diff --git a/build-fail-blacklist b/build-fail-blacklist index f3f7e72ee6305..94d6a11bd8263 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 @@ -1062,3 +1061,6 @@ recipes/mudskipper # md5 mismatch when downloading source recipes/komb + +# duplicate recipe +recipes/treeqmc 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 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 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 diff --git a/recipes/abromics_galaxy_json_extractor/meta.yaml b/recipes/abromics_galaxy_json_extractor/meta.yaml index ab4d067298934..ffb7d367e33e6 100644 --- a/recipes/abromics_galaxy_json_extractor/meta.yaml +++ b/recipes/abromics_galaxy_json_extractor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.3.4" %} +{% 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: '4106ed76eb759f3bd3fcb866d18fdafce64f4ef6d364967f7ccee29b6af06d19' + sha256: '364997088a29c30cdc45d2c66af40a3d6b8e3398efe1d7eb242d31b0e68abd77' build: noarch: python 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 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 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 diff --git a/recipes/agat/meta.yaml b/recipes/agat/meta.yaml index 15d356d0d9d71..a1bae16c77a83 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 = "1.3.3" %} +{% set sha256 = "08fa159f7badb418a681a514d471d7233bb1cc09a5e41d875118eaec4c2ec813" %} package: name: "{{ name|lower }}" 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 ${PREFIX}/bin" + run_exports: + - {{ pin_subpackage('agc', max_pin="x") }} source: - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64-{{ system }}.tar.gz - sha256: {{ sha256 }} + - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_arm_linux.tar.gz # [aarch64] + sha256: 5fee3ccbb2691d82a877987e204c5946dbdbe40b9603af5d2421cb8506577534 # [aarch64] + - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64_linux.tar.gz # [linux64] + sha256: 4868dd45c1ed31a7f36bcbc536174249de27b87ec83858d22b128cbec8deef53 # [linux64] + - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64_mac.tar.gz # [osx and x86_64] + sha256: 0ef911e6bb8df791593ee6e89b5bddbf82b5823684955d249d6a67a39e6d0d4e # [osx and x86_64] + - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_m1_mac.tar.gz # [osx and arm64] + sha256: ff8cc5dd4c5825a41e042567a93e9e01ef43fc91624c983640a29fd3c7ac03e4 # [osx and arm64] requirements: build: - run: + run: about: home: https://github.com/refresh-bio/agc summary: "Assembled Genomes Compressor (AGC) is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans)." @@ -23,6 +29,8 @@ test: commands: - agc extra: + additional-platforms: + - linux-aarch64 skip-lints: - should_be_noarch_generic - should_not_be_noarch_source diff --git a/recipes/akt/build.sh b/recipes/akt/build.sh index 54a4de419bbc8..4eca9aec4baa4 100644 --- a/recipes/akt/build.sh +++ b/recipes/akt/build.sh @@ -1,4 +1,8 @@ #!/bin/bash +if [ `uname -m` == "aarch64" ]; then +sed -i 's/\-mpopcnt//g' Makefile +fi + make \ CC="${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 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 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 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 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 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 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 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 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 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 }} 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 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 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 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' + 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 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: 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 diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index d54840930f3be..b50bcabd479bb 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 = "0.6.1" %} 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: 4892df7c710fe13674047a0059be710eef3e7b93b893167e7930760a62ad6273 + 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: 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 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 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 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 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: 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 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 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 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 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: 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 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 diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index e6f5a9ee840bb..7181cbcc84667 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 = "2.14.0" %} +{% set sha256 = "0ae05ba291a1ad7ae956a42bc7e3123a9789ffcd10bf23f2de4499091b8a9e36" %} 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.* @@ -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.