..2950cd00b8fda 100644 --- a/recipes/nextpolish/build.sh +++ b/recipes/nextpolish/build.sh @@ -1,31 +1,35 @@ #!/usr/bin/env bash +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + # Skip copying of bwa, minimap2, and samtools -sed -i.backup \ +sed -i.bak \ -e "s| bwa samtools minimap2||g" \ Makefile # Use conda's gcc and includes, also skip build of bwa, minimap2, and samtools -sed -i.backup \ +sed -i.bak \ -e "s| bwa_ samtools_ minimap2_||g" \ -e "s|gcc|$CC|g" \ -e "s|-lz|-lz -isystem ${PREFIX}/include|g" \ util/Makefile # Add version info (original required internet connection) -sed -i.backup "s=BIOCONDA_SED_REPLACE=$PKG_VERSION=" lib/kit.py +sed -i.bak "s=BIOCONDA_SED_REPLACE=$PKG_VERSION=" lib/kit.py # Create share directory SHARE_DIR="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}" mkdir -p ${SHARE_DIR}/ -cp -r ./lib ${SHARE_DIR}/ +cp -rf ./lib ${SHARE_DIR}/ # Build -make +make CC="${CC}" CFLAGS="-O3" LDFLAGS="${LDFLAGS}" -j "${CPU_COUNT}" mkdir -p ${PREFIX}/bin -cp bin/* ${PREFIX}/bin +cp -f bin/* ${PREFIX}/bin # fix hardcoded path -sed -i.backup "s=BIOCONDA_SED_REPLACE=$SHARE_DIR=" nextPolish +sed -i.bak "s=BIOCONDA_SED_REPLACE=$SHARE_DIR=" nextPolish chmod 755 nextPolish -cp nextPolish ${PREFIX}/bin +cp -f nextPolish ${PREFIX}/bin diff --git a/recipes/nextpolish/meta.yaml b/recipes/nextpolish/meta.yaml index bee63263c4917..c0220727c74bc 100644 --- a/recipes/nextpolish/meta.yaml +++ b/recipes/nextpolish/meta.yaml @@ -13,20 +13,23 @@ source: - fix_get_version.patch build: - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage('nextpolish', max_pin="x") }} requirements: build: - make - - zlib - {{ compiler('c') }} host: - - zlib + - python + - pip - paralleltask + - bzip2 + - zlib run: - - python >=3.6 + - python - bwa - - bzip2 - minimap2 - paralleltask - samtools @@ -37,16 +40,17 @@ test: - nextPolish --version about: - home: https://github.com/Nextomics/NextPolish - dev_url: https://github.com/Nextomics/NextPolish - doc_url: https://nextpolish.readthedocs.io/en/latest/index.html - summary: Fast and accurately polish the genome generated by long reads - license: GPL-3 - license_family: GPL + home: "https://github.com/Nextomics/NextPolish" + dev_url: "https://github.com/Nextomics/NextPolish" + doc_url: "https://nextpolish.readthedocs.io/en/latest" + summary: "Fast and accurately polish the genome generated by noisy long reads" + license: "GPL-3.0-or-later" + license_family: GPL3 license_file: LICENSE extra: recipe-maintainers: - rpetit3 - container: - extended-base: True + identifiers: + - biotools:NextPolish + - doi:10.1093/bioinformatics/btz891 From ef4e095ef405151e3b149f0315ecb72f3477c373 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 25 Apr 2024 07:03:58 +0300 Subject: [PATCH 1722/1813] comet-ms: add linux-aarch64 build (#47435) Signed-off-by: Martin Tzvetanov Grigorov Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/comet-ms/build.sh | 2 +- recipes/comet-ms/meta.yaml | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/comet-ms/build.sh b/recipes/comet-ms/build.sh index 6ed5c0ccc5bb9..f7a9edbb36ae9 100644 --- a/recipes/comet-ms/build.sh +++ b/recipes/comet-ms/build.sh @@ -11,7 +11,7 @@ export CPPFLAGS="-I${PREFIX}/MSToolkit/include" sed -i.bak "s#gcc#${CC}#;s#g++#${CXX}#" MSToolkit/Makefile sed -i.bak "s#gcc#${CC}#;s#g++#${CXX}#" CometSearch/Makefile -make CXX=${CXX} +make CXX=${CXX} -j ${CPU_COUNT} mkdir -p "$PREFIX"/bin cp comet.exe ${PREFIX}/bin/comet diff --git a/recipes/comet-ms/meta.yaml b/recipes/comet-ms/meta.yaml index e7c9fb4700b11..66057b41ec387 100644 --- a/recipes/comet-ms/meta.yaml +++ b/recipes/comet-ms/meta.yaml @@ -14,7 +14,7 @@ build: run_exports: - {{ pin_subpackage('comet-ms', max_pin=None) }} skip: True # [osx] - number: 0 + number: 1 requirements: build: @@ -36,6 +36,8 @@ about: summary: 'Comet is a command line tool that does MS/MS database search.' extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1007/s13361-015-1179-x - doi:10.1002/pmic.201200439 From 5ad1597dd904ad99abb85cb6ea3f0e2540394dff Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 25 Apr 2024 07:34:11 +0300 Subject: [PATCH 1723/1813] iqtree: add linux-aarch64 build (#46434) * iqtree: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Bump iqtree to 2.3.0 Signed-off-by: Martin Tzvetanov Grigorov * Bump iqtree to 2.3.2 https://github.com/iqtree/iqtree2/pull/148#issuecomment-2046793962 Signed-off-by: Martin Tzvetanov Grigorov * Use GCC 9 for compiling iqtree Signed-off-by: Martin Tzvetanov Grigorov * Try with clang 16 for Linux aarch64 https://github.com/iqtree/iqtree2/issues/173#issuecomment-2047355599 Signed-off-by: Martin Tzvetanov Grigorov * Add libgomp for Linux Signed-off-by: Martin Tzvetanov Grigorov * Try with llvm-openmp for Linux aarch64 Signed-off-by: Martin Tzvetanov Grigorov * Go back to GCC 10 for the Linux build Signed-off-by: Martin Tzvetanov Grigorov * Try with GCC 10.3.0 Signed-off-by: Martin Tzvetanov Grigorov * Depend on `boost` instead of `boost-cpp` Signed-off-by: Martin Tzvetanov Grigorov * Try without boost dependency Signed-off-by: Martin Tzvetanov Grigorov * boost is needed ! Signed-off-by: Martin Tzvetanov Grigorov * Drop -std=c++17 from the CXXFLAGS. It breaks the build on Linux ARM64 Signed-off-by: Martin Tzvetanov Grigorov * Try with a `large` VM at CircleCI Signed-off-by: Martin Tzvetanov Grigorov * Try to build without concurrency `make -j $CPU_COUNT` fails due to out of memory error Signed-off-by: Martin Tzvetanov Grigorov * Revert some not needed changes Signed-off-by: Martin Tzvetanov Grigorov * Use parallel builds on non-aarch64 Signed-off-by: Martin Tzvetanov Grigorov * iqtree: Use latest GCC (12/13) with `-std=c++14` Signed-off-by: Martin Tzvetanov Grigorov * Append `-std=c++14` to CXXFLAGS Signed-off-by: Martin Tzvetanov Grigorov * update to v2.3.3 * revert to -std=c++14 * edit build.sh * try with 1 job * edit build.sh --------- Signed-off-by: Martin Tzvetanov Grigorov Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian --- recipes/iqtree/build.sh | 22 ++++++++++++++++------ recipes/iqtree/meta.yaml | 16 ++++++++++------ 2 files changed, 26 insertions(+), 12 deletions(-) diff --git a/recipes/iqtree/build.sh b/recipes/iqtree/build.sh index 402ef72c00afd..9d0866d98fcbe 100644 --- a/recipes/iqtree/build.sh +++ b/recipes/iqtree/build.sh @@ -1,21 +1,31 @@ #!/bin/bash +set -ex export INCLUDES="-I${PREFIX}/include" export LIBPATH="-L${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3" export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" +export CXXFLAGS="$CXXFLAGS -std=c++14" if [ "$(uname)" == Darwin ]; then export CMAKE_C_COMPILER="clang" export CMAKE_CXX_COMPILER="clang++" fi -mkdir build -cd build +cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DCMAKE_BUILD_TYPE=Release \ + -DUSE_LSD2=ON -DIQTREE_FLAGS=omp -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" -cmake -D CMAKE_INSTALL_PREFIX:PATH="${PREFIX}" -DUSE_LSD2=ON -DIQTREE_FLAGS=omp .. +case $(uname -m) in + aarch64) + JOBS=1 # CircleCI's arm.medium VM runs out of memory with higher values + ;; + *) + JOBS=${CPU_COUNT} + ;; +esac -make --jobs "${CPU_COUNT}" -make install -cp "${PREFIX}"/bin/iqtree2 "${PREFIX}"/bin/iqtree +cmake --build build --target install -j 1 + +cp -f "${PREFIX}"/bin/iqtree2 "${PREFIX}"/bin/iqtree diff --git a/recipes/iqtree/meta.yaml b/recipes/iqtree/meta.yaml index 3f9a392ea0926..66ad8876e27f2 100644 --- a/recipes/iqtree/meta.yaml +++ b/recipes/iqtree/meta.yaml @@ -1,6 +1,6 @@ {% set name = "IQTREE" %} -{% set version = "2.3.0" %} -{% set sha256 = "d55af7fda5a4bbe0bdda7a0e00aa5003bcfe78c771a5f2210b547bf7c7281d63" %} +{% set version = "2.3.3" %} +{% set sha256 = "dace30a921f10380dafdc6d4725254fdcf7611d9f89f7c8e33bb8943bc8e75c7" %} package: name: {{ name|lower }} @@ -12,7 +12,8 @@ build: - {{ pin_subpackage('iqtree', max_pin="x") }} source: - - url: https://github.com/iqtree/iqtree2/archive/refs/tags/v{{ version }}.tar.gz + # v2.3.3 release has an extra "." after "v" + - url: https://github.com/iqtree/iqtree2/archive/refs/tags/v.{{ version }}.tar.gz sha256: {{ sha256 }} - url: https://github.com/tothuhien/lsd2/archive/refs/tags/v.2.4.1.tar.gz sha256: 3d0921c96edb8f30498dc8a27878a76d785516043fbede4a72eefd84b5955458 @@ -23,9 +24,10 @@ requirements: - {{ compiler('cxx') }} - make - cmake + host: + - libgomp # [linux] - llvm-openmp # [osx] - ld64 # [osx] - host: - boost-cpp - eigen - zlib @@ -38,13 +40,15 @@ test: about: home: "http://www.iqtree.org/" dev_url: "https://github.com/iqtree/iqtree2" - license: GPL-2.0-or-later + license: "GPL-2.0-or-later" license_family: GPL2 license_file: LICENSE summary: "Efficient phylogenomic software by maximum likelihood." - doc_url: http://www.iqtree.org/doc/ + doc_url: "http://www.iqtree.org/doc/" extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:iq-tree - doi:10.1093/molbev/msu300 From 146e97348ededf0c5b89563266229e8b2bf31c97 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 25 Apr 2024 07:49:43 +0300 Subject: [PATCH 1724/1813] varlociraptor: add linux-aarch64 build (#46955) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/varlociraptor/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index 393782477f7c8..ba3b7fc4c4bb3 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("varlociraptor", max_pin="x") }} @@ -43,3 +43,7 @@ about: license: GPLv3 license_family: GPL summary: Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control. + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From dd9955eee6bf3dc708c9534ad7d31188ad66bf1b Mon Sep 17 00:00:00 2001 From: Po-E Li Date: Wed, 24 Apr 2024 22:53:49 -0600 Subject: [PATCH 1725/1813] Update gottcha2 to v2.1.8.6 (#47446) * update gottcha2 to v2.1.8.6 * clean up recipe --------- Co-authored-by: mencian --- recipes/gottcha2/meta.yaml | 27 ++++++++++++++++++--------- 1 file changed, 18 insertions(+), 9 deletions(-) diff --git a/recipes/gottcha2/meta.yaml b/recipes/gottcha2/meta.yaml index b86da3424f743..50a0db70f10d7 100644 --- a/recipes/gottcha2/meta.yaml +++ b/recipes/gottcha2/meta.yaml @@ -1,28 +1,34 @@ {% set name = "GOTTCHA2" %} -{% set version = "2.1.8.5p1" %} +{% set version = "2.1.8.6" %} package: name: {{ name|lower }} version: {{ version }} build: - noarch: generic + noarch: python number: 0 - script: {{ PYTHON }} -m pip install -vv --no-deps . + script: {{ PYTHON }} -m pip install -vvv --no-deps --no-build-isolation . + entry_points: + - gottcha2 = cmd:gottcha2_command run_exports: - - {{ pin_subpackage('gottcha2', max_pin='x.x') }} + - {{ pin_subpackage('gottcha2', max_pin='x') }} source: url: https://github.com/poeli/GOTTCHA2/archive/refs/tags/{{ version }}.tar.gz - sha256: 81107fdb32c4da753c02a9973cc7d8ba540ac8255006c57e2f133dbc4c833351 + sha256: 18ae74fa448e837ade605676334c5c37cda07473a6cf0105937d8afe1b017359 requirements: host: - - python + - python >=3.6 + - pip run: + - python >=3.6 - minimap2 >=2.17 - gawk - biom-format >=2.1.7 + - numpy + - pandas - requests - tqdm @@ -33,10 +39,13 @@ test: - gottcha2.py --version about: - home: https://github.com/poeli/gottcha2 - license: BSD 3-clause + home: https://github.com/poeli/GOTTCHA2 + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE summary: 'Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) v2' + dev_url: https://github.com/poeli/GOTTCHA2 extra: identifiers: - - biotools:gottcha2 \ No newline at end of file + - biotools:gottcha2 From 830f3ea602d58ad5824e2607eafbe80b268c6304 Mon Sep 17 00:00:00 2001 From: Jorrit Boekel Date: Thu, 25 Apr 2024 06:58:50 +0200 Subject: [PATCH 1726/1813] Update percolator to version 3.6.5 (#47414) * Percolator version 3.6.5 * Add run_exports * Remove from blacklist, fingers crossed * Maybe it works if I add libboost-devel? * Boost 1.71 has static libraries which percolator needs * Whoops, typo in package version spec * clean up recipe * edit build.sh * revert to skipping osx --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- build-fail-blacklist | 1 - recipes/percolator/build.sh | 38 +++++++++++++++++++++++------------- recipes/percolator/meta.yaml | 22 +++++++++++++-------- 3 files changed, 38 insertions(+), 23 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index e8e163736a075..b2af9f3218d26 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -231,7 +231,6 @@ recipes/bmtool recipes/sibelia recipes/var-agg recipes/wham -recipes/percolator # Segfaults in bulk on Linux 24.3.2021 recipes/dbgraph diff --git a/recipes/percolator/build.sh b/recipes/percolator/build.sh index cd53d08f3084b..5dc597f961637 100644 --- a/recipes/percolator/build.sh +++ b/recipes/percolator/build.sh @@ -1,20 +1,30 @@ #!/bin/bash -mkdir percobuild && cd percobuild -cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$PREFIX -DXML_SUPPORT=ON -DCMAKE_PREFIX_PATH="$PREFIX;$PREFIX/lib" -DCMAKE_CXX_FLAGS="-std=c++14" $SRC_DIR -make && make install -cd .. +export INCLUDES="-I{PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +cmake -S . -B percobuild \ + -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="$PREFIX" -DXML_SUPPORT=ON \ + -DCMAKE_PREFIX_PATH="$PREFIX;$PREFIX/lib" -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="-std=c++14 -O3 -I{PREFIX}/include" +cmake --build percobuild/ --target install -j ${CPU_COUNT} -v # First make sure we dont get problems with truncated PREFIX due to null terminators: # see percolator/percolator#251 and conda/conda-build#1674 -sed -i '54s/WRITABLE_DIR/std::string(WRITABLE_DIR).c_str()/' $SRC_DIR/src/Globals.cpp -mkdir converterbuild && cd converterbuild -cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="$PREFIX" -DBOOST_ROOT=$PREFIX -DBOOST_LIBRARYDIR=$PREFIX/lib -DSERIALIZE="Boost" -DCMAKE_CXX_FLAGS="-std=c++11" -DCMAKE_PREFIX_PATH="$PREFIX" $SRC_DIR/src/converters -make install -cd .. +sed -i.bak '54s/WRITABLE_DIR/std::string(WRITABLE_DIR).c_str()/' $SRC_DIR/src/Globals.cpp + +cmake -S ${SRC_DIR}/src/converters -B converterbuild \ + -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="$PREFIX" -DBOOST_ROOT="$PREFIX" \ + -DBOOST_LIBRARYDIR="$PREFIX/lib" -DSERIALIZE="Boost" \ + -DCMAKE_CXX_FLAGS="-std=c++11 -O3 -I{PREFIX}/include" \ + -DCMAKE_PREFIX_PATH="$PREFIX" -DCMAKE_CXX_COMPILER="${CXX}" +cmake --build converterbuild/ --target install -j ${CPU_COUNT} -v -mkdir $PREFIX/testdata -cp $SRC_DIR/src/converters/data/converters/sqt2pin/target.sqt $PREFIX/testdata/target.sqt -cp $SRC_DIR/src/converters/data/converters/msgf2pin/target.mzid $PREFIX/testdata/target.mzid -cp $SRC_DIR/src/converters/data/converters/tandem2pin/target.t.xml $PREFIX/testdata/target.t.xml -cp $SRC_DIR/data/percolator/tab/percolatorTab $PREFIX/testdata/percolatorTab +mkdir -p $PREFIX/testdata +cp -f $SRC_DIR/src/converters/data/converters/sqt2pin/target.sqt $PREFIX/testdata/target.sqt +cp -f $SRC_DIR/src/converters/data/converters/msgf2pin/target.mzid $PREFIX/testdata/target.mzid +cp -f $SRC_DIR/src/converters/data/converters/tandem2pin/target.t.xml $PREFIX/testdata/target.t.xml +cp -f $SRC_DIR/data/percolator/tab/percolatorTab $PREFIX/testdata/percolatorTab diff --git a/recipes/percolator/meta.yaml b/recipes/percolator/meta.yaml index 20731e041f8b0..c3a9540cf1790 100644 --- a/recipes/percolator/meta.yaml +++ b/recipes/percolator/meta.yaml @@ -1,17 +1,19 @@ {% set name = "percolator" %} -{% set version = "3.5" %} +{% set version = "3.6.5" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/percolator/percolator/archive/rel-3-05.tar.gz - sha256: 5b746bdc0119a40f96bc090e02e27670f91eeb341736911750b170da7e5c06bb + url: https://github.com/percolator/percolator/archive/refs/tags/rel-3-06-05.tar.gz + sha256: e386998046f59c34be01b1b0347709751d92f3a98e9a0079f8e7c5af5e2dcc8f build: - number: 2 - skip: True # [osx] + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('percolator', max_pin="x") }} requirements: build: @@ -19,7 +21,7 @@ requirements: - {{ compiler('cxx') }} - cmake host: - - boost + - boost-cpp 1.71 # last version to have static libs - sqlite - bzip2 - xerces-c @@ -38,13 +40,17 @@ test: about: home: https://github.com/percolator/percolator - license: Apache 2.0 + license: Apache-2.0 + license_family: APACHE license_file: license.txt summary: Semi-supervised learning for peptide identification from shotgun proteomics datasets + dev_url: https://github.com/percolator/percolator + doc_url: http://percolator.ms/ extra: container: - extended-base: true # Add UTF-8 for percolator converters + extended-base: True # Add UTF-8 for percolator converters identifiers: - biotools:Percolator - doi:10.1007/s13361-016-1460-7 + - usegalaxy-eu:percolator From 87992ec3949c93b2f992c22d60f67f9b28940178 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 01:19:45 -0400 Subject: [PATCH 1727/1813] Update rtk2 to 2.11.1 (#47437) * Update rtk2 to 2.11 * Update rtk2 to 2.11.1 * edit build.sh * edit meta.yaml * edit meta.yaml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian --- recipes/rtk2/build.sh | 11 ++++++----- recipes/rtk2/meta.yaml | 17 +++++++++-------- 2 files changed, 15 insertions(+), 13 deletions(-) diff --git a/recipes/rtk2/build.sh b/recipes/rtk2/build.sh index 7961fbb423e85..0b901b830f550 100644 --- a/recipes/rtk2/build.sh +++ b/recipes/rtk2/build.sh @@ -1,15 +1,16 @@ -#!