diff --git a/BioArchLinux/r-raids/PKGBUILD b/BioArchLinux/r-raids/PKGBUILD new file mode 100644 index 0000000000..df5f07b6a1 --- /dev/null +++ b/BioArchLinux/r-raids/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Pekka Ristola + +_pkgname=RAIDS +_pkgver=1.0.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Accurate Inference of Genetic Ancestry from Cancer Sequences" +arch=(any) +url="https://bioconductor.org/packages/${_pkgname}" +license=(Apache) +depends=( + r-annotationdbi + r-annotationfilter + r-bsgenome + r-ensembldb + r-gdsfmt + r-genesis + r-genomicranges + r-iranges + r-matrixgenerics + r-proc + r-rlang + r-s4vectors + r-snprelate + r-variantannotation +) +checkdepends=( + r-testthat +) +optdepends=( + r-biocstyle + r-bsgenome.hsapiens.ucsc.hg38 + r-ensdb.hsapiens.v86 + r-genomeinfodb + r-knitr + r-rmarkdown + r-testthat + r-withr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('768d047b002bb44e1178d69233878818') +sha256sums=('0208eb91f74930bbcebbec4844b708878391831b9097c0080d36cce9c78c5799') + +build() { + mkdir -p build + R CMD INSTALL "$_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-raids/lilac.py b/BioArchLinux/r-raids/lilac.py new file mode 100644 index 0000000000..46d51a28d6 --- /dev/null +++ b/BioArchLinux/r-raids/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 = "Apache License (>= 2)", + ) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-raids/lilac.yaml b/BioArchLinux/r-raids/lilac.yaml new file mode 100644 index 0000000000..4c448d3ab8 --- /dev/null +++ b/BioArchLinux/r-raids/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-annotationdbi +- r-annotationfilter +- r-bsgenome +- r-ensembldb +- r-gdsfmt +- r-genesis +- r-genomicranges +- r-iranges +- r-matrixgenerics +- r-proc +- r-rlang +- r-s4vectors +- r-snprelate +- r-variantannotation +repo_makedepends: +- r-testthat +update_on: +- source: rpkgs + pkgname: RAIDS + repo: bioc + md5: true +- alias: r