* 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: + - $R -e "library('cellhashR')" # [not win] + - "\"%R%\" -e \"library('cellhashR')\"" # [win] + +about: + home: https://github.com/BimberLab/cellhashR + license: MIT + license_family: MIT + summary: "An R package designed to demultiplex cell hashing data.\n More information in https://bimberlab.github.io/cellhashR/Lab B (2024). \n cellhashR: A Package for Demultiplexing Cell Hashing Data.\n" + dev_url: https://github.com/BimberLab/cellhashR diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 29b4cbc81fbe4..c2dea7842a4e5 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8e5876f927b0b0cdfc4a402bfb4fb3d6 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ @@ -54,6 +54,7 @@ requirements: - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'htseq >=2.0.2,<2.1' - r-base - r-hwriter - r-rcolorbrewer @@ -62,6 +63,8 @@ requirements: test: commands: - '$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)' 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 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 }} 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 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: diff --git a/recipes/checkv/meta.yaml b/recipes/checkv/meta.yaml index 50aa0beb676aa..544e4afbcee9f 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 = "1.0.3" %} 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: 2438516f270191267a9860dfe31bf596d64a4fbc16be922b46fb6a4fd98d762a 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 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 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: 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 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 }} diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index 2c1bd818cfbc1..23fad00eb9725 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 = "0.4.3" %} 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: 1a5334a6639f8958e2a8b0254e73066991ff849f00a1194d236a324b3507fbb3 build: entry_points: 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: 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 diff --git a/recipes/dimet/meta.yaml b/recipes/dimet/meta.yaml index 601dacf485321..3dbed3022c530 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 }} @@ -7,12 +7,12 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dimet-{{ version }}.tar.gz - sha256: f5d601a43994705d6bc0cd3948b57756b89dfbd8784266549929a0c8ac3368db + sha256: d394d9a9b1eab5c9cc89f9ac59ff0ee06226b3c6421a6eede001491220fb2642 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 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 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 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 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 }} 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 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 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: 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 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 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 $PREFIX/bin diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index 150a384c7f12c..f10c0fa32a4b2 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -1,7 +1,8 @@ +{% set name = "freebayes" %} {% set version = "1.3.7" %} package: - name: freebayes + name: {{ name }} version: {{ version }} source: @@ -10,10 +11,10 @@ source: patches: - 0001-make-meson-build-conda-friendly.patch - 0002-fix-intervaltree-include-path.patch + - 0003-meson-macos.patch # [osx] build: - number: 0 - skip: true # [osx] + number: 2 run_exports: - {{ pin_subpackage("freebayes", max_pin="x") }} @@ -31,25 +32,32 @@ requirements: - tabixpp - vcflib - simde + - zlib run: - parallel - samtools - tabixpp - vcflib - + - zlib + test: commands: - freebayes --version - freebayes-parallel - + about: - home: https://github.com/ekg/freebayes + home: https://github.com/freebayes/freebayes license: MIT license_file: LICENSE license_family: MIT summary: Bayesian haplotype-based polymorphism discovery and genotyping - maintainers: jpuritz + dev_url: https://github.com/freebayes/freebayes extra: - identifiers: + additional-platforms: + - linux-aarch64 + identifiers: - biotools:freebayes + - usegalaxy-eu:freebayes + recipe-maintainers: + - jpuritz diff --git a/recipes/gb-io/build.sh b/recipes/gb-io/build.sh new file mode 100644 index 0000000000000..a8f3305257de7 --- /dev/null +++ b/recipes/gb-io/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash -e + +set -ex + +# Use a custom temporary directory as home on macOS. +# (not sure why this is useful, but people use it in bioconda recipes) +if [ `uname` == Darwin ]; then + export HOME=`mktemp -d` +fi + +# build statically linked binary with Rust +$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..e346cc5b35e5a --- /dev/null +++ b/recipes/gb-io/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "gb-io" %} +{% set version = "0.3.2" %} + +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: 5bf0a5b2755e5e4aa928184043a44c28e2658158965901abb003ede8c794ad6e + +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. 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 }} 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 }} 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 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" 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 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 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 }} 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} +) 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: 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 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" 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] 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 }} 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 }} 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 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 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 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 ${PREFIX}/lib/igv # Build diff --git a/recipes/igv/meta.yaml b/recipes/igv/meta.yaml index f3a127e2f9d6b..f6b4328bcb2b3 100644 --- a/recipes/igv/meta.yaml +++ b/recipes/igv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "IGV" %} -{% set version = "2.16.2" %} -{% set sha256 = "d08e785d9d44f4e3c16dfe22514133fa0a80d067b677c0cc3c64d2e3d2c12d21" %} +{% set version = "2.17.3" %} +{% set sha256 = "81ab0164014612ff37eea6c7673072fb38ba65b527c05c1197f605c3e9cf3c39" %} package: name: {{ name|lower }} @@ -13,12 +13,14 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: build: - - openjdk 11 + - openjdk 17 run: - - openjdk 11 + - openjdk 17 test: commands: diff --git a/recipes/igvtools/igvtools.sh b/recipes/igvtools/igvtools.sh index 08f3849b0afa5..a2702832d9ce0 100644 --- a/recipes/igvtools/igvtools.sh +++ b/recipes/igvtools/igvtools.sh @@ -16,13 +16,4 @@ while [[ -h "$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: diff --git a/recipes/influx-si-data-manager/meta.yaml b/recipes/influx-si-data-manager/meta.yaml index dade7d4fe4c17..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 = "1.0.0" %} +{% 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: 0cea604084022f74b0886a7ce088cd1966f29cc35b2854b33b62545bafe84eb9 + sha256: 5bac948f0c781e50a7e47f746cb7fc71f1f5de1182356a8b6952f0a622bd8fe8 build: entry_points: 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 }}' 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: diff --git a/recipes/lemur/meta.yaml b/recipes/lemur/meta.yaml new file mode 100644 index 0000000000000..1e8ba3fb9aaa2 --- /dev/null +++ b/recipes/lemur/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "lemur" %} +{% set version = "1.0.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: 'https://github.com/treangenlab/lemur/archive/refs/tags/v{{version}}.tar.gz' + sha256: 190b6302deabe5d09428bc541e5ab924ab6b727c30fc0c93554c2a131e7fd0d7 + +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 diff --git a/recipes/locidex/meta.yaml b/recipes/locidex/meta.yaml new file mode 100644 index 0000000000000..19946a13bd778 --- /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: 1 + 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 >=3.0 + - 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' + 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: 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: diff --git a/recipes/magus-msa/meta.yaml b/recipes/magus-msa/meta.yaml index feb4112d6441e..cde6aeeb6ad37 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 @@ -33,22 +34,30 @@ requirements: 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 + - 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 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 diff --git a/recipes/mappy/meta.yaml b/recipes/mappy/meta.yaml index fd0f7edcf8930..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 }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mappy-{{ version }}.tar.gz - sha256: 47df11e7cecee9138680d6d2312e44397d0484a02ecf1f5908dea50d94a0efe4 + sha256: 0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb build: number: 0 @@ -36,3 +36,7 @@ about: license_family: MIT license_file: LICENSE.txt summary: 'Minimap2 Python binding' + +extra: + additional-platforms: + - linux-aarch64 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: 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 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 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 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") }} 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: 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 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: 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: 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: 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 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 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 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: 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: diff --git a/recipes/ntlink/meta.yaml b/recipes/ntlink/meta.yaml index f67d1d7829657..