/bin/sh - +#!/bin/bash set -euxo pipefail + mkdir -p "$PREFIX"/bin -echo " Setting environment variables" +echo "Setting environment variables" # Fix zlib -export CFLAGS="$CFLAGS -I$PREFIX/include" +export CFLAGS="$CFLAGS -O3 -I$PREFIX/include" export LDFLAGS="$LDFLAGS -L$PREFIX/lib" -export CPATH=${PREFIX}/include +export C_INCLUDE_PATH=${PREFIX}/include echo "RUN MAKE" make test +chmod 755 rtk2 mv rtk2 "$PREFIX"/bin/ diff --git a/recipes/rtk2/meta.yaml b/recipes/rtk2/meta.yaml index 0aebea2760f7b..89654d1a8e8b7 100644 --- a/recipes/rtk2/meta.yaml +++ b/recipes/rtk2/meta.yaml @@ -1,12 +1,13 @@ -{% set version="2.10" %} -{% set name="rtk2" %} +{% set version = "2.11.1" %} +{% set name = "rtk2" %} + package: name: {{ name }} version: {{ version }} source: url: https://github.com/hildebra/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 310cd4bd124f6d976c1f11fdc6a38da2d362942e3ea82a560c0e64cf3f1a9679 + sha256: d816684a1a04f2a48ec2cf605ed33dc938baae01d509ed01e9d84565d54259cc build: number: 0 @@ -19,16 +20,16 @@ requirements: - {{ compiler('cxx') }} host: - zlib - run: - - zlib test: commands: - - {{ name }} -h - - {{ name }} --version | grep -w {{ version }} + - '{{ name }} -h' + #- '{{ name }} --version | grep -w "{{ version }}"' about: home: https://github.com/hildebra/rtk2/ - license: 'GPLv2' + license: 'GPL-2.0-or-later' + license_family: GPL license_file: LICENSE summary: 'rtk2 - a CLI rarefaction toolkit for OTU tables' + dev_url: https://github.com/hildebra/rtk2/ From 1aa6e4a765e334d2bede5200262e99ad8ab0eea4 Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Wed, 24 Apr 2024 23:50:04 -0600 Subject: [PATCH 1728/1813] add recipe for camlhmp (#47453) --- recipes/camlhmp/meta.yaml | 49 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/camlhmp/meta.yaml diff --git a/recipes/camlhmp/meta.yaml b/recipes/camlhmp/meta.yaml new file mode 100644 index 0000000000000..81544753240b8 --- /dev/null +++ b/recipes/camlhmp/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "camlhmp" %} +{% set version = "0.0.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/camlhmp/camlhmp-{{ version }}.tar.gz + sha256: 882013057ea4ff06c84919a71d50309e9db35efae507c1560c4380b0139e0d5e + +build: + noarch: python + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin='x.x.x') }} + +requirements: + host: + - python >=3.8 + - poetry + - pip + run: + - blast + - executor + - pigz + - python >=3.8 + - pyyaml + - rich-click >=1.6.0 + +test: + imports: + - camlhmp + commands: + - pip check + - camlhmp --help + requires: + - pip + +about: + home: https://github.com/rpetit3/camlhmp + summary: Classification through yAML Heuristic Mapping Protocol + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - rpetit3 From 2f7024b26bed717908ac5b71137a5097d67fb362 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Thu, 25 Apr 2024 10:30:09 +0200 Subject: [PATCH 1729/1813] Add tooldistillator recipe (#47443) * Add tooldistillator recipe * Reset build number * Update summary --- recipes/tooldistillator/meta.yaml | 83 +++++++++++++++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 recipes/tooldistillator/meta.yaml diff --git a/recipes/tooldistillator/meta.yaml b/recipes/tooldistillator/meta.yaml new file mode 100644 index 0000000000000..1128ee6930d88 --- /dev/null +++ b/recipes/tooldistillator/meta.yaml @@ -0,0 +1,83 @@ +{% set version = "0.8.4.0" %} +{% set sha256 = " d3e3176f2460f03ad615357869c47ae03d2e4dd14625f5c60016cb56c2ef7969" %} + +context: {} + +package: + name: tooldistillator + version: '{{ version }}' + +source: + url: https://gitlab.com/ifb-elixirfr/abromics/tooldistillator/-/archive/{{ version }}/tooldistillator-{{ version }}.tar.gz + sha256: {{ sha256 }} +build: + noarch: python + number: 0 + script: python -m pip install --no-deps --ignore-installed . + entry_points: + - tooldistillator = tooldistillator.main:main + run_exports: + - {{ pin_subpackage('tooldistillator', max_pin='x.x') }} + +requirements: + host: + - python >=3.10 + - pip >=23.1.2 + run: + - pandas + - biopython + - python + - ld_impl_linux-64 + - _libgcc_mutex + - libstdcxx-ng + - python_abi + - ca-certificates + - libgfortran5 + - libgomp + - libgfortran-ng + - _openmp_mutex + - libgcc-ng + - libopenblas + - openssl + - xz + - ncurses + - libnsl + - libffi + - bzip2 + - libzlib + - libblas + - readline + - tk + - libsqlite + - libcblas + - liblapack + - tzdata + - wheel + - setuptools + - pip + - six + - pytz + - python-tzdata + - python-dateutil + - numpy + +test: + commands: + - tooldistillator --help + - tooldistillator --version + - tooldistillator abricate --help + +about: + dev_url: https://gitlab.com/ifb-elixirfr/abromics/tooldistillator + doc_url: https://gitlab.com/ifb-elixirfr/abromics/tooldistillator/-/blob/main/docs/_build/html/index.html + home: https://gitlab.com/ifb-elixirfr/abromics + license: GPLv3 + license_family: GPL + license_file: LICENSE.txt + summary: Tool to extract and aggregate information from different tool outputs to JSON parsable files + +extra: + recipe-maintainers: + - bebatut + - clsiguret + From af32109863d36cd4d4455465eb4fe08736f352a1 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Thu, 25 Apr 2024 14:08:54 +0200 Subject: [PATCH 1730/1813] [haddock_biobb] update (#47466) --- recipes/haddock_biobb/meta.yaml | 2 +- recipes/haddock_biobb/post-link.sh | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/haddock_biobb/meta.yaml b/recipes/haddock_biobb/meta.yaml index e5511fb188a2c..4ca7ad9ad9dac 100644 --- a/recipes/haddock_biobb/meta.yaml +++ b/recipes/haddock_biobb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "haddock_biobb" %} -{% set version = "3.0.3" %} +{% set version = "3.0.4" %} package: name: '{{ name|lower }}' diff --git a/recipes/haddock_biobb/post-link.sh b/recipes/haddock_biobb/post-link.sh index b634ad9fd28ed..616a2388237eb 100644 --- a/recipes/haddock_biobb/post-link.sh +++ b/recipes/haddock_biobb/post-link.sh @@ -1,2 +1,2 @@ -echo "Before using HADDOCK please install CNS. Instructions: https://github.com/haddocking/haddock3/blob/main/docs/CNS.md" -echo "And create a softlink [ln -s] of the CNS executable to the ${PREFIX}lib/pythonX.XX/bin/ folder (Replace the X by your env python version)" > "${PREFIX}"/.messages.txt +echo "Before using HADDOCK please install CNS. Instructions: https://github.com/haddocking/haddock3/blob/main/docs/CNS.md" > "${PREFIX}"/.messages.txt +echo "And create a softlink [ln -s] of the CNS executable to the ${PREFIX}lib/pythonX.XX/bin/ folder (Replace the X by your env python version)" >> "${PREFIX}"/.messages.txt From 020feb1a08d5cb93dbded959b82fc2683392d177 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Thu, 25 Apr 2024 15:55:58 +0200 Subject: [PATCH 1731/1813] [biobb_pytorch] update 4.1.0 (#47469) --- recipes/biobb_pytorch/meta.yaml | 53 +++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 recipes/biobb_pytorch/meta.yaml diff --git a/recipes/biobb_pytorch/meta.yaml b/recipes/biobb_pytorch/meta.yaml new file mode 100644 index 0000000000000..eb1dde4c40c19 --- /dev/null +++ b/recipes/biobb_pytorch/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "biobb_pytorch" %} +{% set version = "4.1.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 4e55252f16c25f0600ad353ab8e1db96dc4064e5087ea6ca6734fdf5ccb1dbae + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.8 + - setuptools + - biobb_common ==4.1.0 + - pytorch + run: + - python >=3.8 + - biobb_common ==4.1.0 + - pytorch + +test: + imports: + - biobb_pytorch + - biobb_pytorch.mdae + +about: + home: https://github.com/bioexcel/biobb_pytorch + license: Apache Software License + license_family: APACHE + license_file: '' + summary: biobb_pytorch is the Biobb module collection to create and train ML & DL models. + description: "# biobb_pytorch\n\n### Introduction\nBiobb_Pytorch is the Biobb module collection to create and train ML & DL models using the popular [PyTorch](https://pytorch.org/) Python library. + Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb-pytorch.readthedocs.io/en/latest/).\n\ + \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\ + \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\ + Licensed under the\n\ + [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\ + \n\ + ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n" + doc_url: http://biobb_pytorch.readthedocs.io/en/latest/ + dev_url: https://github.com/bioexcel/biobb_pytorch + +extra: + recipe-maintainers: PauAndrio From 7cdc7d055c79e40d4ad8fe307042867d2289399c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Thu, 25 Apr 2024 16:48:44 +0200 Subject: [PATCH 1732/1813] Update ToolDistillator (#47472) --- recipes/tooldistillator/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tooldistillator/meta.yaml b/recipes/tooldistillator/meta.yaml index 1128ee6930d88..08c925278ff6d 100644 --- a/recipes/tooldistillator/meta.yaml +++ b/recipes/tooldistillator/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.4.0" %} -{% set sha256 = " d3e3176f2460f03ad615357869c47ae03d2e4dd14625f5c60016cb56c2ef7969" %} +{% set version = "0.8.4.1" %} +{% set sha256 = "423be625ff79c275f696adc372abed76f82bd1aa4628b91b080070ec77cdb17a" %} context: {} From 048b2b4fba7aa0429c485d8f2cf46ee76beb168d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Salom=C3=A9=20Brunon?= <91611978+Salome-Brunon@users.noreply.github.com> Date: Thu, 25 Apr 2024 17:14:28 +0200 Subject: [PATCH 1733/1813] Updated ToulligQc to v2.5.6 (#47474) * Updated ToulligQc to v2.5.4 * UPDATE: updated ToulligQC to v2.5.5 * UPDATE: updated ToulligQC to v2.5.6 --- recipes/toulligqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/toulligqc/meta.yaml b/recipes/toulligqc/meta.yaml index cf09283366e10..f9d01beea308f 100644 --- a/recipes/toulligqc/meta.yaml +++ b/recipes/toulligqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "toulligqc" %} -{% set version = "2.5.5" %} +{% set version = "2.5.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: aa614700d670218500c436004e1ec7f895f8d95ebf3f95fdbfc7e718be96710b + sha256: 1b6087ccb927e0da6ff8f9c82c166de02d41bc55df9b9d7fc9edf264aec009f9 build: number: 0 From 562ef886f8826fbc91409eea0159be68a582fb4d Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 25 Apr 2024 18:34:59 +0300 Subject: [PATCH 1734/1813] pindel: add linux-aarch64 build (#47456) * pindel: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Add zlib as a host dependency Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/pindel/meta.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/pindel/meta.yaml b/recipes/pindel/meta.yaml index 0a5b46a78ad9d..fc5a2aae1e96c 100644 --- a/recipes/pindel/meta.yaml +++ b/recipes/pindel/meta.yaml @@ -6,8 +6,10 @@ package: version: {{ version }} build: - number: 10 + number: 11 skip: True # [osx] + run_exports: + - {{ pin_subpackage('pindel', max_pin='x.x') }} source: url: https://github.com/genome/pindel/archive/{{ revision }}.tar.gz @@ -23,6 +25,7 @@ requirements: - make host: - htslib + - zlib run: - htslib @@ -37,5 +40,7 @@ about: summary: Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:pindel From e1f0ec18cae86ff135d43b2d12b3b8a956e9157a Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 25 Apr 2024 18:35:42 +0300 Subject: [PATCH 1735/1813] longshot: add linux-aarch64 build (#47454) * longshot: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Update rust-htslib dependency with a patch to fix the build on Linux aarch64 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/longshot/meta.yaml | 6 +++++- recipes/longshot/update-rust-htslib.patch | 23 +++++++++++++++++++++++ 2 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 recipes/longshot/update-rust-htslib.patch diff --git a/recipes/longshot/meta.yaml b/recipes/longshot/meta.yaml index 79ada8afb9463..10c98313b10f1 100644 --- a/recipes/longshot/meta.yaml +++ b/recipes/longshot/meta.yaml @@ -8,9 +8,11 @@ package: source: url: https://github.com/pjedge/longshot/archive/v{{ version }}.tar.gz sha256: f6981892beb966eef40986c46928301dec1fef38591cc291e00a546f9866c5e2 + patches: + - update-rust-htslib.patch build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('longshot', max_pin="x") }} @@ -43,6 +45,8 @@ about: dev_url: https://github.com/pjedge/longshot extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1038/s41467-019-12493-y - biotools:longshot diff --git a/recipes/longshot/update-rust-htslib.patch b/recipes/longshot/update-rust-htslib.patch new file mode 100644 index 0000000000000..1f2ec95d71d9f --- /dev/null +++ b/recipes/longshot/update-rust-htslib.patch @@ -0,0 +1,23 @@ +From 9457f89b8200c238f4696eb86f7e979d23b3ae2c Mon Sep 17 00:00:00 2001 +From: Martin Grigorov +Date: Thu, 25 Apr 2024 11:05:07 +0300 +Subject: [PATCH] Update rust-htslib to 0.46.0 + +This allows building the project on Linux ARM64! +--- + Cargo.toml | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Cargo.toml b/Cargo.toml +index c8592eb..e3a32db 100644 +--- a/Cargo.toml ++++ b/Cargo.toml +@@ -5,7 +5,7 @@ authors = ["Peter Edge "] + + [dependencies] + bio = "0.25.0" +-rust-htslib = "0.38.2" ++rust-htslib = "0.46.0" + clap = "2.26.2" + chrono = "0.4" + rand = { version = "0.8", features = ["std_rng"] } From a6e549d84445828a62807dce684c1b4c846001e9 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 25 Apr 2024 18:36:58 +0300 Subject: [PATCH 1736/1813] gemini: enable linux-aarch64 build (#46360) * gemini: enable linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Try without cyordereddict See: - https://github.com/conda-forge/cyordereddict-feedstock/pull/15#issuecomment-2037338844 - https://github.com/shoyer/cyordereddict/commit/cb271b87e984a2e5c1e5e3bff7cb9dfbd674a1f1 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/gemini/meta.yaml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/recipes/gemini/meta.yaml b/recipes/gemini/meta.yaml index 58e594f5761c1..4208619313276 100644 --- a/recipes/gemini/meta.yaml +++ b/recipes/gemini/meta.yaml @@ -6,9 +6,10 @@ package: version: {{ version }} build: - number: 5 - skip: True # [not py27] + number: 6 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} source: url: https://github.com/arq5x/gemini/archive/v{{ version }}.tar.gz @@ -19,12 +20,11 @@ requirements: - {{ compiler('c') }} host: - pip - - python + - python >=3.8 - setuptools - bcolz - bottle - bx-python - - cyordereddict - cython - cyvcf2 >0.6.5 - geneimpacts @@ -38,18 +38,17 @@ requirements: - openpyxl - pandas - pybedtools - - pysam + - pysam >=0.22 - pyyaml - scipy - unidecode - snappy - python-snappy run: - - python + - python >=3.8 - bcolz - bottle - bx-python - - cyordereddict - cyvcf2 >0.6.5 - geneimpacts - inheritance @@ -63,7 +62,7 @@ requirements: - openpyxl - pandas - pybedtools - - pysam + - pysam >=0.22 - pyyaml - scipy - unidecode @@ -84,6 +83,8 @@ about: summary: a lightweight db framework for disease and population genetics. extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:GEMINI - doi:10.1371/journal.pcbi.1003153 From a21732c6f09c58c3176a86b66a77e16cb9062f0f Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Thu, 25 Apr 2024 13:48:05 -0600 Subject: [PATCH 1737/1813] fix pinning of bactopia-py (#47484) --- recipes/bactopia/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bactopia/meta.yaml b/recipes/bactopia/meta.yaml index df8f01409f6a0..55a6a219c4b5d 100644 --- a/recipes/bactopia/meta.yaml +++ b/recipes/bactopia/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} @@ -17,7 +17,7 @@ source: requirements: run: - - bactopia-py >=1.0.9 + - bactopia-py 1.0.9 - conda >=22.11.0 - coreutils - mamba >=1.1.0 From 067f4271032fc3eb9d4877ad19162fc8f331e22f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 15:56:11 -0400 Subject: [PATCH 1738/1813] Update bactopia-py to 1.1.0 (#47485) --- recipes/bactopia-py/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bactopia-py/meta.yaml b/recipes/bactopia-py/meta.yaml index 751efeead926f..df10918af0a20 100644 --- a/recipes/bactopia-py/meta.yaml +++ b/recipes/bactopia-py/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bactopia-py" %} -{% set version = "1.0.9" %} +{% set version = "1.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/bactopia/bactopia-{{ version }}.tar.gz - sha256: 7f3ff7f1123ad22605098f81686650e3a0631ddcaeaede78dee9e93099d9fdac + sha256: f251c35b1cc69371e7ef93802243570e0942ee2ba066918667380fedb2ee5631 build: noarch: python From 2171f8211a55a2a3f51707c3c51ea8632a91d0ee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 16:43:18 -0400 Subject: [PATCH 1739/1813] Update pyhmmer to 0.10.12 (#47483) --- recipes/pyhmmer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 586e1db28ee9c..ea675212bdbe2 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.11" %} +{% set version = "0.10.12" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c45a2335e6dc5b7d3f3db424e234c398b21b6063ad48b19c90abde0120c3d866 + sha256: 8457547adaa5f570f9a360a015a968b52709634540f95c17f687916640a075d1 build: number: 0 From 67a46afe24f64d5658ca0684d3e7ce611e718743 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 17:02:22 -0400 Subject: [PATCH 1740/1813] Update oakvar to 2.9.111 (#47459) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 79b7a5cf5bee1..e8904c0d61307 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.110" %} -{% set sha256 = "32e96a2fad564a117ea9adc6bf5458a2f98baa6b89a01fded50d84ea716a89ff" %} +{% set version = "2.9.111" %} +{% set sha256 = "2d273a80238654ce5dffb0018d5ace3b1bd925a778e91534efaa083474b535c1" %} package: name: {{ name|lower }} From 3640d04e87ec65754cf98ae6c677a8a00d5cd2ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 17:02:31 -0400 Subject: [PATCH 1741/1813] Update ppx to 1.4.4 (#47457) --- recipes/ppx/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ppx/meta.yaml b/recipes/ppx/meta.yaml index 7666042599d38..468bdacc12df0 100644 --- a/recipes/ppx/meta.yaml +++ b/recipes/ppx/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ppx" %} -{% set version = "1.4.2" %} +{% set version = "1.4.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 4136286d6095ab07930b7df74cf450a938878b2c0e262cbc1987ac03166a16eb + sha256: 97eacbc9272faf98ab2fa16f0949eb55bd0eab5cecf9e8381321e754808e2cd8 build: number: 0 From 10954de5bf43b519f6aac365dccc8de1bce01362 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 17:03:14 -0400 Subject: [PATCH 1742/1813] Update pybiolib to 1.1.2013 (#47471) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index b2b965aa43c9e..39d9de7ef54a2 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.2004" %} +{% set version = "1.1.2013" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 95d6cdae9c6cae98542dc2a44bb197f8e1f1f1240d8a112a7289a8cf446a2135 + sha256: 43d712ee8e801aaa4c53009f48549744cd997d2e43d5a466710e9cf616324491 build: noarch: python From 052642c95d43e2212f6dc50da824fb190390aade Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 17:03:22 -0400 Subject: [PATCH 1743/1813] Update pyensembl to 2.3.13 (#47473) --- recipes/pyensembl/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index b6fdac41746f5..fedc72c441759 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PyEnsembl" %} -{% set version = "2.3.12" %} -{% set sha256 = "bfa3de35a47fe85afa5f8ff39fddd86e2cca6c14c238029c1525b3d3aa8bb089" %} +{% set version = "2.3.13" %} +{% set sha256 = "c70ce760f68fe2a6be871db44e53ce1d4d1227f2ce0578c6b291d5a89f5d1832" %} package: name: {{ name|lower }} From 177febe04fb771dc2f43475ccfb62b8136aaff49 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 17:03:31 -0400 Subject: [PATCH 1744/1813] Update locityper to 0.15.0 (#47478) --- recipes/locityper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/locityper/meta.yaml b/recipes/locityper/meta.yaml index 1849ec8e9da84..291ae3258fcc6 100644 --- a/recipes/locityper/meta.yaml +++ b/recipes/locityper/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.5" %} +{% set version = "0.15.0" %} package: name: locityper @@ -11,7 +11,7 @@ build: source: url: https://github.com/tprodanov/locityper/archive/refs/tags/v{{ version }}.tar.gz - sha256: 968e984f757c3985caa7a02ff87f82b859e0f7c5cf2b2fa80f0393b2e2e9545a + sha256: 23e6505c4e31ad3f27ba9ac86128d3e554012601ea84ebd06d6b2f3b1f067020 requirements: build: From 86dda909e37530fa700acc8dc9b9507b5292efbc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 17:08:37 -0400 Subject: [PATCH 1745/1813] Update cmat to 3.1.2 (#47475) --- recipes/cmat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cmat/meta.yaml b/recipes/cmat/meta.yaml index 22556a626dd0c..ecfe125c94af4 100644 --- a/recipes/cmat/meta.yaml +++ b/recipes/cmat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cmat" %} -{% set version = "3.1.1" %} +{% set version = "3.1.2" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/EBIvariation/CMAT/archive/v{{version}}.tar.gz - sha256: 0ff44acd1a9c1df9ed76804faf62d49716edcc1376679a19b1ef1b5003cde535 + sha256: bac2b83970c76bdb50b18f5555f689b0e8522ddd60fc73ab6a6f16b640c94a73 build: number: 0 From 93786827e874bed20ead1a4d9d55b9d9f23b6a42 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 17:08:46 -0400 Subject: [PATCH 1746/1813] Update galitime to 0.1.3 (#47465) --- recipes/galitime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galitime/meta.yaml b/recipes/galitime/meta.yaml index d14db11964b6c..5f48c03aab361 100644 --- a/recipes/galitime/meta.yaml +++ b/recipes/galitime/meta.yaml @@ -1,5 +1,5 @@ {% set name = "galitime" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 9789a3beec1ce5d1cd588c6bb56012932f69ae3dedbce02a8f4abc0b86ce601a + sha256: 3d2d77adf50d1f40f42b23070d9b7754fc84e6492d0a4cf466d0cad5cd4d569a build: number: 0 From 50ce954287d8a873612ef50d6648a0d02cd12bdf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 17:08:54 -0400 Subject: [PATCH 1747/1813] Update pydeseq2 to 0.4.9 (#47464) --- recipes/pydeseq2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml index cab0312268fa3..245e1501865d3 100644 --- a/recipes/pydeseq2/meta.yaml +++ b/recipes/pydeseq2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydeseq2" %} -{% set version = "0.4.8" %} +{% set version = "0.4.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz - sha256: ae6cb09ce921d866b1d79f2a54bcc6acc61e22d832f1c16e56716ff18e4d35fc + sha256: 0375207775953f43f84ed4279fcb9f11a430d79d038e158bbe74acbc58326d31 build: noarch: python From f623d4e357370116384e0013d09ac73f1231648a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 17:09:05 -0400 Subject: [PATCH 1748/1813] Update tajimas_d to 2.0.2 (#47462) --- recipes/tajimas_d/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tajimas_d/meta.yaml b/recipes/tajimas_d/meta.yaml index 6b5cc9f32216f..f218c3de18a2e 100644 --- a/recipes/tajimas_d/meta.yaml +++ b/recipes/tajimas_d/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tajimas_d" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/not-a-feature/tajimas_d/archive/refs/tags/v{{ version }}.tar.gz - sha256: 11fd47453836d9dc9470a426d52f4889d4c49248dd5c931f66b8907ad9c66656 + sha256: 899cf84e8e89ecccc9fbd106c21ee2777bc7736c163b5470e4cce3b843cbe36a build: noarch: python From a711ee29c2befd57a1bc808953f6d274cc025e44 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 19:49:34 -0400 Subject: [PATCH 1749/1813] Update vcfsim to 1.0.11.alpha (#47488) --- recipes/vcfsim/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vcfsim/meta.yaml b/recipes/vcfsim/meta.yaml index 39949b080fbfe..5a7af5429f034 100644 --- a/recipes/vcfsim/meta.yaml +++ b/recipes/vcfsim/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcfsim" %} -{% set version = "1.0.10.alpha" %} +{% set version = "1.0.11.alpha" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Pie115/VCFSimulator-SamukLab/archive/{{ version }}.tar.gz - sha256: 94125b463150246b9b1109a0d989b5a3e2f8c6fd4f33d9ab203106e242c6a345 + sha256: 9263d88be02a25a4ff9033413ecd2c72807f5ea532434092a35abf96b8858aa0 build: noarch: python From 0e3f004e755dfe71d7dbbe3c791a67b56c5c3221 Mon Sep 17 00:00:00 2001 From: Paul De Geest Date: Fri, 26 Apr 2024 01:50:52 +0200 Subject: [PATCH 1750/1813] Update Astral bioconda package (#47467) * Add recipe for astral 5.7.8 * updated package name as to not conflict with astral in conda-forge channel * updated directory name to match package name * updated astral recipe --- recipes/astral-tree/astral.py | 19 ------------------- recipes/astral-tree/meta.yaml | 6 ++++-- 2 files changed, 4 insertions(+), 21 deletions(-) diff --git a/recipes/astral-tree/astral.py b/recipes/astral-tree/astral.py index f1b2e7421c1e6..2feff928efad7 100755 --- a/recipes/astral-tree/astral.py +++ b/recipes/astral-tree/astral.py @@ -76,24 +76,6 @@ def jvm_opts(argv): return (mem_opts, prop_opts, pass_args, exec_dir) -def def_temp_log_opts(args): - """ - Establish default temporary and log folders. - """ - TEMP = os.getenv("TEMP") - - if TEMP is not None: - if '-log' not in args: - args.append('-log') - args.append(TEMP+'/logs') - - if '-temp_folder' not in args : - args.append('-temp_folder') - args.append(TEMP) - - return args - - def main(): java = java_executable() """ @@ -104,7 +86,6 @@ def main(): we copy the jar file, lib, and resources to the exec_dir directory. """ (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) - pass_args = def_temp_log_opts(pass_args) jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) if pass_args != [] and pass_args[0].startswith('eu'): diff --git a/recipes/astral-tree/meta.yaml b/recipes/astral-tree/meta.yaml index b3d9ae6d5b750..1def11046b60e 100644 --- a/recipes/astral-tree/meta.yaml +++ b/recipes/astral-tree/meta.yaml @@ -1,15 +1,17 @@ # Do not forget to update the version string in the astral_wrapper.py file {% set name = "Astral" %} {% set version = "5.7.8" %} -{% set sha256 = "7284f3f86d4824fb8b80a999f7495245961f2c62943c96c8ad9d626759f65b4e" %} +{% set sha256 = "7b3d89ca4fee42b00e547ed2485e60bebfdf7f0179cfc503f0c522d682483dea" %} package: name: {{ name|lower }}-tree version: {{ version }} build: - number: 0 + number: 1 noarch: generic + run_exports: + - {{ pin_subpackage('astral-tree', max_pin="x") }} source: url: https://github.com/smirarab/ASTRAL/raw/master/{{ name }}.{{ version }}.zip From b9262ebbc4dda01fd51dbbe55f4ce228db13ab3c Mon Sep 17 00:00:00 2001 From: farchaab <116543129+farchaab@users.noreply.github.com> Date: Fri, 26 Apr 2024 01:51:11 +0200 Subject: [PATCH 1751/1813] updated entrypoint and dependencies (#47470) --- recipes/assembly_finder/meta.yaml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index 32b3dd32db53e..4b7311f7dde10 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.6.2" %} +{% set version = "0.7.1" %} package: name: "{{ name|lower }}" @@ -7,28 +7,30 @@ package: source: url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: f3e47042ff6be9fc22cb8a2b695692bd33cefe07b768f17c1b942940f20faa3a + sha256: 52ac47a43399d0d67d45773e613619b3b1e03e2d9654d7cb544a53507bcb4eab build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . -vvv entry_points: - - assembly_finder = assembly_finder.__main__:cli + - assembly_finder=assembly_finder.__main__:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation run_exports: - {{ pin_subpackage('assembly_finder', max_pin="x.x") }} requirements: host: - - python >=3.9,<=3.12 + - python >=3.10 - pip run: - - python >=3.9,<=3.12 - - snakemake-minimal >=7.32.4,<8 + - python >=3.10 + - snakemake-minimal >=7.32.4 - pulp <2.8 + - snaketool-utils >=0.0.4 + - attrmap >=0.0.7 + - pyyaml >=6.0 - pandas >=2.2.1 - rich-click >=1.7.4 - - ncbi-datasets-cli >=16.10.1 test: commands: From 5034a7465e3070d72734ef753df088702859843c Mon Sep 17 00:00:00 2001 From: Abdallah Meknas <139805477+ameknas-phac@users.noreply.github.com> Date: Thu, 25 Apr 2024 19:52:13 -0400 Subject: [PATCH 1752/1813] Update Sequenoscope: Rebuild version 0.0.5 with Updated Dependencies (#47385) * sequenoscope release * fixed build number to 0 * fixed v in version * updated summary * added run export * fixed url * changed python version * changed python version to 3.7.12 restricted * changed build to host and unrestricted python version * changed versions of packages and license * updated steup.py for v0.0.5 * updated license * Rebuild sequenoscope with updated dependencies --------- Co-authored-by: ameknas --- recipes/sequenoscope/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequenoscope/meta.yaml b/recipes/sequenoscope/meta.yaml index 2d9184f285845..59a8abbf2222c 100644 --- a/recipes/sequenoscope/meta.yaml +++ b/recipes/sequenoscope/meta.yaml @@ -9,7 +9,7 @@ source: sha256: aac98d2ab286da78c9c4b621e52cac2a16fd6ea3d1200b05861bf82e3fb49701 build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage("sequenoscope", max_pin="x.x") }} @@ -26,7 +26,7 @@ requirements: - pysam >=0.16.0 - minimap2 >=2.26 - mash >=2.3 - - fastp >=0.22.0 + - fastp >=0.22.0,<=0.23.2 - seqtk >=1.4 - plotly >=5.16.1 - biopython >=1.7 From a65a2e65e82440059d6c619f0fe3ecc21de33e75 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 20:08:17 -0400 Subject: [PATCH 1753/1813] Update snakemake-storage-plugin-fs to 1.0.4 (#47458) --- recipes/snakemake-storage-plugin-fs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-storage-plugin-fs/meta.yaml b/recipes/snakemake-storage-plugin-fs/meta.yaml index 11ffa3559dade..0790f6203c2b5 100644 --- a/recipes/snakemake-storage-plugin-fs/meta.yaml +++ b/recipes/snakemake-storage-plugin-fs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-fs" %} -{% set version = "1.0.3" %} +{% set version = "1.0.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_fs-{{ version }}.tar.gz - sha256: 36086fc8a2970fd89218683655c345907a5834f07416f6c1ddf370489398f9c8 + sha256: d9467d2d8f00689c6af6478f67f693373ce3cb0404d10c6d783997465d5110a9 build: noarch: python From 4f732d5be9921c4ac76d5fb2d3278f0b5e55bb29 Mon Sep 17 00:00:00 2001 From: zhenxian <920596906@qq.com> Date: Fri, 26 Apr 2024 08:32:29 +0800 Subject: [PATCH 1754/1813] Update meta.yaml (#47463) --- recipes/clair3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clair3/meta.yaml b/recipes/clair3/meta.yaml index 4775a888628fd..604a052449a64 100644 --- a/recipes/clair3/meta.yaml +++ b/recipes/clair3/meta.yaml @@ -7,10 +7,10 @@ package: source: url: http://www.bio8.cs.hku.hk/clair3/bioconda/Clair3_v{{ version }}.zip - sha256: 4f688f33c4dfac88924da4374ef43c47a6883b57d461388940e649df102c6d4d + sha256: b34bf1e722dc86a1c5362b4d8aa788a177d998f66c53b6d4ba709962f0926cc4 build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x") }} From 7ea7748721538f7d341c31210979490fdbfb5d6e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 21:05:14 -0400 Subject: [PATCH 1755/1813] Update snakemake to 8.11.0 (#47460) * Update snakemake to 8.11.0 * edit meta.yaml * python not --------- Co-authored-by: mencian --- recipes/snakemake/meta.yaml | 26 ++++++++++++++++---------- 1 file changed, 16 insertions(+), 10 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 53a7d88eb8bb7..fc8fa0f2e0d2a 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,17 +1,18 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.10.8" %} +{% set name = "snakemake" %} +{% set version = "8.11.0" %} package: - name: snakemake + name: {{ name }} version: {{ version }} source: - url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 75711faa668324f9e6c44a860f2f9645be358763a97ee411bb32f7a8f6dca6b7 + url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz + sha256: 1f49ac4fe87886b0c3db45aa2d4b257afa81bea862ac48ab2667b693cad274f0 build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage("snakemake", max_pin="x") }} @@ -44,6 +45,10 @@ test: about: home: https://snakemake.github.io license: MIT + license_family: MIT + license_file: LICENSE.md + dev_url: https://github.com/snakemake/snakemake + doc_url: https://snakemake.readthedocs.io/en/stable/ summary: A popular workflow management system aiming at full in-silico reproducibility. description: | Snakemake is a workflow management system that aims to reduce the complexity of creating @@ -57,11 +62,9 @@ extra: - linux-aarch64 identifiers: - doi:10.1093/bioinformatics/bts480 - - biotools:Snakemake + - biotools:snakemake skip-lints: - - uses_setuptools # uses pkg_resoures during run time - should_be_noarch_python # toplevel metapackage is noarch:generic - - missing_run_exports recipe-maintainers: - johanneskoester - corneliusroemer @@ -71,7 +74,7 @@ outputs: build: noarch: python - script: python -m pip install --no-deps --ignore-installed . + script: python -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv entry_points: - snakemake = snakemake.cli:main run_exports: @@ -81,7 +84,6 @@ outputs: host: - python >=3.11 - pip - - setuptools run: # Keep in sync with snakemake/setup.cfg - python >=3.11,<3.13 @@ -127,6 +129,10 @@ outputs: about: home: https://snakemake.github.io license: MIT + license_family: MIT + license_file: LICENSE.md + dev_url: https://github.com/snakemake/snakemake + doc_url: https://snakemake.readthedocs.io/en/stable/ summary: A popular workflow management system aiming at full in-silico reproducibility. description: | Snakemake is a workflow management system that aims to reduce the complexity From c6a62f0ea8ae82c15a6cf764157fd2fd12e60be9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 21:10:39 -0400 Subject: [PATCH 1756/1813] Update lighter to 1.1.3 (#47487) * Update lighter to 1.1.3 * add run_exports * fix typo --------- Co-authored-by: mencian --- recipes/lighter/build.sh | 10 ++++++---- recipes/lighter/meta.yaml | 16 ++++++++++------ 2 files changed, 16 insertions(+), 10 deletions(-) diff --git a/recipes/lighter/build.sh b/recipes/lighter/build.sh index 5cb63338fa2d8..a4d8ba8f7756a 100644 --- a/recipes/lighter/build.sh +++ b/recipes/lighter/build.sh @@ -1,5 +1,7 @@ -#!