diff --git a/recipes/aletsch/meta.yaml b/recipes/aletsch/meta.yaml index d877735467abd..036c9fa58682e 100644 --- a/recipes/aletsch/meta.yaml +++ b/recipes/aletsch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "aletsch" %} -{% set version = "1.1.2" %} +{% set version = "1.1.3" %} package: name: "{{ name }}" @@ -7,10 +7,10 @@ package: source: url: "https://github.com/Shao-Group/aletsch/releases/download/v{{ version }}/aletsch-{{ version }}.tar.gz" - sha256: "b081cfcbd2f232dcddab4f9c6ce11f15f41e4319e1f977dd955cca240748d4b5" + sha256: "74e1b7e2ff2cb065d02f1e0d45d7e87ae332ccfcef86b6a32af88b2a7005c9f7" build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('aletsch', max_pin="x") }} diff --git a/recipes/aster/meta.yaml b/recipes/aster/meta.yaml index 19c285b795681..6d7dce2306868 100644 --- a/recipes/aster/meta.yaml +++ b/recipes/aster/meta.yaml @@ -1,13 +1,13 @@ -{% set version = "1.16" %} +{% set version = "1.19" %} {% set name = "ASTER" %} -{% set sha256 = "c6e80de483a0a59fc0d3a74465b1f793e773b9d79cbd20756c6766136ffbb1a7" %} +{% set sha256 = "f6d7fd58297ab854a6c869ba5d6715d056a82df8254c0d6cba6d9a6db355f054" %} package: name: "{{ name|lower }}" version: "{{ version }}" build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('aster', max_pin="x") }} diff --git a/recipes/cell2cell/meta.yaml b/recipes/cell2cell/meta.yaml index 0db26e51ae700..5e01f81b216ed 100644 --- a/recipes/cell2cell/meta.yaml +++ b/recipes/cell2cell/meta.yaml @@ -11,7 +11,7 @@ source: build: script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 0 + number: 1 run_exports: - {{ pin_subpackage("cell2cell", max_pin="x.x.x") }} @@ -20,11 +20,11 @@ requirements: - {{ compiler("cxx") }} host: - - python <=3.8 + - python <=3.9 - cython - pip run: - - python <=3.8 + - python <=3.9 - numpy >=1.16,<2.0 - pandas >=1.0.0 - xlrd >=1.1 diff --git a/recipes/gatk4/meta.yaml b/recipes/gatk4/meta.yaml index f588a9884779c..18eb0e910083e 100644 --- a/recipes/gatk4/meta.yaml +++ b/recipes/gatk4/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GATK4" %} -{% set version = "4.5.0.0" %} -{% set sha256 = "dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916" %} +{% set version = "4.6.1.0" %} +{% set sha256 = "ac7015c3f0ef1852745ca0ef647adbf8ddef5db63ab485b00bc1ffe654814155" %} package: name: {{ name|lower }} @@ -18,21 +18,21 @@ build: requirements: host: - - r-base =3.6 + - r-base =4.3.1 - r-gplots - r-ggplot2 - r-gsalib - r-reshape - - gcnvkernel =0.8 + - gcnvkernel =0.9 run: - openjdk >=17,<18 - python - - r-base =3.6 + - r-base =4.3.1 - r-gplots - r-ggplot2 - r-gsalib - r-reshape - - gcnvkernel =0.8 + - gcnvkernel =0.9 test: commands: diff --git a/recipes/gcnvkernel/meta.yaml b/recipes/gcnvkernel/meta.yaml index f8c6448ea98bb..d8488006c2f2f 100644 --- a/recipes/gcnvkernel/meta.yaml +++ b/recipes/gcnvkernel/meta.yaml @@ -1,7 +1,7 @@ {% set name = "gcnvkernel" %} -{% set version = "0.8" %} -{% set gatk_version = "4.5.0.0" %} -{% set gatk_sha256 = "dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916" %} +{% set version = "0.9" %} +{% set gatk_version = "4.6.1.0" %} +{% set gatk_sha256 = "ac7015c3f0ef1852745ca0ef647adbf8ddef5db63ab485b00bc1ffe654814155" %} package: name: {{ name|lower }} @@ -13,47 +13,46 @@ source: build: noarch: python - number: 1 + number: 0 + preserve_egg_dir: true run_exports: - {{ pin_subpackage('gcnvkernel', max_pin="x") }} requirements: build: - - conda-forge::python =3.6.10 + - conda-forge::python =3.10.13 - unzip run: # The following are taken from the GATK python environment: # # https://github.com/broadinstitute/gatk/blob/master/scripts/gatkcondaenv.yml.template - - conda-forge::python =3.6.10 - - pip =21.3.1 - - conda-forge::mkl =2019.5 - - conda-forge::mkl-service =2.3.0 - - conda-forge::numpy =1.17.5 - - conda-forge::theano =1.0.4 - - tensorflow <2 - - conda-forge::scipy =1.0.0 - - conda-forge::pymc3 =3.1 - - conda-forge::h5py =2.10.0 - - conda-forge::keras =2.2.4 - - conda-forge::intel-openmp - - conda-forge::scikit-learn =0.23.1 - - conda-forge::matplotlib =3.2.1 - - conda-forge::pandas =1.0.3 - - conda-forge::typing_extensions =4.1.1 - - conda-forge::dill =0.3.4 - - r-base =3.6.2 - - r-data.table =1.12.8 - - r-dplyr =0.8.5 - - r-getopt =1.20.3 - - r-ggplot2 =3.3.0 - - r-gplots =3.0.3 - - r-gsalib =2.1 - - r-optparse =1.6.4 - - r-backports =1.1.10 - - biopython =1.76 - - pyvcf =0.6.8 - - bioconda::pysam =0.15.3 + - conda-forge::python =3.10.13 + - conda-forge::pip =23.3.1 + - conda-forge:blas =1.0=mkl + - conda-forge::numpy =1.26.2 + - conda-forge::pymc =5.10.1 + - conda-forge::pytensor =2.18.3 + - conda-forge::scipy =1.11.4 + - conda-forge::h5py =3.10.0 + - conda-forge::pytorch =2.1.0=*mkl*100 + - conda-forge::pytorch-lightning =2.4.0 + - conda-forge::scikit-learn =1.3.2 + - conda-forge::matplotlib =3.8.2 + - conda-forge::pandas =2.1.3 + - conda-forge::tqdm =4.66.1 + - conda-forge::dill =0.3.7 + - conda-forge::biopython =1.84 + - r-base =4.3.1 + - r-data.table =1.14.8 + - r-dplyr =1.1.3 + - r-getopt =1.20.4 + - r-ggplot2 =3.4.4 + - r-gplots =3.1.3 + - r-gsalib =2.2.1 + - r-optparse =1.7.3 + - r-backports =1.4.1 + - bioconda::pysam =0.22.0 + - conda-forge::pyvcf =0.6.8 test: imports: diff --git a/recipes/hybpiper/meta.yaml b/recipes/hybpiper/meta.yaml index 9686227d7c7da..4e429ebd0f415 100644 --- a/recipes/hybpiper/meta.yaml +++ b/recipes/hybpiper/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 0f341fb26dffd39c13b3bfc5c1d568936bcd0edbe9064399e4aa947d5882d220 build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir entry_points: @@ -22,6 +22,7 @@ requirements: host: - python >=3.7 - pip + - setuptools run: - bbmap >=38.44 - biopython >=1.80 diff --git a/recipes/liana/meta.yaml b/recipes/liana/meta.yaml new file mode 100644 index 0000000000000..0b735c8ee063e --- /dev/null +++ b/recipes/liana/meta.yaml @@ -0,0 +1,62 @@ +{% set name = "liana" %} +{% set version = "1.4.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/liana-{{ version }}.tar.gz + sha256: 1172a9bef67ee22d5eb3f27144c61dddec3122bd515b131c9ed5b0529fcbf2d1 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage("liana", max_pin="x.x.x") }} + +requirements: + host: + - python >=3.8,<3.12 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.8,<3.12 + - anndata >=0.7.4 + - mudata + - scanpy >=1.8.0 + - numba >=0.54.0 + - plotnine >=0.10.0 + - tqdm >=4.0.0,<5.0.0 + - docrep >=0.3.1 + - pre-commit >=3.0.0 + - omnipath >=1.0.6 + - decoupler >=1.4.0 + - pydeseq2 >=0.3.5 + - cell2cell + - muon + - mofax + - mofapy2 >=0.7.0 + - corneto + - cvxpy >=1.4,<2 + - cylp >=0.91.5,<0.92.0 + - requests >=2.25.1,<3.0.0 + +test: + imports: + - liana + commands: + - pip check + requires: + - pip + +about: + home: https://liana-py.readthedocs.io + summary: 'LIANA+: a one-stop-shop framework for cell-cell communication' + license: GPL-3.0-or-later + license_file: LICENSE + +extra: + recipe-maintainers: + - nilchia diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 6b9359c0a70f9..1650e634f7841 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.11.24" %} -{% set sha256 = "72b3f427b66b2bea8a7b36038f6164e3623b6b6d88c945db659fc06c4d6bed3e" %} +{% set version = "2.11.25" %} +{% set sha256 = "f808922c851b81568107d8013344f233dddbbd9d0c69313a46c3c9f97ef42edd" %} package: name: {{ name|lower }} diff --git a/recipes/pathogen-profiler/meta.yaml b/recipes/pathogen-profiler/meta.yaml index db629d9a89746..0b9f275252bb4 100644 --- a/recipes/pathogen-profiler/meta.yaml +++ b/recipes/pathogen-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pathogen-profiler" %} -{% set version = "4.4.0" %} -{% set sha256 = "42a82777c01f26f1a5c85185960873e173329f9f84e081a1eef0fe66ac940f2e" %} +{% set version = "4.5.0" %} +{% set sha256 = "55b23983ebd1a4de0e9fd9805a0a3a839fdfc89e61f5605bb58a5966b737349c" %} package: name: {{name}} diff --git a/recipes/pbjasmine/build.sh b/recipes/pbjasmine/build.sh index 6b3a4f5a12308..1a89008b66dab 100644 --- a/recipes/pbjasmine/build.sh +++ b/recipes/pbjasmine/build.sh @@ -1,5 +1,5 @@ #!/usr/bin/env bash -mkdir -p "${PREFIX}"/bin -cp jasmine "${PREFIX}"/bin/ -chmod +x "${PREFIX}"/bin/jasmine +mkdir -p "${PREFIX}/"{bin,lib} +cp bin/* "${PREFIX}/bin" +cp lib/* "${PREFIX}/lib" diff --git a/recipes/pbjasmine/meta.yaml b/recipes/pbjasmine/meta.yaml index b78cf8d9ba46b..e73d1f40afbb0 100644 --- a/recipes/pbjasmine/meta.yaml +++ b/recipes/pbjasmine/meta.yaml @@ -1,13 +1,13 @@ {% set name = "pbjasmine" %} -{% set version = "2.0.0" %} -{% set sha256 = "7a93e2b3932ed4701ae437f69a9c82b00b6b0718998ba2b137e0b06df0272e1c" %} +{% set version = "2.4.0" %} +{% set sha256 = "c987777320b8ef5ff838a9a893b3baf0de5aaa58fbcf9a25e6ec7b4ad0b88231" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/PacificBiosciences/jasmine/releases/download/v{{ version }}/jasmine + url: https://github.com/PacificBiosciences/jasmine/releases/download/v{{ version }}/jasmine.tar.xz sha256: {{ sha256 }} about: @@ -26,6 +26,12 @@ extra: build: number: 0 skip: True # [osx] + binary_relocation: False + run_exports: + - {{ pin_subpackage('pbjasmine', max_pin='x.x') }} +requirements: + build: + - {{ compiler('cxx') }} test: commands: diff --git a/recipes/perl-list-moreutils-xs/meta.yaml b/recipes/perl-list-moreutils-xs/meta.yaml index 4d35dd71519b8..4f65724892370 100644 --- a/recipes/perl-list-moreutils-xs/meta.yaml +++ b/recipes/perl-list-moreutils-xs/meta.yaml @@ -11,7 +11,8 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 + run_exports: '{{ pin_subpackage(name, max_pin="x.x") }}' requirements: build: @@ -33,6 +34,10 @@ test: imports: - List::MoreUtils::XS +extra: + additional-platforms: + - linux-aarch64 + about: home: https://metacpan.org/release/List-MoreUtils-XS license: apache_2_0 diff --git a/recipes/seqscreen/meta.yaml b/recipes/seqscreen/meta.yaml index 9c8cbdf6eb2a8..c1d9692c33137 100644 --- a/recipes/seqscreen/meta.yaml +++ b/recipes/seqscreen/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage("seqscreen", max_pin="x.x") }} requirements: @@ -20,7 +20,7 @@ requirements: - scikit-learn - jinja2 - biopython - - nextflow 21.10.6 + - nextflow >=22.0.0,<22.11 - blast >=2.10 - diamond >=2.0.15 - centrifuge-core @@ -36,10 +36,10 @@ requirements: - samtools >=1.15.1 - ete3 >=3.1.2 - minimap2 >=2.24 - - ncbi-datasets-cli 13.20.1 + - ncbi-datasets-cli >=13.20.1 - pandas >=1.4.3 - - bwa 0.7.17 - - pyfasta 0.5.2 + - bwa >=0.7.17 + - pyfasta >=0.5.2 test: commands: diff --git a/recipes/sgdemux/meta.yaml b/recipes/sgdemux/meta.yaml index 6846b7a29256c..7f412931f8a6c 100644 --- a/recipes/sgdemux/meta.yaml +++ b/recipes/sgdemux/meta.yaml @@ -1,3 +1,4 @@ +{% set name = "sgdemux" %} {% set version = "1.2.0" %} package: @@ -5,8 +6,9 @@ package: version: {{ version }} build: - number: 2 - + number: 3 + run_exports: '{{ pin_subpackage(name, max_pin="x.x") }}' + source: url: https://github.com/Singular-Genomics/singular-demux/archive/refs/tags/v{{ version }}.tar.gz sha256: aa7b61b04e40bdd0dba91cfa57874203745506521e17139bbcfa4d36a5811dc5 @@ -35,3 +37,6 @@ about: extra: recipe-maintainers: - nh13 + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml index 0d2dcc79dbf30..a32b773cc9d37 100644 --- a/recipes/tb-profiler/meta.yaml +++ b/recipes/tb-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "tb-profiler" %} -{% set version = "6.3.0" %} -{% set sha256 = "45f3f104a3dd0f2fe07b315e3dc4ab1f0e35be095180363ecc65d41842972140" %} +{% set version = "6.4.0" %} +{% set sha256 = "7868c95b1d2578723622f226f254e6bb7d1f35480a575e235f8e0b9984aca166" %} package: name: {{name}} @@ -19,6 +19,7 @@ build: requirements: host: - python >=3.8 + - setuptools - pip - gatk4 - samtools >=1.10 @@ -28,11 +29,11 @@ requirements: - python >=3.8 - git - jinja2 - - pathogen-profiler =4.3.0 + - pathogen-profiler =4.5.0 - filelock - docxtpl - iqtree - # - usher + - usher - joblib - tqdm - pysam diff --git a/recipes/tirmite/meta.yaml b/recipes/tirmite/meta.yaml index 364f4e5917a39..21ba1c785ed09 100644 --- a/recipes/tirmite/meta.yaml +++ b/recipes/tirmite/meta.yaml @@ -1,8 +1,8 @@ {% set name = "tirmite" %} -{% set version = "1.1.5" %} +{% set version = "1.1.6" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "01d2180d073da1786d5236296e51952281c58cb1124aa254345b3d6ab63a1721" %} +{% set hash_value = "9267c94ec12db1c385a5fd6aca8b85d88005ee69ebf42b5e8dd92418454ae26e" %} package: name: '{{ name|lower }}' @@ -17,7 +17,6 @@ build: number: 0 entry_points: - tirmite=tirmite.cmd_tirmite:main - - tsplit-LTR=tirmite.cmd_LTR:main - tsplit-TIR=tirmite.cmd_TIR:main script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv run_exports: @@ -32,7 +31,7 @@ requirements: - hatch-vcs run: - python >=3.8 - - pandas >=0.20.3 + - pandas >=0.23.4 - biopython >=1.70 - pymummer >=0.10.3 @@ -41,7 +40,6 @@ test: - tirmite commands: - tirmite --help - - tsplit-LTR --help - tsplit-TIR --help about: