-
Notifications
You must be signed in to change notification settings - Fork 3.3k
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge remote-tracking branch 'bioconda_origin/master' into saccharis
# Conflicts: # recipes/saccharis/meta.yaml
- Loading branch information
Showing
164 changed files
with
3,636 additions
and
4,912 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,83 +1,76 @@ | ||
| {% set name = "artic" %} | ||
| {% set version = "1.2.4" %} | ||
| {% set sha256 = "981219a49cec01dc82a9375b16f844278e797ad4034efa1eaa410ccb1849c617" %} | ||
| {% set version = "1.5.3" %} | ||
| {% set sha256 = "107483f22de571c4aafae91c475e453d939e6a8e85a7e2cd2d23ccbca224ef1c" %} | ||
|
|
||
| package: | ||
| name: {{ name|lower }} | ||
| version: {{ version|replace("-", "_") }} | ||
|
|
||
| source: | ||
| url: https://github.com/artic-network/fieldbioinformatics/archive/v{{ version }}.tar.gz | ||
| sha256: {{ sha256 }} | ||
|
|
||
| build: | ||
| number: 1 | ||
| number: 0 | ||
| noarch: python | ||
| run_exports: | ||
| - {{ pin_subpackage('artic', max_pin='x.x') }} | ||
| script: python -m pip install --ignore-installed . | ||
| script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv | ||
| entry_points: | ||
| - artic=artic.pipeline:main | ||
| - align_trim=artic.align_trim:main | ||
| - align_trim_n=artic.align_trim_n:main | ||
| - margin_cons=artic.margin_cons:main | ||
| - margin_cons_medaka=artic.margin_cons_medaka:main | ||
| - vcfextract=artic.vcfextract:main | ||
| - artic_vcf_merge=artic.vcf_merge:main | ||
| - artic_vcf_filter=artic.vcf_filter:main | ||
| - artic_make_depth_mask=artic.make_depth_mask:main | ||
| - artic_fasta_header=artic.fasta_header:main | ||
| - artic_mask=artic.mask:main | ||
| - artic_get_stats=artic.artic_mqc:main | ||
| - artic_get_models=artic.get_models:main | ||
|
|
||
| requirements: | ||
| host: | ||
| - python >=3 | ||
| - python ==3.9 | ||
| - pip | ||
| - setuptools | ||
| run: | ||
| - python | ||
| - artic-porechop >=0.3.2pre | ||
| - artic-tools | ||
| - longshot | ||
| - python ==3.9 | ||
| - bcftools | ||
| - biopython | ||
| - bwa | ||
| - clair3 | ||
| - clint | ||
| - htslib | ||
| - medaka >=1.10.0 | ||
| - minimap2 >=2.26 | ||
| - minimap2 | ||
| - multiqc | ||
| - muscle =3.8 | ||
| - nanopolish >=0.14.0 | ||
| - muscle <5.1 | ||
| - pandas | ||
| - pip | ||
| - pysam | ||
| - pytest | ||
| - pyvcf | ||
| - cyvcf2 | ||
| - pyfaidx =0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE | ||
| - requests | ||
| - samtools | ||
| - tqdm | ||
| - keras-preprocessing >=1.1.2 | ||
|
|
||
|
|
||
| test: | ||
| commands: | ||
| - artic -h | ||
| - align_trim -h | ||
| - align_trim_n -h | ||
| - margin_cons -h | ||
| - margin_cons_medaka -h | ||
| - vcfextract -h | ||
| - artic_vcf_merge -h | ||
| - artic_vcf_filter -h | ||
| - artic_make_depth_mask -h | ||
| - artic_fasta_header -h | ||
| - artic_mask -h | ||
| - artic_get_stats -h | ||
| - artic_get_models -h | ||
|
|
||
| about: | ||
| home: https://github.com/artic-network/fieldbioinformatics | ||
| license: MIT | ||
| license_family: MIT | ||
| license_file: LICENSE | ||
| summary: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore | ||
|
|
||
| summary: "ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore." | ||
| dev_url: https://github.com/artic-network/fieldbioinformatics | ||
| doc_url: https://artic.readthedocs.io/en/latest |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,27 @@ | ||
| #!/bin/bash | ||
|
|
||
| export CFLAGS="$CFLAGS -I$PREFIX/include" | ||
| export LDFLAGS="$LDFLAGS -L$PREFIX/lib" | ||
| export LD_LIBRARY_PATH="${PREFIX}/lib" | ||