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: 3 + number: 0 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: 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 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, + ) + 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 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 }} 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: 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: diff --git a/recipes/pangu/meta.yaml b/recipes/pangu/meta.yaml index dbf8e578c4815..17fe86f5d9ce6 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 = "0.2.6" %} +{% set sha256 = "0484e73185bbed3d54e7a000cf2f0749871589d694dfe7b7d276aaad2892f9a3" %} package: name: pangu 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: 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 }} 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 }} 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 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 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 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: 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 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 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" 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 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 diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index ed079a377b69a..a74e7ad05c86c 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.7.4" %} -{% set sha256 = "bf36ad6246568841a5c4b658fdbbb0bf3a70f6f3b24b31b141f6018de24d4ad8" %} +{% set version = "0.8.1" %} +{% set sha256 = "ec800bd4931a934c09e2cc11e65bd22015fce1bb05898a5605bfb0d5c5502e20" %} package: name: {{ name|lower }} diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 0b30582e2b188..d01b39ef96adc 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 = "1.1.1930" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 09c1c44e4128bdf41798d6327c6cf58192df0a489cfbe5976dc24c4570824f47 + sha256: cf59c083fa15c9c9316b5f95e70fd75560c17545d5bda91959b90fa973056652 build: noarch: python 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 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 }} 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: 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 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 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 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 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 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 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 diff --git a/recipes/r-liger/meta.yaml b/recipes/r-liger/meta.yaml index 47619e1464082..4d150e4e9dfbd 100644 --- a/recipes/r-liger/meta.yaml +++ b/recipes/r-liger/meta.yaml @@ -1,23 +1,24 @@ -{% 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 + number: 1 script: R CMD INSTALL --build . rpaths: - lib/R/lib/ - lib/ run_exports: - - {{ pin_subpackage("r-liger", max_pin="x.x") }} + - {{ pin_subpackage("r-liger", max_pin="x") }} requirements: build: @@ -25,71 +26,65 @@ 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: - $R -e "library('rliger')" about: home: https://github.com/MacoskoLab/liger - license: GPL-3 + license: GPL-3.0-or-later summary: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) , and Liu J, Gao C, Sodicoff J, et al (2020) for more @@ -97,7 +92,12 @@ about: license_family: GPL3 license_file: - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + doc_url: https://welch-lab.github.io/liger/index.html + dev_url: https://github.com/MacoskoLab/liger extra: recipe-maintainers: + - theAeon - raivivek + identifiers: + - doi:10.1016/j.cell.2019.05.006 diff --git a/recipes/rabbitqcplus/build.sh b/recipes/rabbitqcplus/build.sh new file mode 100644 index 0000000000000..28712451f1912 --- /dev/null +++ b/recipes/rabbitqcplus/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +export CC=${CC:-gcc} +export CXX=${CXX:-g++} + +export LIBRARY_DIRS="$LIBRARY_DIRS $PREFIX/lib" + +make +make install + diff --git a/recipes/rabbitqcplus/meta.yaml b/recipes/rabbitqcplus/meta.yaml new file mode 100644 index 0000000000000..3431c61fe6e4b --- /dev/null +++ b/recipes/rabbitqcplus/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.2.8" %} + +package: + name: rabbitqcplus + version: {{ version }} + +source: + url: https://github.com/RabbitBio/RabbitQCPlus/archive/refs/tags/{{ version }}.tar.gz + sha256: 2466f50d735e6445200698ea9ad8041ce93ec8335a94b6181648b44d6a0ee4af + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage("rabbitqcplus", max_pin="x.x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - {{ compiler('c') }} + - make + host: + - zlib + run: + - zlib + +test: + commands: + - rabbitqcplus --help + +about: + home: https://github.com/RabbitBio/RabbitQCPlus + license: MIT + license_file: LICENSE + summary: RabbitQCPlus is an efficient quality control tool for sequencing data diff --git a/recipes/raxml/build.sh b/recipes/raxml/build.sh index 7a51b016595ca..6dd8706245751 100644 --- a/recipes/raxml/build.sh +++ b/recipes/raxml/build.sh @@ -6,10 +6,17 @@ Linux) SUF=.gcc;; *) echo "Unknown architecture"; exit 1;; esac +ARCH=$(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 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 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. 