From e06e9a807fc11c94be42d737ff0b646eae605501 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 14 Oct 2024 13:24:53 -0400 Subject: [PATCH 01/10] Update metabolights-utils to 1.1.12 (#51383) --- recipes/metabolights-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metabolights-utils/meta.yaml b/recipes/metabolights-utils/meta.yaml index 0dcb1851a7712..69e44e55deb2e 100644 --- a/recipes/metabolights-utils/meta.yaml +++ b/recipes/metabolights-utils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metabolights-utils" %} -{% set version = "1.1.11" %} +{% set version = "1.1.12" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metabolights_utils-{{ version }}.tar.gz - sha256: 5290c8c269f5ec3c55d5fc5b24c014c815b24391b831af528a0bec0545337e7e + sha256: a9f482e77df79e1efa6c4884edd9b66f21ac7267cf2d8aa7bf9c018cc9c08788 build: entry_points: From ce5f9a5e583d34d34888bb4d0e64249b6008b4db Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 14 Oct 2024 13:25:13 -0400 Subject: [PATCH 02/10] Update snakemake to 8.23.0 (#51384) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index f467b3193338e..56ad5ea17cf05 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,7 +1,7 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg {% set name = "snakemake" %} -{% set version = "8.22.0" %} +{% set version = "8.23.0" %} package: name: {{ name }} @@ -9,7 +9,7 @@ package: source: url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz - sha256: fe94ee1432ec07af783220bd115ea94b2262072956366a81b6762a9969c11f4a + sha256: 5c4348f55256eb62b2af10c64b0422ca08206193aef725b6412372a7804ef54b build: number: 0 From 11c263790450cc5cb35d61cb9eb09e540fc717d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 14 Oct 2024 13:25:38 -0400 Subject: [PATCH 03/10] Update solvebio to 2.29.2 (#51385) --- recipes/solvebio/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/solvebio/meta.yaml b/recipes/solvebio/meta.yaml index da8e049db6098..d7b1570fc9a6c 100644 --- a/recipes/solvebio/meta.yaml +++ b/recipes/solvebio/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.29.1" %} -{% set sha256 = "e5e1e6eb044fb8300b64af768e1a1cae8ee66d665b55190daa44ec2489f7a2a6" %} +{% set version = "2.29.2" %} +{% set sha256 = "165fe2f9b684d0cab9f7de58315bb3517d02bf6b453398029869b94135e27a30" %} package: name: solvebio From d4726c0e068a97fdaefa0788c13614a09ead29d2 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino <62253982+AndreaGuarracino@users.noreply.github.com> Date: Mon, 14 Oct 2024 12:29:05 -0500 Subject: [PATCH 04/10] add gafpack (#51389) --- recipes/gafpack/build.sh | 7 +++++++ recipes/gafpack/meta.yaml | 38 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 recipes/gafpack/build.sh create mode 100644 recipes/gafpack/meta.yaml diff --git a/recipes/gafpack/build.sh b/recipes/gafpack/build.sh new file mode 100644 index 0000000000000..9f0dcbc83f9ad --- /dev/null +++ b/recipes/gafpack/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash -euo + +set -xe + +# build statically linked binary with Rust +export RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} --no-track diff --git a/recipes/gafpack/meta.yaml b/recipes/gafpack/meta.yaml new file mode 100644 index 0000000000000..9c582610d6aa8 --- /dev/null +++ b/recipes/gafpack/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "gafpack" %} +{% set version = "0.