diff --git a/BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/PKGBUILD b/BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/PKGBUILD new file mode 100644 index 0000000000..0b7316c7dd --- /dev/null +++ b/BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/PKGBUILD @@ -0,0 +1,27 @@ +# Maintainer: Pekka Ristola + +_pkgname=BSgenome.Hsapiens.1000genomes.hs37d5 +_pkgver=0.99.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="1000genomes Reference Genome Sequence (hs37d5)" +arch=(any) +url="https://bioconductor.org/packages/${_pkgname}" +license=(Artistic2.0) +depends=( + r-bsgenome +) +source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('164e1692d38fefa499c2c8ac5fc22793') +sha256sums=('591fb6b984d10c56d6c6efdabcd694414c1a89f7e2c27405f77ceb8a5d79e0b1') + +build() { + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/lilac.py b/BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/lilac.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/lilac.yaml b/BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/lilac.yaml new file mode 100644 index 0000000000..b9a41c3bdb --- /dev/null +++ b/BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/lilac.yaml @@ -0,0 +1,12 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-bsgenome +update_on: +- source: rpkgs + pkgname: BSgenome.Hsapiens.1000genomes.hs37d5 + repo: bioc-data-annotation + md5: true +- alias: r diff --git a/BioArchLinux/r-resolve/PKGBUILD b/BioArchLinux/r-resolve/PKGBUILD new file mode 100644 index 0000000000..aac36f0449 --- /dev/null +++ b/BioArchLinux/r-resolve/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Pekka Ristola + +_pkgname=RESOLVE +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes" +arch=(any) +url="https://bioconductor.org/packages/${_pkgname}" +license=(Apache) +depends=( + r-biostrings + r-bsgenome + r-bsgenome.hsapiens.1000genomes.hs37d5 + r-data.table + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-glmnet + r-gridextra + r-iranges + r-lsa + r-mutationalpatterns + r-nnls + r-reshape2 + r-s4vectors +) +checkdepends=( + r-testthat +) +optdepends=( + r-biocgenerics + r-biocstyle + r-knitr + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('3dd3a656ed19f5faa759f4b37c459f53') +sha256sums=('3fe1a6d0171af5d2ecd111a4bdb690e466081a16d930587eedacba7fb16af3d7') + +build() { + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-resolve/lilac.py b/BioArchLinux/r-resolve/lilac.py new file mode 100644 index 0000000000..c808eaf563 --- /dev/null +++ b/BioArchLinux/r-resolve/lilac.py @@ -0,0 +1,17 @@ +#!/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, + expect_license = "file LICENSE", + ) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-resolve/lilac.yaml b/BioArchLinux/r-resolve/lilac.yaml new file mode 100644 index 0000000000..27f6413a34 --- /dev/null +++ b/BioArchLinux/r-resolve/lilac.yaml @@ -0,0 +1,28 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-biostrings +- r-bsgenome +- r-bsgenome.hsapiens.1000genomes.hs37d5 +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-glmnet +- r-gridextra +- r-iranges +- r-lsa +- r-mutationalpatterns +- r-nnls +- r-reshape2 +- r-s4vectors +repo_makedepends: +- r-testthat +update_on: +- source: rpkgs + pkgname: RESOLVE + repo: bioc + md5: true +- alias: r