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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 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: 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: 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 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 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 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 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 diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index 57275892e7239..288e8d1fc16d8 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 = "0.6.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b21cc15395091da6f094b102e0285c595e7727f1db5ff59b8bcb08cc0b236d29 + 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: 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 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 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 - diff --git a/recipes/skder/meta.yaml b/recipes/skder/meta.yaml index 4dd0dfc2b7538..f89f93f93ff8a 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 = "1.0.10" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/raufs/skDER/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5d48666d6c7db738777c3bbe2601b01707c2c961b987aecde0f4210154605254 + sha256: af12a8a2709709036b84f79e39b7f13f728e45151d62251792991b23d002c54e build: number: 0 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 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 diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index aeea231e43ace..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 = "9.0.0" %} +{% 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: 22b7337d9ea4f9e32679b96fa873337608d73f2d41443cc6bde18de4549acdb7 + sha256: 26da734f7399f5963c5bc7cbcbb51f2d61e3c76298010418d76c48dda92aeb2f build: noarch: python diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index c103bc15844b0..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 = "8.9.0" %} +{% 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: 1c36d231da92a1e37ab9f96d35346f5268949fbd1cebf4c9d429816a05538066 + 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 >=9.0.0,<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 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 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 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 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 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") }} 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: 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 = . 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 diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml index 2af11a447a995..62489b7775eec 100644 --- a/recipes/tb-profiler/meta.yaml +++ b/recipes/tb-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "tb-profiler" %} -{% set version = "6.0.0" %} -{% set sha256 = "a23600831f0e14d604e3a3a9330e61b852a559a539876c49b294ab31c8e8cbcf" %} +{% set version = "6.2.0" %} +{% set sha256 = "23880e0a38541629f5d2b66fd5323dc9df07fb357e359ad3dc640e4c5b77a206" %} package: name: {{name}} @@ -28,7 +28,7 @@ requirements: - python >=3.8 - git - jinja2 - - pathogen-profiler >=4.0.0 + - pathogen-profiler =4.1.0 - filelock - docxtpl - iqtree 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 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: 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 diff --git a/recipes/tree-qmc/build.sh b/recipes/tree-qmc/build.sh index afeec38073355..34621c3bee530 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 +cp tree-qmc $PREFIX/bin/ +chmod a+x $PREFIX/bin/tree-qmc diff --git a/recipes/tree-qmc/meta.yaml b/recipes/tree-qmc/meta.yaml index 66298530a9cb3..e000a16bf22e1 100644 --- a/recipes/tree-qmc/meta.yaml +++ b/recipes/tree-qmc/meta.yaml @@ -1,13 +1,14 @@ {% set name = "TREE-QMC" %} -{% set version = "2.0.0" %} +{% set version = "3.0.4" %} + package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/molloy-lab/{{ name|upper }}/releases/download/{{ version }}/{{ name|upper }}-{{ version }}.zip - sha256: f8530dd6d106c63ffde0d728eeef835b8bded16e69620e78bd45f562129f86a9 + url: https://github.com/molloy-lab/{{ name|upper }}/archive/refs/tags/v{{ version }}.zip + sha256: d7490fb79d23d5aa8c24c661e070c150421b0991464c4a8ae6cc694cd124f83e build: number: 0 @@ -23,7 +24,7 @@ requirements: test: commands: - - TREE-QMC -h + - tree-qmc -h about: home: https://github.com/molloy-lab/TREE-QMC diff --git a/recipes/treeqmc/build.sh b/recipes/treeqmc/build.sh index afeec38073355..56130c62a04c3 100644 --- a/recipes/treeqmc/build.sh +++ b/recipes/treeqmc/build.sh @@ -1,9 +1,15 @@ -cd MQLib -make \ - GXX="${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 $PREFIX/bin/tree-qmc diff --git a/recipes/treeqmc/meta.yaml b/recipes/treeqmc/meta.yaml index 2af0d99783ba1..47e3e64294ac8 100644 --- a/recipes/treeqmc/meta.yaml +++ b/recipes/treeqmc/meta.yaml @@ -1,13 +1,13 @@ {% set name = "TREEQMC" %} -{% set version = "2.0.0" %} +{% set version = "3.0.1" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/molloy-lab/TREE-QMC/releases/download/2.0.0/TREE-QMC-2.0.0.zip - sha256: f8530dd6d106c63ffde0d728eeef835b8bded16e69620e78bd45f562129f86a9 + url: https://github.com/molloy-lab/TREE-QMC/archive/refs/tags/v{{ version }}.zip + sha256: 0fc11b22d981cbf62ee3d832ed79ac7dbf526669231b0137fd4e4756a0af506c build: number: 0 @@ -18,14 +18,14 @@ requirements: build: - make - {{ compiler('cxx') }} - host: - run: test: commands: - - TREE-QMC -h + - tree-qmc -h about: home: https://github.com/molloy-lab/TREE-QMC license: MIT + license_family: MIT summary: TREE-QMC is a quartet-based method for estimating species trees from gene trees. + dev_url: https://github.com/molloy-lab/TREE-QMC diff --git a/recipes/treetime/meta.yaml b/recipes/treetime/meta.yaml index 06d0ced896a94..55bc9b5fb05f4 100644 --- a/recipes/treetime/meta.yaml +++ b/recipes/treetime/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.11.2" %} -{% set sha256 = "c6fe577580a1ed83dcfc7530f85b678bd9d890366ba83d50444cd8e7371a71af" %} +{% set version = "0.11.3" %} +{% set sha256 = "c19b336691fcf3fddbb2b0e55000ff6d4aafca1f2bdf75b4ab39631a57a73e2b" %} package: name: treetime diff --git a/recipes/trinity/build.sh b/recipes/trinity/build.sh index 4d6f8b5e7ea0f..453ee990e1564 100644 --- a/recipes/trinity/build.sh +++ b/recipes/trinity/build.sh @@ -5,7 +5,7 @@ export INCLUDE_PATH="${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 ${TRINITY_HOME} -type f -name "*.bak" -print0 | xargs -0 rm -f # export TRINITY_HOME as ENV variable diff --git a/recipes/trinity/meta.yaml b/recipes/trinity/meta.yaml index c686e8c82f057..721036e21f6e1 100644 --- a/recipes/trinity/meta.yaml +++ b/recipes/trinity/meta.yaml @@ -13,7 +13,9 @@ source: - makefile.patch build: - number: 3 + number: 4 + run_exports: + - {{ pin_subpackage('trinity', max_pin="x") }} requirements: build: @@ -72,9 +74,7 @@ about: home: https://github.com/trinityrnaseq/trinityrnaseq/ license: BSD-3-Clause license_family: BSD - license_file: - - LICENSE - - LICENSE.txt + license_file: LICENSE summary: "Trinity assembles transcript sequences from Illumina RNA-Seq data." doc_url: https://github.com/trinityrnaseq/trinityrnaseq/wiki dev_url: https://github.com/trinityrnaseq/trinityrnaseq/ diff --git a/recipes/trycycler/meta.yaml b/recipes/trycycler/meta.yaml index 6a2dc9921ee6a..54af9c6a1546c 100644 --- a/recipes/trycycler/meta.yaml +++ b/recipes/trycycler/meta.yaml @@ -1,5 +1,5 @@ {% set name="trycycler" %} -{% set version="0.5.4" %} +{% set version="0.5.5" %} package: name: {{ name }} @@ -9,17 +9,19 @@ build: noarch: python number: 0 script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage('trycycler', max_pin="x.x") }} source: url: https://github.com/rrwick/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 6880e6920a5e4f3764fc3c7dd1dfc7ec4c9106eb5eb2ed90ae292e73c74893df + sha256: 5794a4520c3b8673adc69c975cee06d7658cd74ac6d9378d1fc7af860bec1a89 requirements: host: - - python >=3.6 + - python >=3.6,<3.11 - pip run: - - python >=3.6 + - python >=3.6,<3.11 - python-edlib - scipy - numpy diff --git a/recipes/ucsc-bedclip/build.sh b/recipes/ucsc-bedclip/build.sh index af41c472a9323..a0d9457e75286 100644 --- a/recipes/ucsc-bedclip/build.sh +++ b/recipes/ucsc-bedclip/build.sh @@ -1,8 +1,17 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +if [ $(arch) = "aarch64" ] +then + export CFLAGS+=" -O3 " + export CPPFLAGS+=" -O3 " +else + export MACHTYPE=x86_64 +fi + export BINDIR=$(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..b985207becc8a 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: 4 + run_exports: + - {{ pin_subpackage("ucsc-bedclip", max_pin=None) }} requirements: build: @@ -27,7 +30,6 @@ requirements: - mysql-connector-c - openssl - zlib - run: - libpng - libuuid @@ -40,6 +42,10 @@ 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); + } + 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/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 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 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: 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 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 ${CMAKE_INSTALL_BINDIR}) diff --git a/recipes/vcflib/build.sh b/recipes/vcflib/build.sh index c282330d8bd3e..ac929087a86e7 100644 --- a/recipes/vcflib/build.sh +++ b/recipes/vcflib/build.sh @@ -1,12 +1,15 @@ #!/bin/bash set -ex -if [ `uname` == Darwin ]; then +OS=$(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..03b091e5953c1 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: 6 run_exports: - {{ pin_subpackage('vcflib', max_pin="x") }} @@ -34,13 +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 @@ -70,6 +73,8 @@ about: summary: Command-line tools for manipulating VCF files extra: + additional-platforms: + - linux-aarch64 recipe-maintainers: - jpuritz identifiers: 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 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 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 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") }} 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 }} 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" 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: 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 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