From c829cd2d77ad82cdc11b5bebce02ff5352751207 Mon Sep 17 00:00:00 2001 From: root Date: Wed, 9 Oct 2024 11:34:16 +0800 Subject: [PATCH 1/9] bioconductor-affycompatible --- recipes/bioconductor-affycompatible/build.sh | 11 + .../conda_build_config.yaml | 422 ++++++++++++++++++ recipes/bioconductor-affycompatible/meta.yaml | 47 ++ 3 files changed, 480 insertions(+) create mode 100644 recipes/bioconductor-affycompatible/build.sh create mode 100644 recipes/bioconductor-affycompatible/conda_build_config.yaml create mode 100644 recipes/bioconductor-affycompatible/meta.yaml diff --git a/recipes/bioconductor-affycompatible/build.sh b/recipes/bioconductor-affycompatible/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-affycompatible/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affycompatible/conda_build_config.yaml b/recipes/bioconductor-affycompatible/conda_build_config.yaml new file mode 100644 index 0000000000000..6e001efcb7bca --- /dev/null +++ b/recipes/bioconductor-affycompatible/conda_build_config.yaml @@ -0,0 +1,422 @@ +CONDA_BUILD_SYSROOT: '' +MACOSX_DEPLOYMENT_TARGET: '10.9' +VERBOSE_AT: V=1 +VERBOSE_CM: VERBOSE=1 +_libgcc_mutex: 0.1 conda_forge +abseil_cpp: '20211102.0' +alsa_lib: 1.2.6 +antic: '0.2' +arb: '2.22' +arpack: '3.7' +arrow_cpp: 7.0.0 +assimp: 5.2.3 +attr: '2.5' +aws_c_auth: 0.6.15 +aws_c_cal: 0.5.18 +aws_c_common: 0.8.0 +aws_c_event_stream: 0.2.13 +aws_c_http: 0.6.19 +aws_c_io: 0.13.1 +aws_c_mqtt: 0.7.11 +aws_c_s3: 0.1.45 +aws_c_sdkutils: 0.1.2 +aws_checksums: 0.1.12 +aws_crt_cpp: 0.18.2 +aws_sdk_cpp: 1.9.160 +bamtools: 2.5.1 +blas_impl: openblas +boost: 1.74.0 +boost_cpp: 1.74.0 +bzip2: '1' +c_ares: '1' +c_compiler: gcc 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libkml: + max_pin: x.x + libpng: + max_pin: x.x + librsvg: + max_pin: x + libsvm: + max_pin: x.x + libtiff: + max_pin: x + libxml2: + max_pin: x.x + libuuid: + max_pin: x + lzo: + max_pin: x + metis: + max_pin: x.x + mpfr: + max_pin: x + netcdf-cxx4: + max_pin: x.x + netcdf-fortran: + max_pin: x.x + nettle: + max_pin: x.x + nlopt: + max_pin: x.x.x + nss: + max_pin: x + nspr: + max_pin: x + occt: + max_pin: x.x + openturns: + max_pin: x.x + openjpeg: + max_pin: x.x + pango: + max_pin: x.x + poppler: + max_pin: x.x + qt: + max_pin: x.x + qtkeychain: + max_pin: x.x + readline: + max_pin: x + sox: + max_pin: x.x.x + sqlite: + max_pin: x + tk: + max_pin: x.x + tiledb: + max_pin: x.x + vlfeat: + max_pin: x.x.x + vtk: + max_pin: x.x.x + xz: + max_pin: x.x + zeromq: + max_pin: x.x + zlib: + max_pin: x.x + htslib: + max_pin: x.x + bamtools: + max_pin: x.x.x +pixman: '0' +poco: 1.11.1 +poppler: '22.04' +proj: 9.0.1 +ptscotch: 6.0.9 +pulseaudio: '14.0' +pybind11_abi: '4' +python: 3.10.* *_cpython +python_impl: cpython +pytorch: '1.12' +qt: '5.12' +qtkeychain: '0.12' +r_base: 4.2.* +re2: 2022.04.01 +readline: '8' +rocksdb: '6.10' +root_base: 6.26.4 +ruby: '2.6' +rust_compiler: rust +s2n: 1.3.20 +scotch: 6.0.9 +singular: 4.2.1.p3 +slepc: '3.16' +slepc4py: '3.16' +snappy: '1' +soapysdr: '0.8' +sox: 14.4.2 +spdlog: '1.10' +sqlite: '3' +starlink_ast: 9.2.7 +suitesparse: '5' +superlu_dist: 7.1.1 +svt_av1: 1.2.1 +target_goarch: amd64 +target_gobin: ${PREFIX}/bin/ +target_goexe: '' +target_goos: linux +target_platform: linux-aarch64 +tbb: '2021' +tbb_devel: '2021' +thrift_cpp: 0.16.0 +tiledb: '2.10' +tinyxml2: '9' +tk: '8.6' +ucx: 1.12.1 +uhd: 4.2.0 +vlfeat: 0.9.20 +volk: '2.5' +vtk: 9.1.0 +wcslib: '7.7' +wxwidgets: '3.2' +x264: 1!164.