/bin/sh +#!/bin/bash -mkdir -p $PREFIX/bin -make CXX=${CXX} CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" -cp lighter $PREFIX/bin +mkdir -p ${PREFIX}/bin + +make CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +cp -f lighter ${PREFIX}/bin diff --git a/recipes/lighter/meta.yaml b/recipes/lighter/meta.yaml index 11f471c96217b..b33f35505bc38 100644 --- a/recipes/lighter/meta.yaml +++ b/recipes/lighter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "Lighter" %} -{% set version = "1.1.2" %} -{% set sha256 = "89abc34137beffc43382fbe53deb25c3c2f5cee7e6ca2b7f669931d70065993a" %} +{% set version = "1.1.3" %} +{% set sha256 = "c8a251c410805f82dad77e40661f0faf14ec82dedb3ff717094ba8ff4ef94465" %} package: name: '{{ name|lower }}' @@ -13,7 +13,9 @@ source: - 0001-makefile.patch build: - number: 6 + number: 0 + run_exports: + - {{ pin_subpackage('lighter', max_pin="x") }} requirements: build: @@ -21,8 +23,6 @@ requirements: - {{ compiler('cxx') }} host: - zlib - run: - - zlib test: commands: @@ -31,10 +31,14 @@ test: about: home: https://github.com/mourisl/Lighter - license: GPLv3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Lighter is a kmer-based error correction method for whole genome sequencing data + dev_url: https://github.com/mourisl/Lighter extra: identifiers: - biotools:{{ name }} + - doi:10.1186/s13059-014-0509-9 + - usegalaxy-eu:lighter From 3f6de83348675a10364d0c6b5bf97f05305af610 Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Thu, 25 Apr 2024 23:00:32 -0400 Subject: [PATCH 1757/1813] Update BinDash v2.3 (#47290) * Update BinDash v2.3 * clean up recipe * clean up recipe * clean up recipe * clean up recipe * clean up recipe * clean up recipe --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/bindash/build.sh | 1 - recipes/bindash/build_failure.linux-64.yaml | 104 -------------------- recipes/bindash/meta.yaml | 28 +++--- 3 files changed, 17 insertions(+), 116 deletions(-) delete mode 100644 recipes/bindash/build_failure.linux-64.yaml diff --git a/recipes/bindash/build.sh b/recipes/bindash/build.sh index 26b05df755bd5..83f5dedf13ec7 100644 --- a/recipes/bindash/build.sh +++ b/recipes/bindash/build.sh @@ -5,4 +5,3 @@ make VERBOSE=1 -j ${CPU_COUNT} install -d $PREFIX/bin install bindash $PREFIX/bin popd - diff --git a/recipes/bindash/build_failure.linux-64.yaml b/recipes/bindash/build_failure.linux-64.yaml deleted file mode 100644 index 5c45b9976d04e..0000000000000 --- a/recipes/bindash/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: bf400c5d79ff20f338f3a29d4eb02d4a42e02d5f4200e3a4c8fa6d6a9ebb8710 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Diff algorithm options - --minimal produce the smallest possible diff - -w, --ignore-all-space - ignore whitespace when comparing lines - -b, --ignore-space-change - ignore changes in amount of whitespace - --ignore-space-at-eol - ignore changes in whitespace at EOL - --ignore-cr-at-eol ignore carrier-return at the end of line - --ignore-blank-lines ignore changes whose lines are all blank - -I, --ignore-matching-lines - ignore changes whose all lines match - --indent-heuristic heuristic to shift diff hunk boundaries for easy reading - --patience generate diff using the "patience diff" algorithm - --histogram generate diff using the "histogram diff" algorithm - --diff-algorithm - choose a diff algorithm - --anchored generate diff using the "anchored diff" algorithm - --word-diff[=] show word diff, using to delimit changed words - --word-diff-regex - use to decide what a word is - --color-words[=] - equivalent to --word-diff=color --word-diff-regex= - --color-moved[=] - moved lines of code are colored differently - --color-moved-ws - how white spaces are ignored in --color-moved - - Other diff options - --relative[=] - when run from subdir, exclude changes outside and show relative paths - -a, --text treat all files as text - -R swap two inputs, reverse the diff - --exit-code exit with 1 if there were differences, 0 otherwise - --quiet disable all output of the program - --ext-diff allow an external diff helper to be executed - --textconv run external text conversion filters when comparing binary files - --ignore-submodules[=] - ignore changes to submodules in the diff generation - --submodule[=] - specify how differences in submodules are shown - --ita-invisible-in-index - hide 'git add -N' entries from the index - --ita-visible-in-index - treat 'git add -N' entries as real in the index - -S look for differences that change the number of occurrences of the specified string - -G look for differences that change the number of occurrences of the specified regex - --pickaxe-all show all changes in the changeset with -S or -G - --pickaxe-regex treat in -S as extended POSIX regular expression - -O control the order in which files appear in the output - --rotate-to show the change in the specified path first - --skip-to skip the output to the specified path - --find-object - look for differences that change the number of occurrences of the specified object - --diff-filter [(A|C|D|M|R|T|U|X|B)...[*]] - select files by diff type - --output output to a specific file - - -- Configuring done (0.5s) - -- Generating done (0.0s) - -- Build files have been written to: $SRC_DIR/release - $BUILD_PREFIX/bin/cmake -S$SRC_DIR -B$SRC_DIR/release --check-build-system CMakeFiles/Makefile.cmake 0 - $BUILD_PREFIX/bin/cmake -E cmake_progress_start $SRC_DIR/release/CMakeFiles $SRC_DIR/release//CMakeFiles/progress.marks - make -f CMakeFiles/Makefile2 all - make[1]: Entering directory '$SRC_DIR/release' - make -f CMakeFiles/bindash.dir/build.make CMakeFiles/bindash.dir/depend - make[2]: Entering directory '$SRC_DIR/release' - cd $SRC_DIR/release && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR $SRC_DIR/release $SRC_DIR/release $SRC_DIR/release/CMakeFiles/bindash.dir/DependInfo.cmake --color= - make[2]: Leaving directory '$SRC_DIR/release' - make -f CMakeFiles/bindash.dir/build.make CMakeFiles/bindash.dir/build - make[2]: Entering directory '$SRC_DIR/release' - [ 50%] Building CXX object CMakeFiles/bindash.dir/src/bindash.cpp.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DGIT_COMMIT_HASH="" -DGIT_DIFF_SHORTSTAT="" -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bindash-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O3 -DNDEBUG -Ofast -fopenmp -MD -MT CMakeFiles/bindash.dir/src/bindash.cpp.o -MF CMakeFiles/bindash.dir/src/bindash.cpp.o.d -o CMakeFiles/bindash.dir/src/bindash.cpp.o -c $SRC_DIR/src/bindash.cpp - /opt/conda/conda-bld/bindash_1685382869725/work/src/bindash.cpp: In function 'void cmddist(bool, bool, const std::vector&, const std::vector&, const Sketchargs&, const Distargs&)': - /opt/conda/conda-bld/bindash_1685382869725/work/src/bindash.cpp:361:63: error: aggregate 'std::array >, 2048> tophits_arr' has incomplete type and cannot be defined - 361 | std::array, ISIZE> tophits_arr; - | ^~~~~~~~~~~ - make[2]: *** [CMakeFiles/bindash.dir/build.make:76: CMakeFiles/bindash.dir/src/bindash.cpp.o] Error 1 - make[2]: Leaving directory '$SRC_DIR/release' - make[1]: *** [CMakeFiles/Makefile2:83: CMakeFiles/bindash.dir/all] Error 2 - make: *** [Makefile:91: all] Error 2 - make[1]: Leaving directory '$SRC_DIR/release' - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bindash_1685382869725/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/bindash/meta.yaml b/recipes/bindash/meta.yaml index 8e211caaf2494..1b5105f60619d 100644 --- a/recipes/bindash/meta.yaml +++ b/recipes/bindash/meta.yaml @@ -1,7 +1,8 @@ +{% set name = "bindash" %} {% set version = "2.3" %} package: - name: bindash + name: {{ name }} version: {{ version }} source: @@ -10,22 +11,22 @@ source: build: skip: True # [osx] - number: 1 + number: 2 run_exports: - - {{ pin_subpackage('bindash', max_pin="x.x") }} + - {{ pin_subpackage('bindash', max_pin="x") }} requirements: build: - make - - {{ compiler('c') }} - {{ compiler('cxx') }} - cmake - - llvm-openmp # [osx] host: - zlib + - libgomp # [linux] - llvm-openmp # [osx] run: - zlib + - libgomp # [linux] - llvm-openmp # [osx] test: @@ -33,14 +34,19 @@ test: - bindash --help 2>&1 | grep sketch about: - home: https://github.com/zhaoxiaofei/bindash - license: Apache-2.0 - license_family: APACHE - license_file: LICENSE - summary: Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop + home: https://github.com/zhaoxiaofei/bindash + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE + summary: "Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop." + dev_url: https://github.com/zhaoxiaofei/bindash extra: additional-platforms: - linux-aarch64 identifiers: - - doi:10.1371/journal.pgen.1007758 + - doi:10.1093/bioinformatics/bty651 + - doi:10.1101/2024.03.13.584875 + recipe-maintainers: + - jianshu93 + - zhaoxiaofei From f0d578b29bf403c50fff1b79399c3ce9abe2037c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Apr 2024 23:00:44 -0400 Subject: [PATCH 1758/1813] Update seqerakit to 0.4.7 (#47490) --- recipes/seqerakit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqerakit/meta.yaml b/recipes/seqerakit/meta.yaml index 992daf113f85d..d25275da10179 100644 --- a/recipes/seqerakit/meta.yaml +++ b/recipes/seqerakit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqerakit" %} -{% set version = "0.4.6" %} +{% set version = "0.4.7" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqerakit-{{ version }}.tar.gz - sha256: 286a9f7174f7ee242f90a3526dd018b67370a0f8cc9c66c220731b7a741433dd + sha256: ad87c8f9561811b09bb163da29914a9ef16e6b75dd6485bf776236d948a665a3 build: entry_points: From 70580af5e1b30f79c66c3cdabffd552e8af87011 Mon Sep 17 00:00:00 2001 From: Carsten-Ke <163016511+Carsten-Ke@users.noreply.github.com> Date: Fri, 26 Apr 2024 11:25:58 +0200 Subject: [PATCH 1759/1813] Add a new recipe for the radiant program (#46512) * Added a new recipe for the radiant program * radiant recipe: - added run_exports - corrected liscence to be GPLv3+ instead of GPLv3 * Fixing radiant recipe - changed compiler to cxx * fixing recipe - added conda dir as cmake prefix - set minimum-version of boost * trying to fix recipe - removed cmake generator - added cmake mimimum version - added variables at the beginning for easier future updates * added missing '{' * trying to fix cmake * splitting into meta.yaml and build.sh * added missing requirement sqlite * using newer radiant version * updated to correct radiant version * fixed install command * added openmp requirement * Update meta.yaml adden openmp as requirement * updated recipe * updated build for osx * fixes for mac * fixes for mac * removed unnecessary run requirement, changed liscence to SPDX format --------- Co-authored-by: Carsten Kemena --- recipes/radiant/build.sh | 6 ++++++ recipes/radiant/meta.yaml | 44 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 recipes/radiant/build.sh create mode 100644 recipes/radiant/meta.yaml diff --git a/recipes/radiant/build.sh b/recipes/radiant/build.sh new file mode 100644 index 0000000000000..9223f1a6f8a8a --- /dev/null +++ b/recipes/radiant/build.sh @@ -0,0 +1,6 @@ + +export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" +cmake -DCMAKE_INSTALL_PREFIX=$PREFIX -S . -B build +cmake --build build +cmake --install build + diff --git a/recipes/radiant/meta.yaml b/recipes/radiant/meta.yaml new file mode 100644 index 0000000000000..d79fe4d62761d --- /dev/null +++ b/recipes/radiant/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "radiant" %} +{% set version = "1.1.5" %} +{% set sha256 = "e3c37d15cdaf227f88ebd23e7ed55eee6d12c549a3521212f5e0d2655aa4dcad" %} + + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://zivgitlab.uni-muenster.de/domain-world/RADIANT/-/archive/{{ version }}/RADIANT-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('radiant', max_pin="x") }} + +requirements: + build: + - cmake >=3.15 + - make + - {{ compiler('cxx') }} + host: + - sqlite + - bzip2 + - zlib + - openmp + - boost-cpp >=1.77 + run: + - sqlite + - openmp + - boost-cpp >=1.77 +test: + commands: + - radiant -h + +about: + home: https://domainworld.uni-muenster.de/data/radiant-db/index.html + license: GPL-3.0-or-later + license_file: LICENSE + summary: Annotate proteomes with protein domains + description: | + This program rapidly annotates protein sequences with Pfam domains From 8f7d1f7210f1a5e9a3a2b374ff62e95b9f638d99 Mon Sep 17 00:00:00 2001 From: johnrandallia <153721406+johnrandallia@users.noreply.github.com> Date: Fri, 26 Apr 2024 10:26:47 +0100 Subject: [PATCH 1760/1813] Add metamate recipe by tjcreedy (#47380) * added metamate to bioconda * Added run_exports to metamate meta yaml file * changed skip to noarch * changed noarch generic to noarch python * worked on dependency issue with mafft --------- Co-authored-by: johnrandallia --- recipes/metamate/meta.yaml | 69 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 recipes/metamate/meta.yaml diff --git a/recipes/metamate/meta.yaml b/recipes/metamate/meta.yaml new file mode 100644 index 0000000000000..221da4c5f830c --- /dev/null +++ b/recipes/metamate/meta.yaml @@ -0,0 +1,69 @@ +{% set name = "metamate" %} +{% set version = "0.4.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/tjcreedy/metamate/archive/v{{ version }}.tar.gz + sha256: e86a26643f770dae3739d8bd70f1db1a0561ad4554113a5d60b007fd0089cfe3 + +build: + noarch: python + entry_points: + - metamate = metamate.metamate:main + - metaMATE = metamate.metamate:main + - filtertranslate = metamate.filtertranslate:main + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + run_exports: {{ pin_subpackage("metamate", max_pin="x") }} + number: 0 + +requirements: + build: + - python + - mafft + - pysam + - bbmap + - r-base + - biopython + - r-getopt + - r-ape + - r-fastcluster + - r-cluster + host: + - python + - bbmap + - pysam + - mafft + - r-base + - r-getopt + - r-ape + - r-fastcluster + - r-cluster + run: + - python >=3.6 + - biopython >=1.76 + - scipy >=1.4.1 + - pysam + - r-base + - bbmap + - mafft +test: + imports: + - metamate + commands: + - metamate --help + - metaMATE --help + - filtertranslate --help + +about: + home: https://github.com/tjcreedy/metamate + license: GPL-3.0 + license_file: LICENSE + summary: 'metaMATE: your metabarcoding friend!' + +extra: + recipe-maintainers: + - tjcreedy + - johnrandallia From a76f5bffa647502b1a16e55cb5982c59595911f6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Apr 2024 06:21:12 -0400 Subject: [PATCH 1761/1813] Update resistify to 0.1.1 (#47499) --- recipes/resistify/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/resistify/meta.yaml b/recipes/resistify/meta.yaml index ad45a542f97be..47d20d694a4aa 100644 --- a/recipes/resistify/meta.yaml +++ b/recipes/resistify/meta.yaml @@ -1,5 +1,5 @@ {% set name = "resistify" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4fb7a11d524bf740c0832368ca8f5724e29e94f945b81c50062f85c6c719612e + sha256: e4c0714e266d95626e9fcd55db4f2315bc0c2c2e6d953f31aeafe5df4e7ab678 build: noarch: python From d83b80f28a6c4926e0a083472441de5e6f2d6924 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Apr 2024 06:23:13 -0400 Subject: [PATCH 1762/1813] Update oakvar to 2.9.112 (#47496) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index e8904c0d61307..01269e9630b34 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.111" %} -{% set sha256 = "2d273a80238654ce5dffb0018d5ace3b1bd925a778e91534efaa083474b535c1" %} +{% set version = "2.9.112" %} +{% set sha256 = "2d913a92591c8de46a2465b265cf685203eed6a4f866c9b47c416080f88e488f" %} package: name: {{ name|lower }} From 4794828efad720c1db66ddd6216772500f962579 Mon Sep 17 00:00:00 2001 From: Xi Chen <38089207+xinehc@users.noreply.github.com> Date: Fri, 26 Apr 2024 18:24:24 +0800 Subject: [PATCH 1763/1813] update melon to 0.1.4 (#47497) --- recipes/melon/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/melon/meta.yaml b/recipes/melon/meta.yaml index 64f69442d1011..db69fad0e80f4 100644 --- a/recipes/melon/meta.yaml +++ b/recipes/melon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "melon" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/xinehc/melon/archive/refs/tags/v{{ version }}.tar.gz - sha256: 099790947f54cca51ab0a47536cb846f884757db785822f04b540324a0bc6839 + sha256: ccb509d5e2cfbcf1d64af3b9073a0a07fe15d8e724fc12c7a419b9ff52ac1ccb build: noarch: python @@ -28,6 +28,7 @@ requirements: - seqkit - numpy - scipy + - tqdm test: imports: From 8f30f89b55b15a9e87db4b065a198deab6a7b1a7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Apr 2024 07:21:02 -0400 Subject: [PATCH 1764/1813] Update varvamp to 1.1.3 (#47502) --- recipes/varvamp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index 8926113ede596..e3c567cded62a 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "1.1.2" %} +{% set version = "1.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 391281c3f00436f88a63b659afbac5e32a215964e4ee9c0f82cbd0dcc4dcefec + sha256: e65a8af027d32ee6626a8768fe8e373132a3ac8f00845b005b4ed80c5630e041 build: entry_points: From 58ed59b57baafe6a1646f37451eab2e0567012cf Mon Sep 17 00:00:00 2001 From: Lee Katz Date: Fri, 26 Apr 2024 10:14:10 -0400 Subject: [PATCH 1765/1813] Add Perl-bio-kmer Bio::Kmer module (#47486) * perl-bio-seqfeature * address errors for bld.bat and having tests * init from conda-forge * pin package * perl-threaded => perl * remove perl-bio-seqfeature from this specific PR * relax jellyfish vh version * jellyfish => kmer-jellyfish * simplify tests * bump to v0.55 to avoid zcat bug --- recipes/perl-bio-kmer/LICENSE | 21 ++++++++++++ recipes/perl-bio-kmer/meta.yaml | 58 +++++++++++++++++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 recipes/perl-bio-kmer/LICENSE create mode 100644 recipes/perl-bio-kmer/meta.yaml diff --git a/recipes/perl-bio-kmer/LICENSE b/recipes/perl-bio-kmer/LICENSE new file mode 100644 index 0000000000000..85d11a5a1ccef --- /dev/null +++ b/recipes/perl-bio-kmer/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2017 Lee Katz + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/recipes/perl-bio-kmer/meta.yaml b/recipes/perl-bio-kmer/meta.yaml new file mode 100644 index 0000000000000..d894930b001b2 --- /dev/null +++ b/recipes/perl-bio-kmer/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "0.55" %} +{% set sha256 = "268745e0e4e20aad6462c3dd0958ac6a08b3b7eb43c0f326f9bb61e48f6547a0" %} + +# regex to use for Windows build hack +{% set win_patch = "s|C:\\\\strawberry\\\\c|$ENV{LIBRARY_PREFIX}\\\\mingw-w64|g" %} + +package: + name: perl-bio-kmer + version: {{ version }} + +source: + url: https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/Bio-Kmer-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("perl-bio-kmer", max_pin="x.x") }} + # needed for linker to find some m2w64 libs + merge_build_host: True # [win] + script: + - >- + perl Makefile.PL INSTALLDIRS=vendor NO_PERLLOCAL=1 NO_PACKLIST=1 MAKE=make + && (for /r . %%f in (*Makefile) do perl -i -pe "{{ win_patch }}" %%f) # [win] + && make + && make test + && make install VERBINST=1 + +requirements: + build: + - {{ compiler('c') }} # [unix] + - m2w64-gcc # [win] + - make + host: + - perl >=5.26 + - perl-file-which + - perl-bioperl + - kmer-jellyfish >=2 + run: + - perl >=5.26 + - perl-file-which + - perl-bioperl + - kmer-jellyfish >=2 + +test: + imports: + - Bio::Kmer + +about: + home: https://metacpan.org/pod/Bio::Kmer + summary: A perl module for helping with kmer analysis. + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - lskatz + #- conda-forge/perl-packagers From a0fb6339fd5bce40baa7cf928f9fc38b88c684dd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Apr 2024 12:15:28 -0400 Subject: [PATCH 1766/1813] Update mgnify-pipelines-toolkit to 0.1.2 (#47504) --- recipes/mgnify-pipelines-toolkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mgnify-pipelines-toolkit/meta.yaml b/recipes/mgnify-pipelines-toolkit/meta.yaml index 00a8968f37bce..8f1ded523c165 100644 --- a/recipes/mgnify-pipelines-toolkit/meta.yaml +++ b/recipes/mgnify-pipelines-toolkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mgnify-pipelines-toolkit" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgnify_pipelines_toolkit-{{ version }}.tar.gz - sha256: 925b5b154d2858289fc83339fedeb09e58019c0a319edf20d822bc658ff8825b + sha256: d120b42e175468d909c30aeed53c6e7343be57b13cb41a4cd5e7798bfa5e9d78 build: entry_points: From 80a6dc5dcdb99724894687a7fdae433af8464e3c Mon Sep 17 00:00:00 2001 From: John Palmer <32370730+jpalmer37@users.noreply.github.com> Date: Fri, 26 Apr 2024 18:14:00 -0400 Subject: [PATCH 1767/1813] Add tntblast v2.66 (#47477) * added tntblast v2.66 * fixed hash * attempt mpich compilation * minor fix --------- Co-authored-by: John Palmer Co-authored-by: Dan Fornika --- recipes/tntblast/build.sh | 3 ++- recipes/tntblast/meta.yaml | 7 +++++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/tntblast/build.sh b/recipes/tntblast/build.sh index 9faf1b0cc953d..31f9a2bcebb87 100644 --- a/recipes/tntblast/build.sh +++ b/recipes/tntblast/build.sh @@ -1,6 +1,5 @@ #!/bin/bash -sed -i.bak 's/-DUSE_MPI//g' Makefile sed -i.bak '/BLAST_DIR =/d' Makefile export INCLUDE_PATH="${BUILD_PREFIX}/include" @@ -10,6 +9,8 @@ export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BUILD_PREFIX}/lib" export LDFLAGS="-lm -lz -L${BUILD_PREFIX}/lib" export CPPFLAGS="-I${BUILD_PREFIX}/include" +export CXX="${BUILD_PREFIX}/bin/mpicxx" + make CC="${CXX}" INC="${CPPFLAGS}" LIBS="${LDFLAGS}" all mkdir -p $PREFIX/bin diff --git a/recipes/tntblast/meta.yaml b/recipes/tntblast/meta.yaml index 1879071879028..e10695d06f338 100644 --- a/recipes/tntblast/meta.yaml +++ b/recipes/tntblast/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tntblast" %} -{% set version = "2.61" %} +{% set version = "2.66" %} package: name: {{ name|lower }} @@ -12,22 +12,25 @@ build: source: url: https://github.com/jgans/thermonucleotideBLAST/archive/refs/tags/v{{ version }}.tar.gz - sha256: c2c8862ea772e7a655183b037995d02f319a04e3b359b447069b5f8fc0d11ec4 + sha256: 46f4ea4a1a8c3fe1a659cd54da847fd66c6a588d643d90be814412078b92da9e requirements: build: - make - {{ compiler('cxx') }} + - mpich - openmp #[linux] - llvm-openmp #[osx] - zlib host: - openmp #[linux] - llvm-openmp #[osx] + - mpich - zlib run: - openmp #[linux] - llvm-openmp #[osx] + - mpich - zlib test: From 71f363836545ff8699f25d20022f308c153d11ce Mon Sep 17 00:00:00 2001 From: Catherine Chahrour <74187550+CChahrour@users.noreply.github.com> Date: Sat, 27 Apr 2024 13:28:30 +0100 Subject: [PATCH 1768/1813] update seqnado (#47514) * update snakemake dependency * increase build --- recipes/seqnado/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqnado/meta.yaml b/recipes/seqnado/meta.yaml index 0d5423f036b96..96fbd7eb7d54e 100644 --- a/recipes/seqnado/meta.yaml +++ b/recipes/seqnado/meta.yaml @@ -11,7 +11,7 @@ source: build: - number: 0 + number: 1 noarch: python script_env: - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} @@ -42,7 +42,7 @@ requirements: - seaborn - setuptools-scm - singularity - - snakemake >=7.32.4, <8.0.0 + - snakemake >=8, <9 - snakemake-wrapper-utils - tracknado - wget From d4b3572baa696695ea0d5cc4e4aee7e6b26fb7ae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:10:35 -0400 Subject: [PATCH 1769/1813] Update rasusa to 1.0.0 (#47533) * Update rasusa to 1.0.0 * Update min rust version * add testing for subcommands --------- Co-authored-by: Michael Hall --- recipes/rasusa/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/rasusa/meta.yaml b/recipes/rasusa/meta.yaml index b61dc1feb6422..202169f0e6dba 100644 --- a/recipes/rasusa/meta.yaml +++ b/recipes/rasusa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.0" %} +{% set version = "1.0.0" %} {% set name = "rasusa" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: 903fa09fd7f7cc92880953131487186c3fbf539a127dc82f502559f9c1e9c11a + sha256: 7dba1d0cd6776031b13f5ef1e18212c9b37e9fb1fa4c81a1235f2e0460f6d89d build: number: 0 @@ -16,17 +16,20 @@ build: requirements: build: - - rust >=1.70 + - rust >=1.74.1 - {{ compiler('c') }} # [not win] test: commands: - rasusa --help + - rasusa reads --help + - rasusa aln --help + - rasusa cite about: home: https://github.com/mbhall88/rasusa license: MIT - summary: Randomly subsample sequencing reads to a specified coverage + summary: Randomly subsample sequencing reads or alignments license_file: LICENSE extra: From f6d24f5c4a7cbd54462e63b657b597c0a80c8e1e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:24:03 -0400 Subject: [PATCH 1770/1813] Update vsearch to 2.28.1 (#47507) --- recipes/vsearch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index 4f166d6926624..c1aa24bd39cde 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.27.1" %} -{% set sha256 = "54666bcd9434fb7636c5b292a67e7c194e809e631bbe8f4f86b85fb47e863abc" %} +{% set version = "2.28.1" %} +{% set sha256 = "4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c" %} package: name: vsearch From 8d78908c20cb2cdee02be33a249823dc948853c3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:24:15 -0400 Subject: [PATCH 1771/1813] Update ntedit to 2.0.2 (#47513) --- recipes/ntedit/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ntedit/meta.yaml b/recipes/ntedit/meta.yaml index bfca8d2deb1dd..b88758d97416c 100644 --- a/recipes/ntedit/meta.yaml +++ b/recipes/ntedit/meta.yaml @@ -1,18 +1,18 @@ {% set name = "ntedit" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x") }} source: url: https://github.com/bcgsc/ntEdit/releases/download/v{{ version }}/ntEdit-{{ version }}.tar.gz - sha256: e686ef5e49139a50dd3983ac2ac8b2771c918e2b3530884fa0f612d811163111 + sha256: 314bc1a39c2d382786ee64d83a1b8c4519e5c9feb0203b1b7f4ab0d9087cf6c5 requirements: build: From 4261499af847e449e5bd88074fd3a8d07c576b81 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:37:42 -0400 Subject: [PATCH 1772/1813] Update sdeper to 1.2.0 (#47525) --- recipes/sdeper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sdeper/meta.yaml b/recipes/sdeper/meta.yaml index bd72e1eace202..22d7453514edc 100755 --- a/recipes/sdeper/meta.yaml +++ b/recipes/sdeper/meta.yaml @@ -1,7 +1,7 @@ # This is the recipe file to publish SDePER to Bioconda {% set name = "sdeper" %} -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} package: name: "{{ name|lower }}" @@ -9,7 +9,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 9b02688715cf283521102f7a48e260b92b6fb8baf63295158a23d5e91ad96215 + sha256: d4ea77888be125cbebc1185937778d058e065332aac0f991bc67659e8e597161 build: number: 0 From 4d0aa43c2aa4b5fb4ba20064c637c5b90faa1bf9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:37:50 -0400 Subject: [PATCH 1773/1813] Update quatradis to 1.3.0 (#47531) --- recipes/quatradis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/quatradis/meta.yaml b/recipes/quatradis/meta.yaml index 995cf25751c82..a91fb4a8cd361 100644 --- a/recipes/quatradis/meta.yaml +++ b/recipes/quatradis/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.2.0" %} +{% set version="1.3.0" %} package: name: quatradis @@ -6,7 +6,7 @@ package: source: url: https://github.com/quadram-institute-bioscience/QuaTradis/archive/refs/tags/{{ version }}.tar.gz - sha256: f6595d8f69f98a99818fcc3c7797533e663271cfe477c8c3c9c961416c21deb5 + sha256: 8634c61c93073028fc35df46b3d1337e7716924051c336a12172c65e1adb2e74 build: number: 0 From f18a7dce39fdb3010978eb875e8021f8c6620f91 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:37:56 -0400 Subject: [PATCH 1774/1813] Update wgd to 2.0.34 (#47530) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index 5b062a4fafe5c..9e7ab5e50ff1c 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.33" %} +{% set version = "2.0.34" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: d5158f42f536412bdb034dca99d79377a53c45f6450aca0e294bbed7a6a99b07 + sha256: e0afe1ab8b1cd220519d1f562cb899f63d0bdce4ed7664589479a999f66f4d1a build: number: 0 From 9ea573f6a8e65afba4d4a95815ba7c012d05a8ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:38:07 -0400 Subject: [PATCH 1775/1813] Update r-classdiscovery to 3.4.5 (#47529) * Update r-classdiscovery to 3.4.5 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-classdiscovery/meta.yaml | 40 ++++++------------------------ 1 file changed, 7 insertions(+), 33 deletions(-) diff --git a/recipes/r-classdiscovery/meta.yaml b/recipes/r-classdiscovery/meta.yaml index 4993bba3a183f..031a2df080c26 100644 --- a/recipes/r-classdiscovery/meta.yaml +++ b/recipes/r-classdiscovery/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '3.4.0' %} +{% set version = '3.4.5' %} package: name: r-classdiscovery @@ -8,16 +8,17 @@ source: url: - {{ cran_mirror }}/src/contrib/ClassDiscovery_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/ClassDiscovery/ClassDiscovery_{{ version }}.tar.gz - sha256: 5a18e607ba5753bb8026a27ff73df6ad9f77ff186a82050b90d1fac6ee96871a + sha256: 61bcee1d18cb213f4fbe4ca5f6e3051192823a9e919c4010efd5f74aedd1e04c build: noarch: generic - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage("r-classdiscovery", max_pin="x") }} -# Suggests: xtable requirements: host: - r-base @@ -36,39 +37,12 @@ requirements: test: commands: - # You can put additional test commands to be run here. - - $R -e "library('ClassDiscovery')" # [not win] - - "\"%R%\" -e \"library('ClassDiscovery')\"" # [win] + - $R -e "library('ClassDiscovery')" about: home: http://oompa.r-forge.r-project.org/ - license: Apache (== 2.0) + license: Apache-2.0 summary: 'Defines the classes used for "class discovery" problems in the OOMPA project (). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance. ' license_family: APACHE - -# The original CRAN metadata for this package was: - -# Package: ClassDiscovery -# Version: 3.3.9 -# Date: 2018-09-27 -# Title: Classes and Methods for "Class Discovery" with Microarrays or Proteomics -# Author: Kevin R. Coombes -# Maintainer: Kevin R. Coombes -# Depends: R (>= 3.0), cluster, oompaBase (>= 3.0.1) -# Imports: methods, stats, graphics, grDevices, mclust, oompaData, Biobase -# Suggests: xtable -# Description: Defines the classes used for "class discovery" problems in the OOMPA project (). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance. -# License: Apache License (== 2.0) -# LazyLoad: yes -# biocViews: Microarray, Clustering -# URL: http://oompa.r-forge.r-project.org/ -# NeedsCompilation: no -# Packaged: 2018-10-03 11:25:11 UTC; Kevin -# Repository: CRAN -# Date/Publication: 2018-10-03 22:02:55 UTC - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml From 3ccdc9dc80ee85dd695dad3284cf7e02620e780a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:39:04 -0400 Subject: [PATCH 1776/1813] Update sigprofilermatrixgenerator to 1.2.26 (#47515) --- recipes/sigprofilermatrixgenerator/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sigprofilermatrixgenerator/meta.yaml b/recipes/sigprofilermatrixgenerator/meta.yaml index 731b6038b1fc1..e608211acf216 100644 --- a/recipes/sigprofilermatrixgenerator/meta.yaml +++ b/recipes/sigprofilermatrixgenerator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SigProfilerMatrixGenerator" %} -{% set version = "1.2.25" %} +{% set version = "1.2.26" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/SigProfilerMatrixGenerator-{{ version }}.tar.gz - sha256: 6de36147ddd19befe1066d5e482bc9a94a9006a95e757c8e47d52fb5cd2862eb + sha256: c405db79fbe5e42447e3ec2ae8b85519cc2ab8e94b23f66f50e8963345b2f797 build: entry_points: From 157a79842a46b49edd0c1c223deed4399d83c3ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:39:13 -0400 Subject: [PATCH 1777/1813] Update assembly_finder to 0.7.2 (#47512) --- recipes/assembly_finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index 4b7311f7dde10..24c1e9923c775 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.7.1" %} +{% set version = "0.7.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 52ac47a43399d0d67d45773e613619b3b1e03e2d9654d7cb544a53507bcb4eab + sha256: 83476551d22f2336ae40a3412f7b38011341006933d87fc3bb7e6b763a1b89bd build: number: 0 From 776822225e0afde1e3bd4f9c042c1e9f76353218 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:39:25 -0400 Subject: [PATCH 1778/1813] Update mess to 0.8.2 (#47511) --- recipes/mess/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mess/meta.yaml b/recipes/mess/meta.yaml index a3cdfb5f6c92c..5a859cde3d82a 100644 --- a/recipes/mess/meta.yaml +++ b/recipes/mess/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MeSS" %} -{% set version = "0.8.0" %} +{% set version = "0.8.