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/pangenome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 0b78d8047132965c7b0a9b0f3dc26682c1251d08507ebdd98583d9c1b563c758 + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +requirements: + build: + - {{ compiler('rust') }} + +test: + commands: + - gafpack --help + +about: + home: https://github.com/pangenome/{{ name }} + license: MIT + license_family: MIT + license_file: LICENSE + summary: Convert alignments to pangenome variation graphs to coverage maps + dev_url: https://github.com/pangenome/{{ name }} + +extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + recipe-maintainers: + - AndreaGuarracino From 984b6757ef5b2293d7243f42e741df6670b43b0f Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Mon, 14 Oct 2024 22:26:58 +0200 Subject: [PATCH 05/10] add `r-archr` (#51295) * add r-archr * add build.sh * skip build lint * use release; reset build; apply patch * add 0001-cap-threads.patch * patch name * no win * r 4.1 only; tidy quotes * no stdlib func * lint * drop bin patch * squash patch --- recipes/r-archr/build.sh | 3 + recipes/r-archr/meta.yaml | 116 ++++++++++++++++++ .../r-archr/patches/0001-cap-threads.patch | 36 ++++++ 3 files changed, 155 insertions(+) create mode 100644 recipes/r-archr/build.sh create mode 100644 recipes/r-archr/meta.yaml create mode 100644 recipes/r-archr/patches/0001-cap-threads.patch diff --git a/recipes/r-archr/build.sh b/recipes/r-archr/build.sh new file mode 100644 index 0000000000000..b8d2635525637 --- /dev/null +++ b/recipes/r-archr/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash +export DISABLE_AUTOBREW=1 +${R} CMD INSTALL --build . ${R_ARGS} diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml new file mode 100644 index 0000000000000..f5472501bbc18 --- /dev/null +++ b/recipes/r-archr/meta.yaml @@ -0,0 +1,116 @@ +{% set version = '1.0.2' %} +{% set github = 'https://github.com/GreenleafLab/ArchR' %} +{% set posix = 'm2-' if win else '' %} + +package: + name: r-archr + version: {{ version|replace('-', '_') }} + +source: + url: {{ github }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: afe4d82975e9d75018e9ec9fda3d116f34f99ad1d45990cbc5a2be7dea8df352 + patches: + - patches/0001-cap-threads.patch + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: + - {{ pin_subpackage('r-archr', max_pin='x.x') }} + +requirements: + build: + - cross-r-base {{ r_base }} # [build_platform != target_platform] + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - r-base =4.1 + - bioconductor-biocgenerics + - bioconductor-biostrings + - bioconductor-chromvar + - bioconductor-complexheatmap + - bioconductor-genomicranges + - bioconductor-motifmatchr + - bioconductor-rhdf5 + - bioconductor-rsamtools + - bioconductor-s4vectors >=0.9.25 + - bioconductor-summarizedexperiment + - r-data.table + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-gtable + - r-gtools + - r-magrittr + - r-matrix + - r-matrixstats + - r-nabor + - r-plyr + - r-rcpp >=0.12.16 + - r-stringr + - r-uwot + run: + - r-base =4.1 + - bioconductor-biocgenerics + - bioconductor-biostrings + - bioconductor-chromvar + - bioconductor-complexheatmap + - bioconductor-genomicranges + - bioconductor-motifmatchr + - bioconductor-rhdf5 + - bioconductor-rsamtools + - bioconductor-s4vectors >=0.9.25 + - bioconductor-summarizedexperiment + - r-data.table + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-gtable + - r-gtools + - r-magrittr + - r-matrix + - r-matrixstats + - r-nabor + - r-plyr + - r-rcpp >=0.12.16 + - r-stringr + - r-uwot + +test: + commands: + - $R -e "library('ArchR')" + +about: + home: https://www.archrproject.com + dev_url: {{ github }} + doc_url: https://www.archrproject.com/bookdown/index.html + license: GPL-2.0-or-later + summary: This package is designed to streamline scATAC analyses in R. + license_family: GPL2 + license_file: + - {{ environ['PREFIX'] }}/lib/R/share/licenses/GPL-2 + - {{ environ['PREFIX'] }}/lib/R/share/licenses/GPL-3 + +extra: + recipe-maintainers: + - jdblischak + - mfansler + +# Package: ArchR +# Type: Package +# Date: 2022-04-03 +# Title: Analyzing single-cell regulatory chromatin in R. +# Version: 1.0.2 +# Authors@R: c( person("Jeffrey", "Granja", email = "jgranja.stanford@gmail.com", role = c("aut","cre")), person("Ryan", "Corces", role = "aut")) +# Description: This package is designed to streamline scATAC analyses in R. +# Roxygen: list(markdown = TRUE) +# License: GPL (>= 2) +# LinkingTo: Rcpp +# LazyData: TRUE +# RoxygenNote: 7.1.2 +# Encoding: UTF-8 +# Imports: ggplot2, SummarizedExperiment, data.table, Matrix, rhdf5, magrittr, S4Vectors (>= 0.9.25), BiocGenerics, Rcpp (>= 0.12.16), matrixStats, plyr, nabor, motifmatchr, chromVAR, uwot, ggrepel, Rsamtools, gtable, gtools, stringr, grid, gridExtra, Biostrings, ComplexHeatmap, GenomicRanges +# Depends: +# Collate: 'AllClasses.R' 'AnnotationGenome.R' 'AnnotationPeaks.R' 'ArchRBrowser.R' 'ArchRHeatmap.R' 'ArrowRead.R' 'ArrowUtils.R' 'ArrowWrite.R' 'BulkProjection.R' 'Clustering.R' 'ColorPalettes.R' 'CreateArrow.R' 'DoubletsScores.R' 'Embedding.R' 'FilterCells.R' 'Footprinting.R' 'GRangesUtils.R' 'GgplotUtils.R' 'GlobalDefaults.R' 'GroupCoverages.R' 'HelperUtils.R' 'GroupExport.R' 'Harmony.R' 'HiddenUtils.R' 'Imputation.R' 'InputData.R' 'IntegrativeAnalysis.R' 'IterativeLSI.R' 'LoggerUtils.R' 'MarkerFeatures.R' 'MatrixDeviations.R' 'MatrixFeatures.R' 'MatrixGeneExpression.R' 'MatrixGeneScores.R' 'MatrixTiles.R' 'ModuleScore.R' 'MultiModal.R' 'ProjectMethods.R' 'QualityControl.R' 'RNAIntegration.R' 'RcppExports.R' 'ReproduciblePeakSet.R' 'Trajectory.R' 'ValidationUtils.R' 'VisualizeData.R' diff --git a/recipes/r-archr/patches/0001-cap-threads.patch b/recipes/r-archr/patches/0001-cap-threads.patch new file mode 100644 index 0000000000000..b1384bd55b381 --- /dev/null +++ b/recipes/r-archr/patches/0001-cap-threads.patch @@ -0,0 +1,36 @@ +From f512a5eaab8b12ef4c78414ffdf813c7ebc872c5 Mon Sep 17 00:00:00 2001 +From: Mervin Fansler +Date: Fri, 11 Oct 2024 12:50:25 +0200 +Subject: [PATCH] bugfix threads not capped to threads input + +--- + R/CreateArrow.R | 2 +- + R/MatrixGeneScores.R | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/R/CreateArrow.R b/R/CreateArrow.R +index ac0be626..08243139 100644 +--- a/R/CreateArrow.R ++++ b/R/CreateArrow.R +@@ -205,7 +205,7 @@ createArrowFiles <- function( + if(subThreading){ + h5disableFileLocking() + }else{ +- args$threads <- length(inputFiles) ++ args$threads <- min(length(inputFiles), threads) + } + + args$minTSS <- NULL +diff --git a/R/MatrixGeneScores.R b/R/MatrixGeneScores.R +index 1d1d10b3..fd342a1a 100644 +--- a/R/MatrixGeneScores.R ++++ b/R/MatrixGeneScores.R +@@ -125,7 +125,7 @@ addGeneScoreMatrix <- function( + if(subThreading){ + h5disableFileLocking() + }else{ +- args$threads <- length(ArrowFiles) ++ args$threads <- min(length(ArrowFiles), threads) + } + + #Remove Input from args From 9ee882ee36efe7a5da8e1c269ced89e4ec5ee39b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 14 Oct 2024 16:27:08 -0400 Subject: [PATCH 06/10] Update oakvar to 2.11.12 (#51387) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 1c79b821bf1a9..bd744ba3f9fc8 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.11.11" %} -{% set sha256 = "16ac185b5e26e422111f7d7e568bd602e972ac2a91feeb4ee61a2193d47cd9a7" %} +{% set version = "2.11.12" %} +{% set sha256 = "eb979f31a9291c8285d0ec335102455e8ad0210f59ffddf8074b1fabf76061a3" %} package: name: {{ name|lower }} From 7bf863a38a5f4fe0feeb2d7db8f50a8391e46a91 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 14 Oct 2024 23:27:19 +0300 Subject: [PATCH 07/10] merquryfk & fastk: add linux-aarch64 build (#51369) * merquryfk: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * fastk: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/fastk/build.sh | 9 ++++++--- recipes/fastk/meta.yaml | 6 +++++- recipes/merquryfk/build.sh | 5 ++++- recipes/merquryfk/meta.yaml | 6 +++++- 4 files changed, 20 insertions(+), 6 deletions(-) diff --git a/recipes/fastk/build.sh b/recipes/fastk/build.sh index c198ff512ee83..5faab284224fd 100644 --- a/recipes/fastk/build.sh +++ b/recipes/fastk/build.sh @@ -1,16 +1,19 @@ #!