diff --git a/BioArchLinux/r-extrachips/PKGBUILD b/BioArchLinux/r-extrachips/PKGBUILD new file mode 100644 index 0000000000..3c15b9499c --- /dev/null +++ b/BioArchLinux/r-extrachips/PKGBUILD @@ -0,0 +1,85 @@ +# Maintainer: Pekka Ristola + +_pkgname=extraChIPs +_pkgver=1.6.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Additional functions for working with ChIP-Seq data" +arch=(x86_64) +url="https://bioconductor.org/packages/${_pkgname}" +license=(GPL3) +depends=( + r-biocio + r-biocparallel + r-broom + r-complexupset + r-csaw + r-dplyr + r-edger + r-enrichedheatmap + r-forcats + r-genomeinfodb + r-genomicinteractions + r-genomicranges + r-ggforce + r-ggplot2 + r-ggrepel + r-ggside + r-glue + r-gviz + r-interactionset + r-iranges + r-limma + r-matrixstats + r-patchwork + r-rcolorbrewer + r-rlang + r-rsamtools + r-rtracklayer + r-s4vectors + r-scales + r-stringr + r-summarizedexperiment + r-tibble + r-tidyr + r-tidyselect + r-vctrs + r-venndiagram +) +checkdepends=( + r-harmonicmeanp + r-testthat +) +optdepends=( + r-biocstyle + r-covr + r-cqn + r-harmonicmeanp + r-here + r-knitr + r-magrittr + r-plyranges + r-quantro + r-rmarkdown + r-testthat + r-tidyverse +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('462672c12f16f912b7e3d4b30a07162f') +sha256sums=('92031cff96880e0e7c1cfa46084ec580991c01a7e23c0734f1802778a1e0c47e') + +build() { + mkdir -p build + R CMD INSTALL "$_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-extrachips/lilac.py b/BioArchLinux/r-extrachips/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-extrachips/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-extrachips/lilac.yaml b/BioArchLinux/r-extrachips/lilac.yaml new file mode 100644 index 0000000000..165ee44adc --- /dev/null +++ b/BioArchLinux/r-extrachips/lilac.yaml @@ -0,0 +1,50 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-biocio +- r-biocparallel +- r-broom +- r-complexupset +- r-csaw +- r-dplyr +- r-edger +- r-enrichedheatmap +- r-forcats +- r-genomeinfodb +- r-genomicinteractions +- r-genomicranges +- r-ggforce +- r-ggplot2 +- r-ggrepel +- r-ggside +- r-glue +- r-gviz +- r-interactionset +- r-iranges +- r-limma +- r-matrixstats +- r-patchwork +- r-rcolorbrewer +- r-rlang +- r-rsamtools +- r-rtracklayer +- r-s4vectors +- r-scales +- r-stringr +- r-summarizedexperiment +- r-tibble +- r-tidyr +- r-tidyselect +- r-vctrs +- r-venndiagram +repo_makedepends: +- r-harmonicmeanp +- r-testthat +update_on: +- source: rpkgs + pkgname: extraChIPs + repo: bioc + md5: true +- alias: r