add r-bsgenome

1 files changed, 53 insertions, 0 deletions

diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..908fa8b1ba78
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,53 @@
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+
+_pkgname=BSgenome
+_pkgver=1.64.0
+pkgname=r-${_pkgname,,}
+pkgver=1.64.0
+pkgrel=1
+pkgdesc='Software infrastructure for efficient representation of full genomes and their SNPs'
+arch=('any')
+url="https://bioconductor.org/packages/${_pkgname}"
+license=('Artistic2.0')
+depends=(
+  r
+  r-biocgenerics
+  r-biostrings
+  r-genomeinfodb
+  r-genomicranges
+  r-iranges
+  r-matrixstats
+  r-rsamtools
+  r-rtracklayer
+  r-s4vectors
+  r-xvector
+)
+optdepends=(
+  r-biobase
+  r-biocmanager
+  r-bsgenome.celegans.ucsc.ce2
+  r-bsgenome.hsapiens.ncbi.grch38
+  r-bsgenome.hsapiens.ucsc.hg38
+  r-bsgenome.hsapiens.ucsc.hg38.masked
+  r-bsgenome.mmusculus.ucsc.mm10
+  r-bsgenome.rnorvegicus.ucsc.rn5
+  r-bsgenome.scerevisiae.ucsc.saccer1
+  r-hgu95av2probe
+  r-runit
+  r-snplocs.hsapiens.dbsnp144.grch38
+  r-txdb.hsapiens.ucsc.hg38.knowngene
+  r-txdb.mmusculus.ucsc.mm10.knowngene
+  r-xtrasnplocs.hsapiens.dbsnp144.grch38
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('ace392a9db183effb8a55c1f74719ef00dee5ea2da2af6f383af77e354cdf89d')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et: