PKGBUILD


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# Maintainer: peippo <christoph+aur@christophfink.com>
# Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
# Contributor: Grey Christoforo <first name at last name dot net>

_bcname=GenomicAlignments
_bcver=1.38.2
pkgname=r-${_bcname,,}
pkgver=${_bcver//[:-]/.}
pkgrel=1
pkgdesc="Representation and manipulation of short genomic alignments"
arch=(i686 x86_64)
url="https://bioconductor.org/packages/release/bioc/html/${_bcname}.html"
license=(Artistic2.0)
depends=(
    "r>=4.0.0"
    "r-biocgenerics>=0.37.0"
    "r-biocparallel"
    "r-biostrings>=2.55.7"
    "r-genomeinfodb>=1.13.1"
    "r-genomicranges>=1.41.5"
    "r-iranges>=2.23.9"
    "r-rsamtools>=1.31.2"
    "r-s4vectors>=0.27.12"
    "r-summarizedexperiment>=1.9.13"
)
optdepends=(
    "r-biocstyle"
    "r-bsgenome"
    "r-bsgenome.dmelanogaster.ucsc.dm3"
    "r-bsgenome.hsapiens.ucsc.hg19"
    "r-deseq2"
    "r-edger"
    "r-genomicfeatures"
    "r-pasillabamsubset"
    "r-rnaseqdata.hnrnpc.bam.chr14"
    "r-rtracklayer"
    "r-runit"
    "r-shortread"
    "r-txdb.dmelanogaster.ucsc.dm3.ensgene"
    "r-txdb.hsapiens.ucsc.hg19.knowngene"
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_bcname}_${_bcver}.tar.gz")
b2sums=("dc7d683f9cb8fca40a7eacf8f73ac4da1de59b81584f5cac2c7132b16cd1a2ee57485cac46af01acb9b3332578863eee6f0b542fa1d1097727ecf18b8de01f78")

build() {
  R CMD INSTALL ${_bcname}_${_bcver}.tar.gz -l "${srcdir}"
}

package() {
  install -dm0755 "${pkgdir}/usr/lib/R/library"

  cp -a --no-preserve=ownership "${_bcname}" "${pkgdir}/usr/lib/R/library"
}