Merge branch 'bioconda:master' into master

bioconda · Dec 24, 2024 · d7eafe9 · d7eafe9
2 parents 13771c6 + 8874e29
commit d7eafe9
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -607,7 +607,6 @@ recipes/fastuniq
 recipes/fgap
 recipes/funcannot
 recipes/genepender
-recipes/ghostx
 recipes/ls-gkm
 recipes/mosaik
 recipes/ngmerge

diff --git a/recipes/captus/meta.yaml b/recipes/captus/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.0.1" %}
-{% set sha256 = "a9331d4a3d8d967e4b679c14e5af6fd98539659de3b740da876b1fa5c8dd0ba3" %}
+{% set version = "1.1.0" %}
+{% set sha256 = "7a82c26cca9c56dec5e0ddc65bc5ae13cd2beb01719bd621c2cd6bf01d1bfe3e" %}
 
 package:
   name: captus
@@ -10,7 +10,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 4
+  number: 0
   noarch: python
   run_exports:
     - {{ pin_subpackage("captus", max_pin="x.x") }}

diff --git a/recipes/flexynesis/meta.yaml b/recipes/flexynesis/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "flexynesis" %}
-{% set version = "0.2.10" %}
+{% set version = "0.2.11" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/flexynesis-{{ version }}.tar.gz
-  sha256: e6faea383272ee0bdd2792a2d11e4c1682d898eea09008990aa1132a93e72b34
+  sha256: 075ed19b40b5187d96162eaa56ba4e663f284ce04bfc3e5aa64c0a005cf17c6a
 
 build:
   entry_points:
@@ -34,6 +34,7 @@ requirements:
     - scikit-optimize
     - scipy
     - seaborn
+    - xgboost
     - pytorch
     - torchvision
     - tqdm

diff --git a/recipes/ghostx/build.sh b/recipes/ghostx/build.sh
@@ -1,6 +1,10 @@
+#!/usr/bin/env bash
+
+set -xe
+
 cd ./src/
 
-make
-mkdir -p $PREFIX/bin
+CC="${CC}" CXX="${CXX}" CC_FLAGS="${CFLAGS}" make -j"${CPU_COUNT}"
 
-cp ghostx $PREFIX/bin
+mkdir -p $PREFIX/bin
+install -m 755 ghostx $PREFIX/bin
diff --git a/recipes/ghostx/ghostx-makefile.patch b/recipes/ghostx/ghostx-makefile.patch
@@ -0,0 +1,39 @@
+diff --git i/src/Makefile w/src/Makefile
+index 8844e0a..3248657 100644
+--- i/src/Makefile
++++ w/src/Makefile
+@@ -1,9 +1,9 @@
+ LAST_CC=g++
+-CC=gcc
+-CXX=g++
++CC?=gcc
++CXX?=g++
+ COMMON_FLAGS=-Wall -Wextra -pedantic -fopenmp -O3
+ INCLUDES = -I ../ext/boost
+-CC_FLAGS=${COMMON_FLAGS} 
++CC_FLAGS?=${COMMON_FLAGS}
+ LDLIBS	=-lm -fopenmp
+
+ ifeq ($(PROFILE), Yes)
+@@ -69,18 +69,18 @@ OBJS += $(CPP_SRC:%.cpp=%.o)
+ all:ghostx
+
+ ghostx: $(OBJS)
+-	$(LAST_CC) -o $@ $(OBJS) $(LDFLAGS) $(LDLIBS)
++	$(CXX) -std=c++14 -o $@ $(OBJS) $(LDFLAGS) $(LDLIBS)
+
+ .c.o:
+ 	$(CC) -c $(CC_FLAGS) $< -o $@  $(INCLUDES)
+
+ .cpp.o:
+-	$(CXX) -c $(CC_FLAGS) $< -o $@  $(INCLUDES)
++	$(CXX) -std=c++14 -c $(CC_FLAGS) $< -o $@  $(INCLUDES)
+
+
+
+ .PHONY: clean
+ clean:
+-	rm ghostx
+ 	rm -f *.o
+ 	rm -f *~
++	rm ghostx
diff --git a/recipes/ghostx/meta.yaml b/recipes/ghostx/meta.yaml
@@ -8,16 +8,22 @@ package:
 source:
   url: http://www.bi.cs.titech.ac.jp/{{ name }}/releases/{{ name }}-{{ version }}.tar.gz
   sha256: c2bd846e2d7c648931601578501db3aea89c4c5af8fa5f3fa79680c8fe0755bf
+  patches:
+    - ghostx-makefile.patch
 
 build:
-  number: 1
+  number: 2
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x') }}
 
 requirements:
   build:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-  run:
+  host:
+    - libgomp # [linux]
+    - llvm-openmp # [osx]
 
 test:
   commands:
@@ -30,6 +36,9 @@ about:
   summary: "GHOSTX is a homology search tool which can detect remote homologues like BLAST and is about 100 times more efficient than BLAST by using suffix arrays. GHOSTX outputs search results in the format similar to BLAST-tabular format."
 
 extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
   recipe-maintainers:
     - tomkinsc
   identifiers:

diff --git a/recipes/lodei/meta.yaml b/recipes/lodei/meta.yaml
@@ -0,0 +1,39 @@
+{% set version = "1.0.0" %}
+
+package:
+  name: lodei
+  version: {{version}}
+
+source:
+  url: https://github.com/rna-editing1/lodei/archive/refs/tags/v{{version}}.tar.gz
+  sha256: e71d7bbd28a8227c8e5757c79f4c94f1bf9e1db278782cb82e5bcc2147721dfe
+
+build:
+  noarch: python
+  number: 0
+  script: python -m pip install . --no-deps --no-build-isolation -vvv
+  run_exports:
+    - {{ pin_subpackage('lodei', max_pin="x") }}
+
+requirements:
+  host:
+    - python
+    - pip
+  run:
+    - pysamstats 
+    - pandas
+    - matplotlib-base
+
+test:
+  commands:
+    - lodei --help
+
+about:
+  home: https://github.com/rna-editing1/lodei
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+  doi: 10.1038/s41467-024-53298-y
+  summary: Analyze differentially edited A-to-I regions in two sets of RNA-seq samples.
+  details: |
+    LoDEI - the local differential editing index - offers a collection of programs 
+    to detect and analyze differentially edited A-to-I regions in two sets of RNA-seq samples.
diff --git a/recipes/phasius/build.sh b/recipes/phasius/build.sh
@@ -1,11 +1,12 @@
-#!/bin/bash -euo
+#!/bin/bash
+
+set -xeuo
+
 export CFLAGS="${CFLAGS} -fcommon"
 export CXXFLAGS="${CFLAGS} -fcommon"
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
-# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
+cargo-bundle-licenses --format yaml --output THIRDPARTY.yml
 
 # build statically linked binary with Rust
 export LD=$CC
-C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path .
+C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . --no-track
diff --git a/recipes/phasius/meta.yaml b/recipes/phasius/meta.yaml
@@ -1,26 +1,30 @@
-{% set version = "0.1.0" %}
+{% set name = "phasius" %}
+{% set version = "0.2.0" %}
 
 package:
-  name: phasius
+  name: {{ name }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   skip: true  # [osx]
-#  script: cargo install --path . --root ${PREFIX}
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
 
 source:
-  url: https://github.com/wdecoster/phasius/archive/v{{ version }}d.tar.gz
-  sha256: fc210f31c06f5437264cabff9be785e708a293f945b9e865c2bd964fdb61f9c7
+  url: https://github.com/wdecoster/phasius/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: a5b320303383b473661fccf7ec93f3b555b21d86d78d9cdaf5317cc9bcf3cb0e
 
 requirements:
   build:
-    - rust >=1.60  
     - autoconf
     - make
+    - {{ compiler('rust') }}
     - {{ compiler('cxx') }}
     - pkg-config
     - cmake
+    - cargo-bundle-licenses
+    - clangdev
   host:
   run:
 
@@ -32,5 +36,11 @@ test:
 about:
   home: https://github.com/wdecoster/phasius
   license: MIT
-  license_file: LICENSE
+  license_file: 
+    - LICENSE
+    - THIRDPARTY.yml
   summary: A rust tool to create phase-block maps from phased cram/bam files
+
+extra:
+  additional-platforms:
+   - linux-aarch64
diff --git a/recipes/pylibseq/meta.yaml b/recipes/pylibseq/meta.yaml
@@ -12,9 +12,11 @@ source:
     - patch
 
 build:
-  number: 7
-  skip: True  # [py<30 or osx]
+  number: 8
+  skip: True  # [osx]
   script: {{ PYTHON }} -m pip install . --no-deps -vv
+  run_exports:
+      - {{ pin_subpackage('pylibseq', max_pin="x.x") }}
 
 requirements:
   build:
@@ -36,7 +38,11 @@ test:
 
 about:
   home: http://pypi.python.org/pypi/pylibseq
-  license: GPLv3+
-  license_family: GPL
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: COPYING
   summary: 'A Python interface to libsequence'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/revbayes/build.sh b/recipes/revbayes/build.sh
@@ -24,8 +24,7 @@ fi
 	-j "${CPU_COUNT}" \
 	"${CONFIG_ARGS}"
 
-chmod 0755 rb-mpi rb-mpi-help2yml
-mv rb-mpi rb-mpi-help2yml $PREFIX/bin/
+install -v -m 0755 build-mpi/rb-mpi rb-mpi-help2yml "${PREFIX}/bin"
 