* +x265: '3.5' +xerces_c: '3.2' +xrootd: '5' +xz: '5.2' +zeromq: 4.3.4 +zfp: '1.0' +zip_keys: +- - python + - numpy + - python_impl +- - c_compiler_version + - cxx_compiler_version + - fortran_compiler_version +- - abseil_cpp + - grpc_cpp +zlib: '1.2' +zlib_ng: '2.0' +zstd: '1.5' diff --git a/recipes/bioconductor-affycompatible/meta.yaml b/recipes/bioconductor-affycompatible/meta.yaml new file mode 100644 index 0000000000000..d18415c44b234 --- /dev/null +++ b/recipes/bioconductor-affycompatible/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.58.0" %} +{% set name = "AffyCompatible" %} +{% set bioc = "3.16" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ba2f2f8dd8d5a678dc41d5fa86b322f8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - bioconductor-biostrings + - r-base + - 'r-rcurl >=0.8-1' + - 'r-xml >=2.8-1' + run: + - bioconductor-biostrings + - r-base + - 'r-rcurl >=0.8-1' + - 'r-xml >=2.8-1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix GeneChip software compatibility' + description: 'This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.' +extra: + identifiers: + - biotools:affycompatible + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-affycompatible + path: recipes/bioconductor-affycompatible + version: 1.40.0 + From eab41db893dfb79a3c6c2b620de444a43e35b3a5 Mon Sep 17 00:00:00 2001 From: root Date: Wed, 9 Oct 2024 14:32:31 +0800 Subject: [PATCH 2/9] bioconductor-gofuncr --- recipes/bioconductor-gofuncr/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-gofuncr/meta.yaml b/recipes/bioconductor-gofuncr/meta.yaml index 71d2d0bf7bc4f..0b6878a68f918 100644 --- a/recipes/bioconductor-gofuncr/meta.yaml +++ b/recipes/bioconductor-gofuncr/meta.yaml @@ -53,4 +53,6 @@ about: summary: 'Gene ontology enrichment using FUNC' description: 'GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (''Homo.sapiens'' by default); the GO-graph is included in the package and updated regularly (01-May-2021). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher''s exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - +extra: + additional-platforms: + - linux-aarch64 From c8baba4b522e698cce7cd76cc367fe79106921a9 Mon Sep 17 00:00:00 2001 From: root Date: Wed, 9 Oct 2024 16:03:04 +0800 Subject: [PATCH 3/9] bioconductor-awfisher --- recipes/bioconductor-awfisher/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-awfisher/meta.yaml b/recipes/bioconductor-awfisher/meta.yaml index cc019247c8442..6f7660944b298 100644 --- a/recipes/bioconductor-awfisher/meta.yaml +++ b/recipes/bioconductor-awfisher/meta.yaml @@ -43,4 +43,6 @@ about: summary: 'An R package for fast computing for adaptively weighted fisher''s method' description: 'Implementation of the adaptively weighted fisher''s method, including fast p-value computing, variability index, and meta-pattern.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - +extra: + additional-platforms: + - linux-aarch64 From e6bb9fdc96227b1af73116e97d958719898d20e1 Mon Sep 17 00:00:00 2001 From: root Date: Wed, 9 Oct 2024 17:03:00 +0800 Subject: [PATCH 4/9] bioconductor-bacon --- recipes/bioconductor-bacon/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-bacon/meta.yaml b/recipes/bioconductor-bacon/meta.yaml index 350eb69311bf0..1060c777455cd 100644 --- a/recipes/bioconductor-bacon/meta.yaml +++ b/recipes/bioconductor-bacon/meta.yaml @@ -51,4 +51,5 @@ extra: name: bioconductor-bacon path: recipes/bioconductor-bacon version: 1.8.0 - + additional-platforms: + - linux-aarch64 From c95cac7a247cd6675c67e0db283d26ed49029aec Mon Sep 17 00:00:00 2001 From: root Date: Wed, 9 Oct 2024 17:46:11 +0800 Subject: [PATCH 5/9] bioconductor-bags --- recipes/bioconductor-bags/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-bags/meta.yaml b/recipes/bioconductor-bags/meta.yaml index 9aa67ffe4f606..7e09fd6453a1e 100644 --- a/recipes/bioconductor-bags/meta.yaml +++ b/recipes/bioconductor-bags/meta.yaml @@ -40,4 +40,6 @@ about: license: Artistic-2.0 summary: 'A Bayesian Approach for Geneset Selection' description: 'R package providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.' - +extra: + additional-platforms: + - linux-aarch64 From 5c2e3a353c8baddc189466df57b1b5feafdde370 Mon Sep 17 00:00:00 2001 From: root Date: Wed, 9 Oct 2024 17:50:27 +0800 Subject: [PATCH 6/9] bioconductor-bambu --- recipes/bioconductor-bambu/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-bambu/meta.yaml b/recipes/bioconductor-bambu/meta.yaml index 0a5192523653c..7a4d5a652e222 100644 --- a/recipes/bioconductor-bambu/meta.yaml +++ b/recipes/bioconductor-bambu/meta.yaml @@ -73,4 +73,6 @@ about: summary: 'Context-Aware Transcript Quantification from Long Read RNA-Seq data' description: 'bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.' license_file: LICENSE - +extra: + additional-platforms: + - linux-aarch64 From ba070e61b25e51b274fd7fd2809b8a9afa1e50b2 Mon Sep 17 00:00:00 2001 From: root Date: Thu, 10 Oct 2024 11:22:31 +0800 Subject: [PATCH 7/9] bioconductor-baynorm --- recipes/bioconductor-baynorm/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-baynorm/meta.yaml b/recipes/bioconductor-baynorm/meta.yaml index 32927dab2124f..d1eaf542b5513 100644 --- a/recipes/bioconductor-baynorm/meta.yaml +++ b/recipes/bioconductor-baynorm/meta.yaml @@ -67,4 +67,6 @@ about: summary: 'Single-cell RNA sequencing data normalization' description: 'bayNorm is used for normalizing single-cell RNA-seq data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - +extra: + additional-platforms: + - linux-aarch64 From 6ce3ea3e846f808c35bac3c4104b6477bd92d8a4 Mon Sep 17 00:00:00 2001 From: root Date: Thu, 10 Oct 2024 15:27:48 +0800 Subject: [PATCH 8/9] bioconductor-beachmat.hdf5 --- recipes/bioconductor-beachmat.hdf5/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-beachmat.hdf5/meta.yaml b/recipes/bioconductor-beachmat.hdf5/meta.yaml index d26114501a536..5a463500078dc 100644 --- a/recipes/bioconductor-beachmat.hdf5/meta.yaml +++ b/recipes/bioconductor-beachmat.hdf5/meta.yaml @@ -50,4 +50,6 @@ about: summary: 'beachmat bindings for HDF5-backed matrices' description: 'Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - +extra: + additional-platforms: + - linux-aarch64 From 9c03dabfb86562bd4b0db6588b890aaa1160e5a4 Mon Sep 17 00:00:00 2001 From: root Date: Thu, 10 Oct 2024 20:09:30 +0800 Subject: [PATCH 9/9] bioconductor-bicare --- recipes/bioconductor-bicare/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-bicare/meta.yaml b/recipes/bioconductor-bicare/meta.yaml index e703872a25ea2..7d035520f0a85 100644 --- a/recipes/bioconductor-bicare/meta.yaml +++ b/recipes/bioconductor-bicare/meta.yaml @@ -54,4 +54,5 @@ extra: name: bioconductor-bicare path: recipes/bioconductor-bicare version: 1.38.0 - + additional-platforms: + - linux-aarch64