diff --git a/BioArchLinux/r-hicdoc/PKGBUILD b/BioArchLinux/r-hicdoc/PKGBUILD new file mode 100644 index 0000000000..bccbfb5d92 --- /dev/null +++ b/BioArchLinux/r-hicdoc/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Pekka Ristola + +_pkgname=HiCDOC +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="A/B compartment detection and differential analysis" +arch=(x86_64) +url="https://bioconductor.org/packages/${_pkgname}" +license=(LGPL3) +depends=( + r-biocgenerics + r-biocparallel + r-cowplot + r-data.table + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-gtools + r-interactionset + r-multihiccompare + r-pbapply + r-rcpp + r-s4vectors + r-summarizedexperiment + r-zlibbioc + zlib +) +checkdepends=( + r-testthat +) +optdepends=( + r-biocmanager + r-biocstyle + r-knitr + r-rhdf5 + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('334df180a7e5e2851bbf6724e8537ffd') +sha256sums=('237724013ba999d39bc69394adc52b83bb29e9618b552bae00114aaa4653edf8') + +build() { + mkdir -p build + R CMD INSTALL "$_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-hicdoc/lilac.py b/BioArchLinux/r-hicdoc/lilac.py new file mode 100644 index 0000000000..76084a6c1f --- /dev/null +++ b/BioArchLinux/r-hicdoc/lilac.py @@ -0,0 +1,18 @@ +#!/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", + expect_systemrequirements = "C++11", + ) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-hicdoc/lilac.yaml b/BioArchLinux/r-hicdoc/lilac.yaml new file mode 100644 index 0000000000..60e897f5ff --- /dev/null +++ b/BioArchLinux/r-hicdoc/lilac.yaml @@ -0,0 +1,34 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-cowplot +- r-data.table +- r-genomeinfodb +- r-genomicranges +- r-ggplot2 +- r-gridextra +- r-gtools +- r-interactionset +- r-multihiccompare +- r-pbapply +- r-rcpp +- r-s4vectors +- r-summarizedexperiment +- r-zlibbioc +repo_makedepends: +- r-testthat +update_on: +- source: rpkgs + pkgname: HiCDOC + repo: bioc + md5: true +- alias: r +- source: alpm + alpm: zlib + repo: core + provided: libz.so + strip_release: true