 
 # Non-mpi version
@@ -41,7 +40,6 @@ rm -rf build-mpi
         -j "${CPU_COUNT}" \
         "${CONFIG_ARGS}"
 
-chmod 0755 rb rb-help2yml
-mv rb rb-help2yml $PREFIX/bin/
+install -v -m 0755 build/rb rb-help2yml "${PREFIX}/bin"
 
 rm -rf build
diff --git a/recipes/revbayes/meta.yaml b/recipes/revbayes/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "revbayes" %}
-{% set version = "1.2.4" %}
+{% set version = "1.2.5" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/revbayes/revbayes/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 020aa32b32db5896b081e14613c754fbb5523f01fa64262f502a6b693db9058a
+  sha256: 547fc4b9f7d3bd9ebc6ea7dd3e2d7ff824955d49a879b47d0bd6018f6e48b9f7
 
 build:
   number: 0
@@ -54,4 +54,6 @@ extra:
     - doi:10.1093/sysbio/syw021
     - doi:10.1093/sysbio/syu039
   additional-platforms:
-    - osx-arm64
+    # Times out
+    #- osx-arm64
+    #- linux-aarch64
diff --git a/recipes/sc-musketeers/meta.yaml b/recipes/sc-musketeers/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "sc-musketeers" %}
-{% set version = "0.3.7" %}
+{% set version = "0.4.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/sc_musketeers-{{ version }}.tar.gz
-  sha256: e1480895be92b54762b09cb48886c9e68f5ec72e7cf8e48d938c22ada26ca94a
+  sha256: bd9033c4c2c1afb5ef84e3b066e5fbfc93f134c044461172e86665490c6199e1
 
 build:
   entry_points:
@@ -27,10 +27,8 @@ requirements:
     - python >=3.10.0,<4.0.0
     - poetry >=1.8.1,<2.0.0
     - numpy >=1.23.0,<2.0.0
-    - pytorch >=2.3.1,<3.0.0
     - keras >=3.3.3,<4.0.0
     - scanpy >=1.10.1,<2.0.0
-    - ax-platform >=0.4.0,<0.5.0
     - neptune >=1.10.4,<2.0.0
     - pympler >=1.0.1,<2.0.0
     - tensorflow >=2.10.0,<3.0.0

diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml
@@ -1,15 +1,15 @@
 # Attention: when upgrading the version, please compare below dependencies with
 # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg
 {% set name = "snakemake" %}
-{% set version = "8.25.5" %}
+{% set version = "8.26.0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz
-  sha256: 62a2009a28b6738aa189e3c04b9366713f2efe8085b6facb2b4655643549fd51
+  sha256: b52390cd6c3b591e5c4a0977df93d8f25a4a38a5c43dee4c7e2093393cb1f053
 
 build:
   number: 0

diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh
@@ -25,10 +25,10 @@ make CC=${CC} CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" all -j "${CPU_COUNT}"
 cd ..
 
 # Compile readskmercount as an object first if it doesn't have a main
-${CXX}  -c readskmercount.opt.cpp -I./kmc3
+${CXX}  -c readskmercount.opt.parameter.cpp -I./kmc3
 
 # Then link it to create the executable
-${CXX}  -o readskmercount readskmercount.opt.o -L./kmc3/bin -lkmc_core -pthread
+${CXX}  -o readskmercount readskmercount.opt.parameter.o -L./kmc3/bin -lkmc_core -pthread
 
 # Copy everything to the Conda environments bin directory to ensure they're accessible
 echo "Copying binaries to PREFIX..."
@@ -46,7 +46,7 @@ for file in *.r; do
 done
 
 
-cp graph.plot.r readskmercount TIPP.pl TIPP_polish.pl html2repeatbed.pl MSA.plot.r TIPP_plastid.pl TIPP_telomere_backup.pl readskmercount.cpp telomeres.visulization.r TIPP_plastid.v2.1.pl TIPP_telomere.pl TIPPo.v2.3.pl TIPPo.v2.2.pl "$PREFIX/bin/" || { echo "Failed to copy specific binaries to PREFIX"; exit 1; }
+cp graph.plot.r readskmercount TIPP.pl TIPP_polish.pl html2repeatbed.pl MSA.plot.r TIPP_plastid.pl TIPP_telomere_backup.pl readskmercount.cpp telomeres.visulization.r asm_defaults.cfg asm_hifi.cfg TIPP_plastid.v2.1.pl TIPP_telomere.pl TIPPo.v2.4.pl TIPPo.v2.3.pl TIPPo.v2.2.pl "$PREFIX/bin/" || { echo "Failed to copy specific binaries to PREFIX"; exit 1; }
 cp -r kmc3/bin $PREFIX/bin/kmc3/
 cp seqtk/seqtk $PREFIX/bin/seqtk/