diff --git a/BioArchLinux/r-rnaseqcovarimpute/PKGBUILD b/BioArchLinux/r-rnaseqcovarimpute/PKGBUILD new file mode 100644 index 0000000000..8d119540cb --- /dev/null +++ b/BioArchLinux/r-rnaseqcovarimpute/PKGBUILD @@ -0,0 +1,51 @@ +# Maintainer: Pekka Ristola + +_pkgname=RNAseqCovarImpute +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Impute Covariate Data in RNA Sequencing Studies" +arch=(any) +url="https://bioconductor.org/packages/${_pkgname}" +license=(GPL3) +depends=( + r-biobase + r-biocparallel + r-dplyr + r-edger + r-foreach + r-limma + r-magrittr + r-mice + r-rlang +) +checkdepends=( + r-testthat +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-stringr + r-testthat + r-tidyr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('17d14273ae359562d3f0cbf1c45b10a7') +sha256sums=('f163be9e6155e9d27b2f06c8326b3c0691ad05525d2598ad1187e6925310d65e') + +build() { + mkdir -p build + R CMD INSTALL "$_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-rnaseqcovarimpute/lilac.py b/BioArchLinux/r-rnaseqcovarimpute/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-rnaseqcovarimpute/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-rnaseqcovarimpute/lilac.yaml b/BioArchLinux/r-rnaseqcovarimpute/lilac.yaml new file mode 100644 index 0000000000..7e866ef9a9 --- /dev/null +++ b/BioArchLinux/r-rnaseqcovarimpute/lilac.yaml @@ -0,0 +1,22 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-biobase +- r-biocparallel +- r-dplyr +- r-edger +- r-foreach +- r-limma +- r-magrittr +- r-mice +- r-rlang +repo_makedepends: +- r-testthat +update_on: +- source: rpkgs + pkgname: RNAseqCovarImpute + repo: bioc + md5: true +- alias: r