diff --git a/BioArchLinux/r-ataccogaps/PKGBUILD b/BioArchLinux/r-ataccogaps/PKGBUILD new file mode 100644 index 0000000000..30432b2448 --- /dev/null +++ b/BioArchLinux/r-ataccogaps/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Pekka Ristola + +_pkgname=ATACCoGAPS +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Analysis Tools for scATACseq Data with CoGAPS" +arch=(any) +url="https://bioconductor.org/packages/${_pkgname}" +license=(Artistic2.0) +depends=( + r-bsgenome.hsapiens.ucsc.hg19 + r-bsgenome.mmusculus.ucsc.mm10 + r-chromvar + r-cogaps + r-dplyr + r-fgsea + r-geneoverlap + r-genomicfeatures + r-genomicranges + r-gplots + r-gtools + r-homo.sapiens + r-iranges + r-jaspar2016 + r-motifmatchr + r-msigdbr + r-mus.musculus + r-projectr + r-rgreat + r-stringr + r-tfbstools + r-tidyverse +) +optdepends=( + r-knitr + r-viridis +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('f8cf8dd559b05caf23934090510297de') +sha256sums=('caaeb2de0ecf051edce19095d387547617d7d500ed606205293b029d364c2aed') + +build() { + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-ataccogaps/lilac.py b/BioArchLinux/r-ataccogaps/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-ataccogaps/lilac.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-ataccogaps/lilac.yaml b/BioArchLinux/r-ataccogaps/lilac.yaml new file mode 100644 index 0000000000..06b8fcbcba --- /dev/null +++ b/BioArchLinux/r-ataccogaps/lilac.yaml @@ -0,0 +1,33 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-bsgenome.hsapiens.ucsc.hg19 +- r-bsgenome.mmusculus.ucsc.mm10 +- r-chromvar +- r-cogaps +- r-dplyr +- r-fgsea +- r-geneoverlap +- r-genomicfeatures +- r-genomicranges +- r-gplots +- r-gtools +- r-homo.sapiens +- r-iranges +- r-jaspar2016 +- r-motifmatchr +- r-msigdbr +- r-mus.musculus +- r-projectr +- r-rgreat +- r-stringr +- r-tfbstools +- r-tidyverse +update_on: +- source: rpkgs + pkgname: ATACCoGAPS + repo: bioc + md5: true +- alias: r diff --git a/BioArchLinux/r-jaspar2016/PKGBUILD b/BioArchLinux/r-jaspar2016/PKGBUILD new file mode 100644 index 0000000000..682bb41b97 --- /dev/null +++ b/BioArchLinux/r-jaspar2016/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Pekka Ristola + +_pkgname=JASPAR2016 +_pkgver=1.30.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Data package for JASPAR 2016" +arch=(any) +url="https://bioconductor.org/packages/${_pkgname}" +license=(GPL2) +depends=( + r +) +source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('2976e4678291944f664396385049180b') +sha256sums=('fefe5f2854ac17a1f9995578d1ab9f22c2cb24a2d90b599064d85b795c12dd37') + +build() { + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-jaspar2016/lilac.py b/BioArchLinux/r-jaspar2016/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-jaspar2016/lilac.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-jaspar2016/lilac.yaml b/BioArchLinux/r-jaspar2016/lilac.yaml new file mode 100644 index 0000000000..7458b8b2e7 --- /dev/null +++ b/BioArchLinux/r-jaspar2016/lilac.yaml @@ -0,0 +1,10 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +update_on: +- source: rpkgs + pkgname: JASPAR2016 + repo: bioc-data-experiment + md5: true +- alias: r