| export LIBRARY_PATH="${PREFIX}/lib" | ||
| export CPATH="${PREFIX}/include" | ||
| export INCLUDES="-I${PREFIX}/include" | ||
| export LIBPATH="-L${PREFIX}/lib" | ||
| export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" | ||
| export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" | ||
|
|
||
| sed -i.bak 's/^GIT_HEADER/#GIT_HEADER/' makefile | ||
| if [[ `uname` == "Darwin" ]]; then | ||
| export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" | ||
| export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" | ||
| else | ||
| export CONFIG_ARGS="" | ||
| fi | ||
|
|
||
| make CXX=$CXX ARM=false | ||
| cmake . -GNinja \ | ||
| -DCONDA=ON \ | ||
| -DCMAKE_BUILD_TYPE=Release \ | ||
| -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ | ||
| -DCMAKE_CXX_COMPILER="${CXX}" \ | ||
| -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ | ||
| "${CONFIG_ARGS}" | ||
|
|
||
| mkdir -p $PREFIX/bin | ||
| cp atlas $PREFIX/bin | ||
| ninja || exit 1 | ||
|
|
||
| mkdir -p ${PREFIX}/bin | ||
| cp atlas ${PREFIX}/bin || exit 1 | ||
| chmod +x ${PREFIX}/bin/atlas |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,39 +1,65 @@ | ||
| {% set version = "0.9.9" %} | ||
| {% set version = "2.0.0" %} | ||
|
|
||
| package: | ||
| package: | ||
| name: atlas | ||
| version: {{ version }} | ||
|
|
||
| source: | ||
| url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}.tar.gz | ||
| sha256: 7b65eae5ab7ff439accd53febf8caa15ad9d8230278eee31fd5c2e95bf021990 | ||
| url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}-rc.6.tar.gz | ||
| sha256: 017235049dddfac88fedf16bfc444cf38aed25ac84df084dc555736b5d48d6a3 | ||
|
|
||
| build: | ||
| number: 3 | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage("atlas", max_pin="x") }} | ||
|
|
||
| requirements: | ||
| build: | ||
| - make | ||
| - {{ compiler('cxx') }} | ||
| - zlib | ||
| - armadillo | ||
| - libblas | ||
| - openblas | ||
| host: | ||
| - zlib | ||
| - armadillo | ||
| - libblas | ||
| - openblas | ||
| run: | ||
| - libblas | ||
| - zlib | ||
| - armadillo | ||
| build: | ||
| - {{ compiler('cxx') }} | ||
| - cmake | ||
| - git | ||
| - ninja | ||
| - sysroot_linux-64 =2.17 # [linux] | ||
| host: | ||
| - armadillo | ||
| - fmt | ||
| - htslib | ||
| - lapack | ||
| - libgomp # [linux] | ||
| - llvm-openmp # [osx] | ||
| - nlohmann_json | ||
| - openblas | ||
| - sysroot_linux-64 =2.17 # [linux] | ||
| - jsoncpp | ||
| - zlib | ||
| run: | ||
| - armadillo | ||
| - fmt | ||
| - htslib | ||
| - lapack | ||
| - libgomp # [linux] | ||
| - llvm-openmp # [osx] | ||
| - nlohmann_json | ||
| - openblas | ||
| - sysroot_linux-64 =2.17 # [linux] | ||
| - jsoncpp | ||
|
|
||
| test: | ||
| commands: | ||
| - atlas task=recal | grep Wegmann | ||
|
|
||
| commands: | ||
| - atlas | grep "successfully" | ||
| - atlas simulate | ||
| - atlas HKY85 --bam ATLAS_simulations.bam --fasta ATLAS_simulations.fasta | ||
| - atlas GLF --bam ATLAS_simulations.bam | ||
| - atlas saf --glf ATLAS_simulations.glf.gz --fasta ATLAS_simulations.fasta | ||
| - atlas majorMinor --glf ATLAS_simulations.glf.gz | ||
| - rm ATLAS_* *.parameters saf.saf.* || exit 1 | ||
|
|
||
| about: | ||
| home: https://bitbucket.org/wegmannlab/atlas/wiki/Home | ||
| license: GPLv3 | ||
| summary: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" | ||
| home: https://atlaswiki.netlify.app | ||
| license: MPL-2.0 | ||
| summary: "ATLAS: Analysis Tools for Ancient and Low-depth Samples" | ||
|
|
||
| extra: | ||
| additional-platforms: | ||
| - linux-aarch64 | ||
| - osx-arm64 |
Oops, something went wrong.