/bin/bash + +set -xe + export LDFLAGS="-L$SRC_DIR/HTSLIB -L$PREFIX/lib" export CFLAGS="-I$SRC_DIR -I$SRC_DIR/HTSLIB -I$SRC_DIR/LIBDEFLATE -I$SRC_DIR/LIBDEFLATE/common -I$PREFIX/include -L$SRC_DIR/HTSLIB -L$PREFIX/lib" export CPPFLAGS="-I$SRC_DIR -I$SRC_DIR/HTSLIB -I$SRC_DIR/LIBDEFLATE -I$SRC_DIR/LIBDEFLATE/common -I$PREFIX/include -L$SRC_DIR/HTSLIB -L$PREFIX/lib" # build HTSLIB cd HTSLIB -make lib-static +make -j"${CPU_COUNT}" lib-static cd - # build LIBDEFLATE cd LIBDEFLATE -make +make -j"${CPU_COUNT}" cd - # build fastk -make +make -j"${CPU_COUNT}" make install diff --git a/recipes/fastk/meta.yaml b/recipes/fastk/meta.yaml index 74ea8e5805c91..a3a85c9b9151d 100644 --- a/recipes/fastk/meta.yaml +++ b/recipes/fastk/meta.yaml @@ -13,7 +13,7 @@ source: - patch build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage("fastk", max_pin="x") }} @@ -36,3 +36,7 @@ about: license: https://github.com/thegenemyers/FASTK/blob/master/LICENSE summary: FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode. home: https://github.com/thegenemyers/FASTK + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file diff --git a/recipes/merquryfk/build.sh b/recipes/merquryfk/build.sh index 9f9bb40388aae..1a36f7f00fc94 100644 --- a/recipes/merquryfk/build.sh +++ b/recipes/merquryfk/build.sh @@ -1,8 +1,11 @@ #!/bin/bash + +set -xe + export LDFLAGS="$LDFLAGS -L$PREFIX/lib" export CPATH=${PREFIX}/include -make +make -j"${CPU_COUNT}" mkdir -p $PREFIX/bin cp HAPmaker $PREFIX/bin diff --git a/recipes/merquryfk/meta.yaml b/recipes/merquryfk/meta.yaml index b9b8a27e24ca9..97923a411e0ae 100644 --- a/recipes/merquryfk/meta.yaml +++ b/recipes/merquryfk/meta.yaml @@ -13,7 +13,7 @@ source: - patch build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("merquryfk", max_pin="x") }} @@ -50,3 +50,7 @@ about: license: https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE summary: MerquryFK replaces meryl with the FastK k-mer counter suite to considerably speed up analyses. home: https://github.com/thegenemyers/MERQURY.FK + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 75f8ccdb8e221b518ca6a0f6595ed4c7c611101b Mon Sep 17 00:00:00 2001 From: Xiangyang1984 <58356520+Xiangyang1984@users.noreply.github.com> Date: Tue, 15 Oct 2024 04:49:06 +0800 Subject: [PATCH 08/10] Xiangyang1984 patch 10 (#51382) * add pneumo-typer recipes * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml * Update the lastest meta.yaml * Update meta.yaml#8 * Update meta.yaml * Update meta.yaml --- recipes/pneumo-typer/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/pneumo-typer/meta.yaml b/recipes/pneumo-typer/meta.yaml index 676037376f5f9..815d6fcdac78e 100644 --- a/recipes/pneumo-typer/meta.yaml +++ b/recipes/pneumo-typer/meta.yaml @@ -1,17 +1,18 @@ {% set name = "pneumo-typer" %} {% set version = "1.0.2" %} -{% set sha256 = "5ba1aa25862376d44f612c1f9d25ac9fa9ab76aa10dc88939fb27518bf70e013" %} + +{% set sha256 = "755584efcb967c3afe260650af905123f81e192707ee8078ed9d1db22bbfad41" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://www.microbialgenomic.cn/temp_dir/pneumo-typer-v{{ version }}.tar.gz + url: https://www.microbialgenomic.cn/gz/pneumo-typer-v{{ version }}.tar.gz sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('pneumo-typer', max_pin="x") }} @@ -41,7 +42,7 @@ test: about: home: 'https://www.microbialgenomic.cn/Pneumo-Typer.html' - summary: 'Pneumo-Typer is a comprehensive prediction and visualization of serotype and sequence type for streptococcus pneumoniae using assembled genomes.' + summary: 'Pneumo-Typer: An integrated tool for simultaneous identification of serotype, sequence type, and capsule genotype in Streptococcus pneumoniae.' description: 'Pneumo-Typer is a stand-alone perl application, which requires blat, prodigal, NCBI BLAST+, and several perl Modules (GD, GD::SVG) to be installed before use.' doc_url: 'https://github.com/Xiangyang1984/Pneumo-Typer' license: GNU General Public License v3.0 or any later version (GPL-3.0-or-later) From 4e780977259d1c80e1cadf07f09e5f6227d3c7ef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 14 Oct 2024 18:00:13 -0400 Subject: [PATCH 09/10] Update sourcepredict to 0.5.1 (#51388) * Update sourcepredict to 0.5.1 * add run_exports * add run_exports * add setuptools to host --------- Co-authored-by: mencian --- recipes/sourcepredict/meta.yaml | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/recipes/sourcepredict/meta.yaml b/recipes/sourcepredict/meta.yaml index a4ce14bbeed4e..7ff49466c2665 100644 --- a/recipes/sourcepredict/meta.yaml +++ b/recipes/sourcepredict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sourcepredict" %} -{% set version = "0.5" %} +{% set version = "0.5.1" %} package: name: {{ name|lower }} @@ -7,22 +7,25 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sourcepredict-{{ version }}.tar.gz - sha256: d6eb89492b266c33fdf61121de849fdcdc1bdcd692227f559c63f74a9059d3ad + sha256: 6e3e5a418e73f55e6a518e53d5f28838bcdad6307e481d755ad907d2a76b74c9 build: entry_points: - sourcepredict= sourcepredict.__main__:main noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv number: 0 + run_exports: + - {{ pin_subpackage('sourcepredict', max_pin="x.x") }} requirements: host: - python >=3.6 - pip + - setuptools run: - python >=3.6 - - numpy <1.24.0 + - numpy >=1.16.4 - pandas >=0.24.1 - scikit-learn >=0.20.1 - scikit-bio >=0.5.5 @@ -34,15 +37,15 @@ test: imports: - sourcepredict commands: - - pip check - sourcepredict --help - requires: - - pip about: home: https://github.com/maxibor/sourcepredict - summary: Classification and prediction of the origin of metagenomic samples + summary: "Classification and prediction of the origin of metagenomic samples." license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + dev_url: https://github.com/maxibor/sourcepredict extra: recipe-maintainers: From fdbcbe859837ee2f880a5618e68c6a08bab20ccc Mon Sep 17 00:00:00 2001 From: Neng Huang Date: Tue, 15 Oct 2024 06:02:18 +0800 Subject: [PATCH 10/10] Add recipe for longcallr_nn (#51355) * Add recipe for longcallr_nn * clean up pip install command --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/longcallr_nn/meta.yaml | 51 ++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 recipes/longcallr_nn/meta.yaml diff --git a/recipes/longcallr_nn/meta.yaml b/recipes/longcallr_nn/meta.yaml new file mode 100644 index 0000000000000..387e4451d9830 --- /dev/null +++ b/recipes/longcallr_nn/meta.yaml @@ -0,0 +1,51 @@ +{% set name = "longcallr_nn" %} +{% set version = "0.0.1" %} +{% set hash = "294155357b7165b127fc821b06dcdbeee28c108a0caf442b28992a5a5cc3e583" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://github.com/huangnengCSU/longcallR-nn/archive/refs/tags/v{{ version }}.tar.gz" + sha256: {{ hash }} + +build: + number: 0 + noarch: python + entry_points: + - longcallR_nn=longcallR_nn.longcallR_nn:main + script: + - {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - pip + - python 3.9.* + run: + - python 3.9.* + - numpy 1.21.0 + - pyyaml + - pysam + - tensorboardX + - pytorch 1.13.* + - torchvision + - torchmetrics + +test: + commands: + - longcallR_nn --help + +about: + home: "https://github.com/huangnengCSU/longcallR-nn" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "longcallR_nn is a variant caller specifically designed for long-read RNA-seq data utilizing a ResNet model." + dev_url: "https://github.com/huangnengCSU/longcallR-nn" + +extra: + recipe-maintainers: + - huangnengCSU