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3fc888a31f6c9acd71552b26f9e42f963a34382eeccb2215afcc872ba0f54c3e + sha256: 157ce1f1426211ead7deebf5da1620d65de2b3f89cc3cf20fdf55a42df146a6d build: number: 0 From 4fd433e34d32eb293d63b746b3c31f400039d927 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:39:37 -0400 Subject: [PATCH 1779/1813] Update pyteomics to 4.7.2 (#47510) --- recipes/pyteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyteomics/meta.yaml b/recipes/pyteomics/meta.yaml index feb0274d684e9..cdc52d031adeb 100644 --- a/recipes/pyteomics/meta.yaml +++ b/recipes/pyteomics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.7.1" %} +{% set version = "4.7.2" %} package: name: pyteomics @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz - sha256: e5e5d3204af3050b9bf95bb64941b6156331335216e125ac253e7c8dfb1cf0ab + sha256: 9c2cc22f0e45574c62a8e8628a8412d7b5688ccdd679b2f6ddc6fbbee2abb26d build: noarch: python From dcb35b9d6b61b52d983ef2b5ca7e61887bc0735b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:39:48 -0400 Subject: [PATCH 1780/1813] Update pybiolib to 1.1.2017 (#47508) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 39d9de7ef54a2..d120e0ac38eba 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.2013" %} +{% set version = "1.1.2017" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 43d712ee8e801aaa4c53009f48549744cd997d2e43d5a466710e9cf616324491 + sha256: 97d0a1b00973038dd7d29cccaec6dbf4d711137c4d6fb8073291596ce5f91490 build: noarch: python From 75ec76c69eeca8458c4c97d0fd23cca822ce772d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:39:58 -0400 Subject: [PATCH 1781/1813] Update melon to 0.1.5 (#47506) --- recipes/melon/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/melon/meta.yaml b/recipes/melon/meta.yaml index db69fad0e80f4..1859cf993abd9 100644 --- a/recipes/melon/meta.yaml +++ b/recipes/melon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "melon" %} -{% set version = "0.1.4" %} +{% set version = "0.1.5" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/xinehc/melon/archive/refs/tags/v{{ version }}.tar.gz - sha256: ccb509d5e2cfbcf1d64af3b9073a0a07fe15d8e724fc12c7a419b9ff52ac1ccb + sha256: 4cd77a0262e589c125627d89fea9a340ccbf0dc53b67bfc40f907008c95864da build: noarch: python From f7f9f8747b35e1cbd0c4d9fffd809ac280bb35a6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Apr 2024 22:40:54 -0400 Subject: [PATCH 1782/1813] Update snakemake-storage-plugin-gcs to 1.0.0 (#47503) --- recipes/snakemake-storage-plugin-gcs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-storage-plugin-gcs/meta.yaml b/recipes/snakemake-storage-plugin-gcs/meta.yaml index ce5f67acc91ae..b269805339223 100644 --- a/recipes/snakemake-storage-plugin-gcs/meta.yaml +++ b/recipes/snakemake-storage-plugin-gcs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-gcs" %} -{% set version = "0.1.4" %} +{% set version = "1.0.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_gcs-{{ version }}.tar.gz - sha256: f8c2ebbc2b44ff5a87f7507b26bd1176de98ae80e93339b2ae65f722d17dbc24 + sha256: a5ca15813a74ae18d41cc5dbde0792e2ec5bfc32e8615d458b41dded1b430e14 build: noarch: python From 9ca2fc7b3428fee635aca66904f2d4d2497832b9 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 05:42:36 +0300 Subject: [PATCH 1783/1813] trf: add linux-aarch64 build (#47518) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/trf/build.sh | 2 +- recipes/trf/meta.yaml | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/trf/build.sh b/recipes/trf/build.sh index bc49ad10f8798..50dcf40faed52 100644 --- a/recipes/trf/build.sh +++ b/recipes/trf/build.sh @@ -1,5 +1,5 @@ #!/bin/sh ./configure --prefix=$PREFIX CPPFLAGS=-DUNIXCONSOLE -make +make -j ${CPU_COUNT} make install diff --git a/recipes/trf/meta.yaml b/recipes/trf/meta.yaml index ed87b9b7fba4e..ad38c60967d71 100644 --- a/recipes/trf/meta.yaml +++ b/recipes/trf/meta.yaml @@ -11,7 +11,9 @@ source: build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} requirements: build: @@ -30,5 +32,7 @@ about: summary: 'Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:Trf From 3bcfe88557aaae749d9305db62df6e9143137942 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 05:42:46 +0300 Subject: [PATCH 1784/1813] gappa: add linux-aarch64 build (#47517) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/gappa/build.sh | 2 +- recipes/gappa/meta.yaml | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/gappa/build.sh b/recipes/gappa/build.sh index 27a186617836b..2456a7bb675f9 100644 --- a/recipes/gappa/build.sh +++ b/recipes/gappa/build.sh @@ -4,7 +4,7 @@ if [ "$(uname)" == Darwin ] ; then CXXFLAGS="$CXXFLAGS -fopenmp" fi -make +make -j ${CPU_COUNT} mkdir -p $PREFIX/bin diff --git a/recipes/gappa/meta.yaml b/recipes/gappa/meta.yaml index f0fd77ade36d8..e2fc50494968b 100644 --- a/recipes/gappa/meta.yaml +++ b/recipes/gappa/meta.yaml @@ -3,7 +3,9 @@ package: version: "0.8.4" build: - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('gappa', max_pin='x.x') }} source: url: https://github.com/lczech/gappa/archive/refs/tags/v0.8.4.tar.gz @@ -31,5 +33,7 @@ about: summary: Genesis Applications for Phylogenetic Placement Analysis extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1093/bioinformatics/bty767 From 588a8074f8e51d8d8e777a54269cba64482b94d5 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 05:51:00 +0300 Subject: [PATCH 1785/1813] ska2: add linux-aarch64 build (#47522) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ska2/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/ska2/meta.yaml b/recipes/ska2/meta.yaml index 5351d482863ab..99e4a3aa8967f 100644 --- a/recipes/ska2/meta.yaml +++ b/recipes/ska2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ea7234428f253638b2093abdd6c8b1e8362ecad0ba56e3b29700af9a4481d911 build: - number: 0 + number: 1 script: "cargo install --no-track --locked --verbose --root \"${PREFIX}\" --path ." run_exports: - {{ pin_subpackage("ska2", max_pin="x.x") }} @@ -29,3 +29,7 @@ about: license_family: APACHE license_file: LICENSE summary: SKA (Split Kmer Analysis) version 2 + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From d6c8a5929cb577ae0c415f56d46b46861714c36f Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 05:51:11 +0300 Subject: [PATCH 1786/1813] raxml-ng: add linux-aarch64 build (#47521) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/raxml-ng/build.sh | 4 ++-- recipes/raxml-ng/meta.yaml | 14 ++++++++------ 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/recipes/raxml-ng/build.sh b/recipes/raxml-ng/build.sh index 6209021d02b11..1ad4779811365 100644 --- a/recipes/raxml-ng/build.sh +++ b/recipes/raxml-ng/build.sh @@ -4,7 +4,7 @@ mkdir build_pthreads pushd build_pthreads cmake .. - make + make -j ${CPU_COUNT} install -d ${PREFIX}/bin install ../bin/raxml-ng ${PREFIX}/bin popd @@ -15,7 +15,7 @@ then mkdir build_mpi pushd build_mpi CXX=mpicxx cmake -DUSE_MPI=ON .. - make + make -j ${CPU_COUNT} install -d ${PREFIX}/bin install ../bin/raxml-ng-mpi ${PREFIX}/bin popd diff --git a/recipes/raxml-ng/meta.yaml b/recipes/raxml-ng/meta.yaml index 0da1caa7dbbc0..a662b76ebaf8e 100644 --- a/recipes/raxml-ng/meta.yaml +++ b/recipes/raxml-ng/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e14ec2233f0c9d9f497eab8f77c73512c8c787e44ed3839bd25fd35658ef89e3 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('raxml-ng', max_pin="x") }} @@ -40,8 +40,10 @@ about: summary: "RAxML Next Generation: faster, easier-to-use and more flexible" extra: - container: - # openmpi needs ssh client - extended-base: true - identifiers: - - doi:10.1093/bioinformatics/btz305 + additional-platforms: + - linux-aarch64 + container: + # openmpi needs ssh client + extended-base: true + identifiers: + - doi:10.1093/bioinformatics/btz305 From ea48038ae734e87eb2509c76378c91be3fde4734 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 05:51:19 +0300 Subject: [PATCH 1787/1813] ucsc-bigwigsummary: add linux-aarch64 build (#47520) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-bigwigsummary/build.sh | 12 ++++++------ recipes/ucsc-bigwigsummary/htmshell.patch | 11 +++++++++++ recipes/ucsc-bigwigsummary/meta.yaml | 9 ++++++++- 3 files changed, 25 insertions(+), 7 deletions(-) create mode 100644 recipes/ucsc-bigwigsummary/htmshell.patch diff --git a/recipes/ucsc-bigwigsummary/build.sh b/recipes/ucsc-bigwigsummary/build.sh index 6f51d7e922ae0..bc10870454d00 100644 --- a/recipes/ucsc-bigwigsummary/build.sh +++ b/recipes/ucsc-bigwigsummary/build.sh @@ -1,13 +1,13 @@ #!/bin/bash mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export L="${LDFLAGS}" mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bigWigSummary && make) +(cd kent/src/lib && make -j ${CPU_COUNT}) +(cd kent/src/htslib && make -j ${CPU_COUNT}) +(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) +(cd kent/src/hg/lib && make -j ${CPU_COUNT}) +(cd kent/src/utils/bigWigSummary && make -j ${CPU_COUNT}) cp bin/bigWigSummary "$PREFIX/bin" chmod +x "$PREFIX/bin/bigWigSummary" diff --git a/recipes/ucsc-bigwigsummary/htmshell.patch b/recipes/ucsc-bigwigsummary/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-bigwigsummary/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-bigwigsummary/meta.yaml b/recipes/ucsc-bigwigsummary/meta.yaml index 1f60c5321b8a9..ca2ca18d6646b 100644 --- a/recipes/ucsc-bigwigsummary/meta.yaml +++ b/recipes/ucsc-bigwigsummary/meta.yaml @@ -12,10 +12,13 @@ source: sha256: {{ sha256 }} patches: - include.patch + - htmshell.patch build: - number: 0 + number: 1 skip: True # [osx] + run_exports: + - {{ pin_subpackage(package|lower, max_pin=None) }} requirements: build: @@ -45,3 +48,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "Extract summary information from a bigWig file." + +extra: + additional-platforms: + - linux-aarch64 From 21d2de75fa259a3778f1591e25745f1b6ac508af Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 05:51:29 +0300 Subject: [PATCH 1788/1813] ucsc-twobittofa: add linux-aarch64 build (#47519) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-twobittofa/build.sh | 12 ++++++------ recipes/ucsc-twobittofa/htmshell.patch | 11 +++++++++++ recipes/ucsc-twobittofa/meta.yaml | 7 ++++++- 3 files changed, 23 insertions(+), 7 deletions(-) create mode 100644 recipes/ucsc-twobittofa/htmshell.patch diff --git a/recipes/ucsc-twobittofa/build.sh b/recipes/ucsc-twobittofa/build.sh index 56c2c2edc3e97..8f25dc11367ae 100644 --- a/recipes/ucsc-twobittofa/build.sh +++ b/recipes/ucsc-twobittofa/build.sh @@ -1,13 +1,13 @@ #!/bin/bash mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export L="${LDFLAGS}" mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/twoBitToFa && make) +(cd kent/src/lib && make -j ${CPU_COUNT}) +(cd kent/src/htslib && make -j ${CPU_COUNT}) +(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) +(cd kent/src/hg/lib && make -j ${CPU_COUNT}) +(cd kent/src/utils/twoBitToFa && make -j ${CPU_COUNT}) cp bin/twoBitToFa "$PREFIX/bin" chmod +x "$PREFIX/bin/twoBitToFa" diff --git a/recipes/ucsc-twobittofa/htmshell.patch b/recipes/ucsc-twobittofa/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-twobittofa/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-twobittofa/meta.yaml b/recipes/ucsc-twobittofa/meta.yaml index 60da0e0bea610..9469bbbab5f7e 100644 --- a/recipes/ucsc-twobittofa/meta.yaml +++ b/recipes/ucsc-twobittofa/meta.yaml @@ -12,10 +12,11 @@ source: sha256: {{ sha256 }} patches: - include.patch + - htmshell.patch build: skip: True # [osx] - number: 0 + number: 1 ignore_run_exports: - libpng - libuuid @@ -50,3 +51,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "Convert all or part of .2bit file to fasta" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 92d5bf0e7c4d5c217b020f7a34f290bda8776da7 Mon Sep 17 00:00:00 2001 From: JohannesGawron <93670909+JohannesGawron@users.noreply.github.com> Date: Mon, 29 Apr 2024 04:53:26 +0200 Subject: [PATCH 1789/1813] Add r-dsb recipe (#47505) * added r-dsb recipe * shortened summary * removed *.bat files * added run_exports and noarch specification to recipe --- recipes/r-dsb/build.sh | 22 ++++++++ recipes/r-dsb/meta.yaml | 110 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 132 insertions(+) create mode 100644 recipes/r-dsb/build.sh create mode 100644 recipes/r-dsb/meta.yaml diff --git a/recipes/r-dsb/build.sh b/recipes/r-dsb/build.sh new file mode 100644 index 0000000000000..df943f40e3e3d --- /dev/null +++ b/recipes/r-dsb/build.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +# 'Autobrew' is being used by more and more packages these days +# to grab static libraries from Homebrew bottles. These bottles +# are fetched via Homebrew's --force-bottle option which grabs +# a bottle for the build machine which may not be macOS 10.9. +# Also, we want to use conda packages (and shared libraries) for +# these 'system' dependencies. See: +# https://github.com/jeroen/autobrew/issues/3 +export DISABLE_AUTOBREW=1 + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION +# shellcheck disable=SC2086 +${R} CMD INSTALL --build . ${R_ARGS} + +# Add more build steps here, if they are necessary. + +# See +# https://docs.conda.io/projects/conda-build +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-dsb/meta.yaml b/recipes/r-dsb/meta.yaml new file mode 100644 index 0000000000000..953d980c21491 --- /dev/null +++ b/recipes/r-dsb/meta.yaml @@ -0,0 +1,110 @@ +{% set version = '1.0.3' %} + +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-dsb + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/dsb_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/dsb/dsb_{{ version }}.tar.gz + sha256: 6287a25d1f67f5a5dfc8af5558e884c59d7ea7fea49a9c08c53b30023069f0f7 + +build: + merge_build_host: True # [win] + # If this is a new build for the same version, increment the build number. + number: 0 + # no skip + noarch: generic + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + run_exports: + - {{ pin_subpackage('r-dsb', max_pin="x") }} + +# Suggests: testthat, knitr, rmarkdown, ggplot2, cowplot, spelling +requirements: + build: + - {{ posix }}zip # [win] + + host: + - r-base + - bioconductor-limma + - r-magrittr + - r-mclust + + run: + - r-base + - bioconductor-limma + - r-magrittr + - r-mclust + +test: + commands: + # You can put additional test commands to be run here. + - $R -e "library('dsb')" # [not win] + - "\"%R%\" -e \"library('dsb')\"" # [win] + + # You can also put a file called run_test.py, run_test.sh, or run_test.bat + # in the recipe that will be run at test time. + + # requires: + # Put any additional test requirements here. + +about: + home: https://github.com/niaid/dsb + license: CC0 | file LICENSE + summary: "Normalizing and denoising protein expression data from droplet-based single cell profiling" + description: "This lightweight R package provides a method for normalizing and denoising protein + expression data from droplet based single cell experiments. Raw protein Unique Molecular + Index (UMI) counts from sequencing DNA-conjugated antibody derived tags (ADT) in + droplets (e.g. 'CITE-seq') have substantial measurement noise. Our experiments and + computational modeling revealed two major components of this noise: 1) protein-specific + noise originating from ambient, unbound antibody encapsulated in droplets that can + be accurately inferred via the expected protein counts detected in empty droplets, + and 2) droplet/cell-specific noise revealed via the shared variance component associated + with isotype antibody controls and background protein counts in each cell. This + package normalizes and removes both of these sources of noise from raw protein data + derived from methods such as 'CITE-seq', 'REAP-seq', 'ASAP-seq', 'TEA-seq', 'proteogenomic' + data from the Mission Bio platform, etc. See the vignette for tutorials on how to + integrate dsb with 'Seurat' and 'Bioconductor' and how to use dsb in 'Python'. Please + see our paper Mul\xE8 M.P., Martins A.J., and Tsang J.S. Nature Communications 2022 + for more details on the method." + license_family: CC + license_file: + - LICENSE + +# The original CRAN metadata for this package was: + +# Package: dsb +# Type: Package +# Title: Normalize & Denoise Droplet Single Cell Protein Data (CITE-Seq) +# Version: 1.0.3 +# Authors@R: c(person(given = "Matthew", family = "Mule", role = c("aut", "cre"), email = "mattmule@gmail.com", comment = c(ORCID = "0000-0001-8457-2716")), person(given = "Andrew", family = "Martins", role = "aut", email = "andrew.martins@nih.gov", comment = c(ORCID = "0000-0002-1832-1924")), person(given = "John", family = "Tsang", role = "pdr", email = "john.tsang@nih.gov", comment = c(ORCID = "0000-0003-3186-3047"))) +# Description: This lightweight R package provides a method for normalizing and denoising protein expression data from droplet based single cell experiments. Raw protein Unique Molecular Index (UMI) counts from sequencing DNA-conjugated antibody derived tags (ADT) in droplets (e.g. 'CITE-seq') have substantial measurement noise. Our experiments and computational modeling revealed two major components of this noise: 1) protein-specific noise originating from ambient, unbound antibody encapsulated in droplets that can be accurately inferred via the expected protein counts detected in empty droplets, and 2) droplet/cell-specific noise revealed via the shared variance component associated with isotype antibody controls and background protein counts in each cell. This package normalizes and removes both of these sources of noise from raw protein data derived from methods such as 'CITE-seq', 'REAP-seq', 'ASAP-seq', 'TEA-seq', 'proteogenomic' data from the Mission Bio platform, etc. See the vignette for tutorials on how to integrate dsb with 'Seurat' and 'Bioconductor' and how to use dsb in 'Python'. Please see our paper Mule M.P., Martins A.J., and Tsang J.S. Nature Communications 2022 for more details on the method. +# License: CC0 | file LICENSE +# Encoding: UTF-8 +# LazyData: true +# RoxygenNote: 7.1.1 +# Depends: R (>= 2.10) +# biocViews: +# Imports: magrittr, limma, mclust, stats +# Suggests: testthat, knitr, rmarkdown, ggplot2, cowplot, spelling +# URL: https://github.com/niaid/dsb +# BugReports: https://github.com/niaid/dsb/issues +# VignetteBuilder: knitr, rmarkdown +# Language: en-US +# NeedsCompilation: no +# Packaged: 2023-03-17 16:55:52 UTC; matthewmule +# Author: Matthew Mule [aut, cre] (), Andrew Martins [aut] (), John Tsang [pdr] () +# Maintainer: Matthew Mule +# Repository: CRAN +# Date/Publication: 2023-03-17 23:20:02 UTC + +# See +# https://docs.conda.io/projects/conda-build for +# more information about meta.yaml From 9bd5c6fdd6f838d66a16093599ee3d7a57f2bd68 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 05:54:06 +0300 Subject: [PATCH 1790/1813] fastani: add linux-aarch64 build (#47455) * fastani: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Replace openmp with libgomp for Linux Signed-off-by: Martin Tzvetanov Grigorov * Try without re-defining memcpy on Linux ARM64 Signed-off-by: Martin Tzvetanov Grigorov * Wrap memcpy() only for Linux x86_64 Signed-off-by: Martin Tzvetanov Grigorov * Update the patch - created with `diff -u old new` Signed-off-by: Martin Tzvetanov Grigorov * Apply the patch only for Linux ARM64 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/fastani/build.sh | 2 +- recipes/fastani/meta.yaml | 10 ++++++++-- .../wrap-memcpy-only-for-linux-x86_64.patch | 16 ++++++++++++++++ 3 files changed, 25 insertions(+), 3 deletions(-) create mode 100644 recipes/fastani/wrap-memcpy-only-for-linux-x86_64.patch diff --git a/recipes/fastani/build.sh b/recipes/fastani/build.sh index 72d67bb7674dc..8008be92c6a0a 100644 --- a/recipes/fastani/build.sh +++ b/recipes/fastani/build.sh @@ -12,5 +12,5 @@ mkdir -p $PREFIX/bin ./bootstrap.sh ./configure --prefix=$PREFIX --with-gsl=$PREFIX -make +make -j ${CPU_COUNT} make install diff --git a/recipes/fastani/meta.yaml b/recipes/fastani/meta.yaml index c24fad941222f..82c05c4c98336 100644 --- a/recipes/fastani/meta.yaml +++ b/recipes/fastani/meta.yaml @@ -7,13 +7,15 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('fastani', max_pin="x") }} source: url: https://github.com/ParBLiSS/{{ name }}/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} + patches: + - wrap-memcpy-only-for-linux-x86_64.patch # [linux and aarch64] requirements: build: @@ -24,7 +26,7 @@ requirements: host: - zlib - gsl >=2.6, <2.7.1 - - openmp # [linux] + - libgomp # [linux] - llvm-openmp # [osx] - clangdev # [osx] - libcxx >=4.0 # [osx] @@ -44,3 +46,7 @@ about: license_family: Apache license_file: LICENSE summary: 'FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).' + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file diff --git a/recipes/fastani/wrap-memcpy-only-for-linux-x86_64.patch b/recipes/fastani/wrap-memcpy-only-for-linux-x86_64.patch new file mode 100644 index 0000000000000..4e0f3cd97e967 --- /dev/null +++ b/recipes/fastani/wrap-memcpy-only-for-linux-x86_64.patch @@ -0,0 +1,16 @@ +--- Makefile.in 2024-04-27 14:58:06.238060909 +0300 ++++ Makefile.in.new 2024-04-27 14:58:01.910293221 +0300 +@@ -2,10 +2,11 @@ + CPPFLAGS += @amcppflags@ + + UNAME_S=$(shell uname -s) ++UNAME_M=$(shell uname -m) + + ifeq ($(UNAME_S),Darwin) #macOS clang + CXXFLAGS += -mmacosx-version-min=10.7 -stdlib=libc++ -Xpreprocessor -fopenmp -lomp +-else ++elif ($(UNAME_M),x86_64) + CXXFLAGS += -include src/common/memcpyLink.h -Wl,--wrap=memcpy + CFLAGS += -include src/common/memcpyLink.h + endif + From b2483ffa95e5220c5028fc1ab1f18922dfdb8a58 Mon Sep 17 00:00:00 2001 From: Kristina Gagalova Date: Mon, 29 Apr 2024 11:42:26 +0800 Subject: [PATCH 1791/1813] Ripcal recipe 2.0 (#46792) * occultercut recepy added * updated occultercut * update for run_exports * adding gcc libs * updated meta * test with excluded prefix * lint test * clean up recipe * edit build.sh * recipe ripcal-derip * fixing errors * correct recipe and name coincidence * attempt to fix run_exports * removed packeges that are not necessary * source fixed * fix link download * remove unzip from build * fixing path install * new attempt to change path to perl scripts * change syntax of build * attempt to correct path * attempt to fix path * fix path * fix syntax * attempt to fix * fix typo * fix path * license file added * licence file fixed * fix path perl * bioperlcore added * remove cpan module * fix perl version * test perl without version * try again by removing versions * attempt fixing variable * attempt to fix bioperl path * fix BioPerl --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ripcal/LICENSE | 674 +++++++++++++++++++++++++++++++++++++++ recipes/ripcal/build.sh | 26 ++ recipes/ripcal/meta.yaml | 45 +++ 3 files changed, 745 insertions(+) create mode 100644 recipes/ripcal/LICENSE create mode 100644 recipes/ripcal/build.sh create mode 100644 recipes/ripcal/meta.yaml diff --git a/recipes/ripcal/LICENSE b/recipes/ripcal/LICENSE new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/ripcal/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/ripcal/build.sh b/recipes/ripcal/build.sh new file mode 100644 index 0000000000000..b1d42ef3349f2 --- /dev/null +++ b/recipes/ripcal/build.sh @@ -0,0 +1,26 @@ +#!/bin/bash + +export LANGUAGE=en_US.UTF-8 +export LC_ALL=en_US.UTF-8 + +# Creating necessary directories +mkdir -p "${PREFIX}/bin" + +# Copying executable files to bin directory +cp "${SRC_DIR}/perl/"* "${PREFIX}/bin/" + +# Fixing permissions +chmod +x "${PREFIX}/bin/deripcal" +chmod +x "${PREFIX}/bin/ripcal" +chmod +x "${PREFIX}/bin/ripcal_summarise" + +sed -i "s:/usr/bin/perl:/usr/bin/env perl:" "${PREFIX}/bin/ripcal" +sed -i "s/use Bio::Perl;/use BioPerl;/" "${PREFIX}/bin/ripcal" + +sed -i "s:/usr/bin/perl:/usr/bin/env perl:" "${PREFIX}/bin/deripcal" +sed -i "s:/usr/bin/perl:/usr/bin/env perl:" "${PREFIX}/bin/ripcal_summarise" + +export "PERL5LIB=${PREFIX}/lib/perl5/site_perl/5.32.1/:${PERL5LIB}" + +sed -i.bak '/^use Tk/ s/^/# /' "${PREFIX}/bin/ripcal" + diff --git a/recipes/ripcal/meta.yaml b/recipes/ripcal/meta.yaml new file mode 100644 index 0000000000000..47583a3f8627d --- /dev/null +++ b/recipes/ripcal/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "ripcal" %} +{% set version = "2.0" %} +{% set sha256 = "6f18af1c6fedde17430e023e3a5c1ab56f14910694d83ba90ee738d8d48188bd" %} + +package: + name: '{{ name }}' + version: '{{ version }}' + +source: + url: "https://sourceforge.net/projects/ripcal/files/RIPCAL/RIPCAL_{{ version }}/{{ name }}2_install.zip" + sha256: '{{ sha256 }}' + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('ripcal', max_pin="x") }} + +requirements: + run: + - perl >=5.32.1 + - perl-math-round + - perl-bioperl >=1.7.2 + - perl-bioperl-core >=1.7.2 + - perl-getopt-long + - perl-mime-base64 + - perl-gd + +test: + commands: + - 'ripcal --help' + - 'deripcal --help' + +about: + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: 'RIPCAL is used for the bioinformatic analysis of repeat-induced point mutation (RIP) in fungal genome sequences' + home: https://sourceforge.net/projects/ripcal + +extra: + identifiers: + - https://doi.org/10.1186/1471-2105-9-478 + recipe-maintainers: + - KristinaGagalova From bb9f1fe1d57a0fd66474ddbe82826ec6d462aed8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Apr 2024 02:03:43 -0400 Subject: [PATCH 1792/1813] Update r-pathfindr to 2.4.0 (#47527) * Update r-pathfindr to 2.4.0 * clean up recipe * add java back * edit build.sh --------- Co-authored-by: mencian --- recipes/r-pathfindr/build.sh | 2 +- recipes/r-pathfindr/meta.yaml | 32 +++++++++++++++----------------- 2 files changed, 16 insertions(+), 18 deletions(-) diff --git a/recipes/r-pathfindr/build.sh b/recipes/r-pathfindr/build.sh index dadf215407d10..e19c0e9e0c900 100644 --- a/recipes/r-pathfindr/build.sh +++ b/recipes/r-pathfindr/build.sh @@ -1,6 +1,6 @@ #!/bin/bash +export LC_ALL=en_US.UTF-8 export DISABLE_AUTOBREW=1 ${R} CMD INSTALL --build . ${R_ARGS} - diff --git a/recipes/r-pathfindr/meta.yaml b/recipes/r-pathfindr/meta.yaml index 4a76e0d8a98db..9cb3d79495a58 100644 --- a/recipes/r-pathfindr/meta.yaml +++ b/recipes/r-pathfindr/meta.yaml @@ -1,22 +1,20 @@ -{% set version = '2.3.1' %} - -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} +{% set name = "r-pathfindr" %} +{% set version = "2.4.0" %} package: - name: r-pathfindr - version: {{ version|replace("-", "_") }} + name: {{ name }} + version: {{ version }} source: url: - {{ cran_mirror }}/src/contrib/pathfindR_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/pathfindR/pathfindR_{{ version }}.tar.gz - sha256: 03b766e4799dbf2083717cd9a8a302beaaa58eaec9499b3b9b9e5e55e50c5694 + sha256: 9e03c7c189857097c0f6645599d9c8ed0738b6e68b077baa481ef17a068dfef6 build: - merge_build_host: True # [win] number: 0 noarch: generic + merge_build_host: True # [win] rpaths: - lib/R/lib/ - lib/ @@ -24,11 +22,6 @@ build: - {{ pin_subpackage("r-pathfindr", max_pin="x") }} requirements: - build: - - {{ posix }}zip # [win] - - cross-r-base {{ r_base }} # [build_platform != target_platform] - - openjdk 8.* - host: - r-base - openjdk 8.* @@ -36,6 +29,8 @@ requirements: - r-dbi - bioconductor-keggrest - bioconductor-kegggraph + - bioconductor-ggkegg + - r-httr - r-r.utils - r-doparallel - r-foreach @@ -50,7 +45,6 @@ requirements: - bioconductor-org.hs.eg.db - r-pathfindr.data >=2.0 - r-rmarkdown - run: - r-base - openjdk 8.* @@ -58,6 +52,8 @@ requirements: - r-dbi - bioconductor-keggrest - bioconductor-kegggraph + - bioconductor-ggkegg + - r-httr - r-r.utils - r-doparallel - r-foreach @@ -75,11 +71,10 @@ requirements: test: commands: - - $R -e "library('pathfindR')" # [not win] - - "\"%R%\" -e \"library('pathfindR')\"" # [win] + - $R -e "library('pathfindR')" about: - home: https://egeulgen.github.io/pathfindR/, https://github.com/egeulgen/pathfindR + home: "https://github.com/egeulgen/pathfindR" license: MIT summary: 'Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein @@ -99,6 +94,9 @@ about: license_file: - '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT' - LICENSE + doc_url: "https://egeulgen.github.io/pathfindR/" + dev_url: "https://github.com/egeulgen/pathfindR" + extra: recipe-maintainers: - egeulgen From 5fd5087113e2030db85980ffe9d87c24f1a8f1ff Mon Sep 17 00:00:00 2001 From: Andrea Guarracino <62253982+AndreaGuarracino@users.noreply.github.com> Date: Mon, 29 Apr 2024 01:22:48 -0500 Subject: [PATCH 1793/1813] add `wgatools` (#47528) * add wgatools * add `run_exports` * fix `sha256` * add `cmake` * add `pkg-config`, `openssl`, and `perl` * `export`s * `make` * try `export`s * host and run * remove compiler in host and run * clean up recipe --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/wgatools/build.sh | 14 +++++++++++++ recipes/wgatools/meta.yaml | 43 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 recipes/wgatools/build.sh create mode 100644 recipes/wgatools/meta.yaml diff --git a/recipes/wgatools/build.sh b/recipes/wgatools/build.sh new file mode 100644 index 0000000000000..2fd3e311f3e0a --- /dev/null +++ b/recipes/wgatools/build.sh @@ -0,0 +1,14 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +export LIBRARY_PATH="${PREFIX}/lib" +export INCLUDE_PATH="${PREFIX}/include" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/wgatools/meta.yaml b/recipes/wgatools/meta.yaml new file mode 100644 index 0000000000000..7b3eeaf7aaf9c --- /dev/null +++ b/recipes/wgatools/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "wgatools" %} +{% set version = "0.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/wjwei-handsome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: a03f0b6c843f8566aebaa9486292fbcb37d7e900c2f1c4691b0c9340b96fd892 + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('rust') }} + - make + - cmake + - pkg-config + host: + - openssl + run: + - perl + +test: + commands: + - wgatools --help + +about: + home: https://github.com/wjwei-handsome/{{ name }} + license: MIT + license_family: MIT + license_file: LICENSE + summary: "A Rust library and tools for whole genome alignment files" + dev_url: https://github.com/wjwei-handsome/{{ name }} + +extra: + recipe-maintainers: + - AndreaGuarracino From 49a05f7cc8fd61aa2848dd9708fe719cc17781b4 Mon Sep 17 00:00:00 2001 From: Tom Stanton Date: Mon, 29 Apr 2024 17:18:00 +1000 Subject: [PATCH 1794/1813] Update kaptive (#47524) * Update kaptive * Update meta.yaml * Update meta.yaml * clean up recipe * clean up recipe --------- Co-authored-by: mencian --- recipes/kaptive/build.sh | 9 -------- recipes/kaptive/meta.yaml | 43 +++++++++++++++++++++++++----------- recipes/kaptive/post-link.sh | 5 ----- 3 files changed, 30 insertions(+), 27 deletions(-) delete mode 100644 recipes/kaptive/build.sh delete mode 100644 recipes/kaptive/post-link.sh diff --git a/recipes/kaptive/build.sh b/recipes/kaptive/build.sh deleted file mode 100644 index 8792b601d75fa..0000000000000 --- a/recipes/kaptive/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash -mkdir -p $PREFIX/bin -mv kaptive.py $PREFIX/bin -chmod +x $PREFIX/bin/kaptive.py -mkdir -p $PREFIX/opt/kaptive_reference_database -mkdir -p $PREFIX/opt/kaptive_sample_data - -mv $SRC_DIR/reference_database/*.* $PREFIX/opt/kaptive_reference_database/ -mv $SRC_DIR/sample_data/*.* $PREFIX/opt/kaptive_reference_database/ diff --git a/recipes/kaptive/meta.yaml b/recipes/kaptive/meta.yaml index 84ac9c281a046..60b9b840802d8 100644 --- a/recipes/kaptive/meta.yaml +++ b/recipes/kaptive/meta.yaml @@ -1,30 +1,47 @@ -{% set version = "2.0.6" %} +{% set name = "kaptive" %} +{% set version = "3.0.0b1" %} package: - name: kaptive + name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/katholt/Kaptive/archive/v{{ version }}.tar.gz - sha256: 53a90693c00a05b55e7ebb6f2eb999a89f47f6c279600ac2018f831287119019 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/kaptive-{{ version }}.tar.gz + sha256: ee3f4dc710b91580db84f9eb24bfc8adf6bc9d52871a018f0aabb0c4b6dd5790 build: + entry_points: + - kaptive = kaptive.__main__:main + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir number: 0 - noarch: generic + run_exports: + - {{ pin_subpackage('kaptive', max_pin="x") }} requirements: + host: + - python >=3.9 + - pip run: - - python >=3 - - biopython <1.78 - - numpy - - blast >=2.3.0 + - python >=3.9 + - biopython + - dna_features_viewer test: + imports: + - kaptive commands: - - kaptive.py -h + - kaptive --help about: - home: https://github.com/katholt/Kaptive - license: GPL3 + home: "https://kaptive.readthedocs.io/en/latest" + dev_url: "https://github.com/klebgenomics/Kaptive" + summary: "Reports information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies." + license: "GPL-3.0-or-later" + license_family: GPL3 license_file: LICENSE - summary: Reports information about surface polysaccharide loci for Klebsiella and Acinetobacter baumannii genome assemblies + doc_url: "https://kaptive.readthedocs.io/en/latest" + +extra: + recipe-maintainers: + - tomdstanton diff --git a/recipes/kaptive/post-link.sh b/recipes/kaptive/post-link.sh deleted file mode 100644 index 04984ece131ff..0000000000000 --- a/recipes/kaptive/post-link.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash -echo "Kaptive is installed with its database at...$PREFIX/opt/kaptive_reference_database. When you run kaptive.py, you can specify -path to one of the databases as the following example: -kaptive.py -fa /path/to/a/file.fasta -k $PREFIX/opt/kaptive_reference_database/Klebsiella_k_locus_primary_reference.gbk -o output -" From f29127ff3b16c4e225405f969851c70a41b1d5d6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Apr 2024 03:45:05 -0400 Subject: [PATCH 1795/1813] Update riassigner to 0.4.1 (#47535) --- recipes/riassigner/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/riassigner/meta.yaml b/recipes/riassigner/meta.yaml index 25837214f09ca..deaa6d07bf1c6 100644 --- a/recipes/riassigner/meta.yaml +++ b/recipes/riassigner/meta.yaml @@ -1,5 +1,5 @@ {% set name = "riassigner" %} -{% set version = "0.4.0" %} +{% set version = "0.4.1" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/riassigner-{{ version }}.tar.gz - sha256: 32d0306ba76feb7d470eb504b2bd382f0d78c85f7795bc275abad0c874ee7d61 + sha256: 316bc4399f0de586a8ba31e3d38b834307277bf84b7dcc2b51dfe2cead807299 build: noarch: python From f9975d80c8a094c6ded0766dc9148b74e31a1a86 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Mon, 29 Apr 2024 09:59:18 +0200 Subject: [PATCH 1796/1813] Update mosdepth to 0.3.8 (#47494) * Update mosdepth to 0.3.8 * Unpinning nim * Trying nim <=1.6.20 * Fixing nim to v1.6.20 * Trying nim v2.0.0 * Trying nim v2.0.2 * Trying to skip build for osx * Trying to build nim v1.6 from source * Another attempt at building nim v1.6 from source * debug * DEBUG2 * DEBUG3 * A bit of cleanup * Removing debug statements --- recipes/mosdepth/build.sh | 5 +++++ recipes/mosdepth/meta.yaml | 3 +-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/mosdepth/build.sh b/recipes/mosdepth/build.sh index ae5ff06f5f3cb..8d17d6407e85d 100755 --- a/recipes/mosdepth/build.sh +++ b/recipes/mosdepth/build.sh @@ -1,6 +1,11 @@ #!/bin/sh if [[ ${target_platform} == osx-64 ]] ; then + curl -SL https://github.com/nim-lang/nightlies/releases/download/latest-version-1-6/macosx_x64.tar.xz -o macosx_x64.tar.xz + tar -xzf macosx_x64.tar.xz + cd nim-1.6.* + export PATH="$PWD/bin:$PATH" + cd .. curl -SL https://github.com/brentp/mosdepth/archive/refs/tags/v${PKG_VERSION}.tar.gz -o mosdepth-latest.tar.gz tar -xzf mosdepth-latest.tar.gz cd mosdepth-${PKG_VERSION} diff --git a/recipes/mosdepth/meta.yaml b/recipes/mosdepth/meta.yaml index 14d5aaa549798..a1a2bd00817be 100755 --- a/recipes/mosdepth/meta.yaml +++ b/recipes/mosdepth/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.7" %} +{% set version = "0.3.8" %} package: name: mosdepth @@ -13,7 +13,6 @@ requirements: build: - {{ compiler('c') }} - curl - - nim <=1.6.2 host: - htslib >=1.19.1 run: From 02c4cd11f6e2d2db949d61a28d218a310b89bb61 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 11:32:26 +0300 Subject: [PATCH 1797/1813] pysamstats: add linux-aarch64 build (#47536) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/pysamstats/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/pysamstats/meta.yaml b/recipes/pysamstats/meta.yaml index f6f765ba811b1..e0e59504cd7e9 100644 --- a/recipes/pysamstats/meta.yaml +++ b/recipes/pysamstats/meta.yaml @@ -7,7 +7,9 @@ source: md5: 050294fe9fe99aae3b07ea28f6cbe449 build: - number: 10 + number: 11 + run_exports: + - {{ pin_subpackage('pysamstats', max_pin="x") }} requirements: build: @@ -41,5 +43,7 @@ about: on sequence alignments from a SAM, BAM or CRAM file. extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:pysamstats From 8236a6238ee678ea9ecd028148d1c6062da46f16 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 11:32:42 +0300 Subject: [PATCH 1798/1813] ucsc-bigwigtowig: add linux-aarch64 build (#47538) * ucsc-bigwigtowig: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Add run_exports for ucsc-bigwigtowig Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/ucsc-bigwigtowig/build.sh | 12 ++++++------ recipes/ucsc-bigwigtowig/htmshell.patch | 11 +++++++++++ recipes/ucsc-bigwigtowig/meta.yaml | 9 ++++++++- 3 files changed, 25 insertions(+), 7 deletions(-) create mode 100644 recipes/ucsc-bigwigtowig/htmshell.patch diff --git a/recipes/ucsc-bigwigtowig/build.sh b/recipes/ucsc-bigwigtowig/build.sh index 41c737003ef7d..a437ceb086a47 100644 --- a/recipes/ucsc-bigwigtowig/build.sh +++ b/recipes/ucsc-bigwigtowig/build.sh @@ -1,13 +1,13 @@ #!/bin/bash mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export L="${LDFLAGS}" mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bigWigToWig && make) +(cd kent/src/lib && make -j ${CPU_COUNT}) +(cd kent/src/htslib && make -j ${CPU_COUNT}) +(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) +(cd kent/src/hg/lib && make -j ${CPU_COUNT}) +(cd kent/src/utils/bigWigToWig && make -j ${CPU_COUNT}) cp bin/bigWigToWig "$PREFIX/bin" chmod +x "$PREFIX/bin/bigWigToWig" diff --git a/recipes/ucsc-bigwigtowig/htmshell.patch b/recipes/ucsc-bigwigtowig/htmshell.patch new file mode 100644 index 0000000000000..1e6f87375ed01 --- /dev/null +++ b/recipes/ucsc-bigwigtowig/htmshell.patch @@ -0,0 +1,11 @@ +--- kent/src/lib/htmshell.c 2024-03-27 10:56:44.493892141 +0200 ++++ kent/src/lib/htmshell.c 2024-03-27 10:57:01.073792396 +0200 +@@ -713,7 +713,7 @@ + puts("Status: 400\r"); + puts("Content-Type: text/plain; charset=UTF-8\r"); + puts("\r"); +-if (format != NULL && args != NULL) ++if (format != NULL) + { + vfprintf(stdout, format, args); + fprintf(stdout, "\n"); diff --git a/recipes/ucsc-bigwigtowig/meta.yaml b/recipes/ucsc-bigwigtowig/meta.yaml index 72927f2fed2f3..31e4bcee47493 100644 --- a/recipes/ucsc-bigwigtowig/meta.yaml +++ b/recipes/ucsc-bigwigtowig/meta.yaml @@ -12,10 +12,13 @@ source: sha256: {{ sha256 }} patches: - include.patch + - htmshell.patch build: - number: 0 + number: 1 skip: True # [osx] + run_exports: + - {{ pin_subpackage(package, max_pin="x") }} requirements: build: @@ -45,3 +48,7 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "Convert bigWig to wig. This will keep more of the same structure of the original wig than bigWigToBedGraph does, but still will break up large stepped sections into smaller ones." + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From f4f9beb26002649efbaf3dbe08ef4da0cd02e096 Mon Sep 17 00:00:00 2001 From: Rafael Mamede Date: Mon, 29 Apr 2024 15:00:13 +0100 Subject: [PATCH 1799/1813] Update chewBBACA to v3.3.5 (#47509) * Updated chewBBACA recipe. * Updated Biopython and Pandas versions. * Updated recipe URL. * Updated hash. --- recipes/chewbbaca/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index 8dbb1f8eacb80..8d41f613a5ce0 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,13 +1,15 @@ {% set name = 'chewBBACA' %} -{% set version = '3.3.4' %} +{% set version = '3.3.5' %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 3e9debdd29fe67741b81041ffeb3b05946018ef273b7876daf033ec433f6e293 + url: https://github.com/B-UMMI/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + # url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 6cf063286b55f55e33f75789eb5beaa59a1b7ca454f1a8bd89bb84a67aef1cde + # sha256: b54c5f4fb2f3c943f9ec51e5b81f4fb9a312fcc87fdea6e0a9f3edbebdf62308 build: number: 0 @@ -27,8 +29,8 @@ requirements: - python >=3.7 - numpy >=1.24.3 - scipy >=1.10.1 - - biopython >=1.78 - - pandas >=1.5.1 + - biopython >=1.79 + - pandas >=1.5.1,<2.1 - plotly >=5.8.0 - requests >=2.27.1 - sparqlwrapper >=2.0.0 From 3bf333bece7025401ba3ba8751c2795394b79d07 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 19:31:54 +0300 Subject: [PATCH 1800/1813] mmseqs2: re-build for linux-aarch64 support (#47549) mmseqs2 added `linux-aarch64` as an additional platform with 51b9013 but the build infrastructure wasn't ready at the time Signed-off-by: Martin Tzvetanov Grigorov --- recipes/mmseqs2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/mmseqs2/meta.yaml b/recipes/mmseqs2/meta.yaml index ff7ace052d96d..7343528cfb308 100644 --- a/recipes/mmseqs2/meta.yaml +++ b/recipes/mmseqs2/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('mmseqs2', max_pin=None) }} From 14d32d27e00ce20e0a19541513178783a81772c2 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 29 Apr 2024 19:32:44 +0300 Subject: [PATCH 1801/1813] samsum: add linux-aarch64 build (#47551) Signed-off-by: Martin Tzvetanov Grigorov --- recipes/samsum/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/samsum/meta.yaml b/recipes/samsum/meta.yaml index 6988988dd4f66..74767cb6d3564 100644 --- a/recipes/samsum/meta.yaml +++ b/recipes/samsum/meta.yaml @@ -10,11 +10,13 @@ source: sha256: 36b1fc0eaa4da1b7a70d2791357c7547612c9653e4e0ea7db39ba96cdd03ffc5 build: - number: 3 + number: 4 skip: True # [py2k] entry_points: - samsum = samsum.__main__:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: @@ -45,5 +47,7 @@ about: summary: A light-weight python package for summarizing sequence coverage from SAM and BAM files extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - cmorganl From 135c13ef93b58e4a71da986d5126b88e3a19f2cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Apr 2024 12:36:13 -0400 Subject: [PATCH 1802/1813] Update sylph to 0.6.1 (#47558) --- recipes/sylph/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml index b15925877f40c..06ecabc04a199 100644 --- a/recipes/sylph/meta.yaml +++ b/recipes/sylph/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.0" %} +{% set version = "0.6.1" %} package: name: sylph @@ -11,7 +11,7 @@ build: source: url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz - sha256: 751a6ab193d8f35c8ff65d3da6fd9ab29c9132e004b32b3159d2bedf371a05eb + sha256: 9f384ecf33d5eed57e518c1cc238ffb5ac68948dcf921731ba77ccbd02b57bdb requirements: build: From b6f621b6edaf5757df5296b52fef32e5384a9d82 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Apr 2024 14:29:52 -0400 Subject: [PATCH 1803/1813] Update ncbi-datasets-pylib to 16.6.1 (#47562) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index b2054dbde9eb1..9c5c206587b6f 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.6.0" %} -{% set sha256 = "5c5e0afef07ab5e28de96aff4f600316a82570fc0f233a0ba9daf531e92c475f" %} +{% set version = "16.6.1" %} +{% set sha256 = "06ab4409a00ac4c89465dea774558f8e51bc759f869072332399e5dcca0dded8" %} package: name: {{ name|lower }} From 5f219ef0f64384484d66b16bdd549881c6fa1c4b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Apr 2024 14:30:01 -0400 Subject: [PATCH 1804/1813] Update dxpy to 0.374.0 (#47563) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 3116782ae7bc7..422bee812a140 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.373.0" %} +{% set version = "0.374.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 060fb6d03ea0b76ddf6f5c553a39bb1100bf3dbdcc2761881a8860a8f0cccddd + sha256: 2e1f049d28815ae7c3a67f4e2302bc9fe23bd235780c927b82122d52badf9fcb build: number: 0 From 5a27385291a03a2360c098c97a8a802c425659c7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Apr 2024 17:59:41 -0400 Subject: [PATCH 1805/1813] Update clipkit to 2.3.0 (#47565) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index de6539728c1bd..f1259b6f9302f 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.2.6" %} +{% set version = "2.3.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 04564dc5399e1cd41ef812a5dc7865a23912b81ef423cbf07a9476ed4b84067b + sha256: 6e4f39f7b0e99b89de17aa57a26d1a7c6a1c064203b4fd436b413ad7d2e57ce5 build: number: 0 From fb46859103dcfc6b3ed272e05c3e096495b9bfa4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Apr 2024 18:00:15 -0400 Subject: [PATCH 1806/1813] Update phykit to 1.19.3 (#47566) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index 1544d1303dc18..718064f631068 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.19.2" %} +{% set version = "1.19.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 90a21339828521aca055257a08846099134889f274b1584f0d989e891a921cd3 + sha256: a23386e7913a42051c5b4d8e63abc3da3fe80c5bad1c5ac8834da636610ecc33 build: noarch: python From 4079afe585767bd0ab94a5bc3043ecb3c285a267 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Tue, 30 Apr 2024 00:00:36 +0200 Subject: [PATCH 1807/1813] fix python version dependency (#47544) --- recipes/hicmatrix/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hicmatrix/meta.yaml b/recipes/hicmatrix/meta.yaml index 6d8a5deba2f6a..827c3e2f7aeda 100644 --- a/recipes/hicmatrix/meta.yaml +++ b/recipes/hicmatrix/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8f431725f7aa548c9774c18e052dabfab10da72e0f0edf0f9dc512b66a4d9df4 build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv run_exports: @@ -18,7 +18,7 @@ build: requirements: host: - - python >=3.7 + - python >=3.8 - numpy >=1.20 - scipy >=1.2.* - intervaltree >=3.0.* @@ -26,7 +26,7 @@ requirements: - pandas >=0.25.* - cooler >=0.8.10 run: - - python >=3.7 + - python >=3.8 - numpy >=1.20 - scipy >=1.2.* - intervaltree >=3.0.* From 48b69e2e175aa8c57e1aa67662caef40b44f3df4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Apr 2024 18:05:17 -0400 Subject: [PATCH 1808/1813] Update snakemake to 8.11.1 (#47553) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index fc8fa0f2e0d2a..408d9f3f9b50b 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,7 +1,7 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg {% set name = "snakemake" %} -{% set version = "8.11.0" %} +{% set version = "8.11.1" %} package: name: {{ name }} @@ -9,7 +9,7 @@ package: source: url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz - sha256: 1f49ac4fe87886b0c3db45aa2d4b257afa81bea862ac48ab2667b693cad274f0 + sha256: 54df0a2fab378f334741459a48c5293f05ae372b31ac0fd4c3ec8d19f2309356 build: number: 0 From 535d6323b6ad8f2817a03b50a2021403128d9fc2 Mon Sep 17 00:00:00 2001 From: Moray Smith <65286772+SwiftSeal@users.noreply.github.com> Date: Tue, 30 Apr 2024 04:53:14 +0100 Subject: [PATCH 1809/1813] bump resistify to v0.1.1 (#47501) From 3244a399905724cad9ca2da6b2d75945ea7c9af9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Apr 2024 23:53:43 -0400 Subject: [PATCH 1810/1813] Update mitos to 2.1.9 (#47564) --- recipes/mitos/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index 23b7f8a7d3a1f..666d07b5d40bf 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "2.1.8" %} +{% set version = "2.1.9" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b97a1bb0270676816dcca73487d92e9794676327862dc059f797ac1df81bf3c1 + sha256: 88fc8980c815ae8497518ee7ff58ff69e51b1a35c1efe2ae9b0925b7c4f364f5 build: number: 0 From 4da359a55da3630ea5a97f6be591c7133c248077 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino <62253982+AndreaGuarracino@users.noreply.github.com> Date: Mon, 29 Apr 2024 23:12:49 -0500 Subject: [PATCH 1811/1813] Add `impg` (#47570) * `impg` recipe * update `sha256` --- recipes/impg/build.sh | 9 +++++++++ recipes/impg/meta.yaml | 35 +++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 recipes/impg/build.sh create mode 100644 recipes/impg/meta.yaml diff --git a/recipes/impg/build.sh b/recipes/impg/build.sh new file mode 100644 index 0000000000000..d70db500fe871 --- /dev/null +++ b/recipes/impg/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/impg/meta.yaml b/recipes/impg/meta.yaml new file mode 100644 index 0000000000000..04999b4407314 --- /dev/null +++ b/recipes/impg/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "impg" %} +{% set version = "0.2.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/pangenome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: ad2f4f4ea68e0c3feb5ecef5b408bb8649c4a67f5203ca7320434ed9a070c7ee + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +requirements: + build: + - {{ compiler('rust') }} + +test: + commands: + - impg --help + +about: + home: https://github.com/pangenome/{{ name }} + license: MIT + license_family: MIT + license_file: LICENSE + summary: "impg: implicit pangenome graphs" + dev_url: https://github.com/pangenome/{{ name }} + +extra: + recipe-maintainers: + - AndreaGuarracino From 82b3a2905a2a65ff738d361e3ac284f2f7a89ef9 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 30 Apr 2024 11:31:40 +0200 Subject: [PATCH 1812/1813] Bump bedgovcf to v0.1.1 (#47580) --- recipes/bedgovcf/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bedgovcf/meta.yaml b/recipes/bedgovcf/meta.yaml index 8fd41cd2aadef..8be27b7e3ba9a 100644 --- a/recipes/bedgovcf/meta.yaml +++ b/recipes/bedgovcf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.0' %} +{% set version = '0.1.1' %} {% set name = 'bedgovcf' %} package: @@ -7,9 +7,9 @@ package: source: - url: https://github.com/nvnieuwk/bedgovcf/releases/download/{{ version }}/bedgovcf-{{ version }}-darwin-amd64.tar.gz # [osx-amd64] - md5: 9e57370c3b7eced5da92cd11dc1984e5 # [osx] + md5: 978e24745b517395eb6d50cd0f8cdb1d # [osx] - url: https://github.com/nvnieuwk/bedgovcf/releases/download/{{ version }}/bedgovcf-{{ version }}-linux-amd64.tar.gz # [linux] - md5: bbe8e249c655a276657c6602524f7e39 # [linux] + md5: ca7b377c7c751b45daaf533bedbcc3d4 # [linux] build: number: 0 From 7fa774367d38af2a65f564b6a94f22b9da344ace Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 30 Apr 2024 12:05:02 +0100 Subject: [PATCH 1813/1813] Update shinyngs (#47582) --- recipes/r-shinyngs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-shinyngs/meta.yaml b/recipes/r-shinyngs/meta.yaml index 2c7fd3512a809..eacf45100bbe9 100644 --- a/recipes/r-shinyngs/meta.yaml +++ b/recipes/r-shinyngs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.8.5' %} +{% set version = '1.8.6' %} {% set d3heatmap_version = '0.6.1.2' %} package: @@ -7,7 +7,7 @@ package: source: - url: https://github.com/pinin4fjords/shinyngs/archive/refs/tags/v{{ version }}.tar.gz - sha256: "79d5da8cb976c3752e925da34d475ab1dac5837e83544bbced4486b10e165909" + sha256: "97b7bb4439c16c7f2c0d8fc521e13b7797a8e1ec6641ba1006aedb95fefe7c58" folder: shinyngs - url: https://github.com/cran/d3heatmap/archive/refs/tags/{{ d3heatmap_version }}.tar.gz sha256: "bda213c4d335b199c38a48cb8e60027c929a8ba8ef6e14dc7de692967777c25a"