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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=Rsamtools
_bcver=2.18.0
pkgname=r-${_bcname,,}
pkgver=${_bcver//[:-]/.}
pkgrel=1
pkgdesc="Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import"
arch=(i686 x86_64)
url="https://bioconductor.org/packages/release/bioc/html/${_bcname}.html"
license=("Artistic2.0")
depends=(
"r>=3.5.0"
"r-biocgenerics>=0.25.1"
"r-biocparallel"
"r-biostrings>=2.47.6"
"r-bitops"
"r-genomeinfodb>=1.1.3"
"r-genomicranges>=1.31.8"
"r-iranges>=2.13.12"
"r-rhtslib>=1.99.3"
"r-s4vectors>=0.17.25"
"r-xvector>=0.19.7"
"r-zlibbioc"
)
makedepends=(make)
optdepends=(
"r-biocstyle"
"r-bsgenome.hsapiens.ucsc.hg19"
"r-genomicalignments"
"r-genomicfeatures"
"r-knitr"
"r-rnaseqdata.hnrnpc.bam.chr14"
"r-runit"
"r-shortread>=1.19.10"
"r-txdb.dmelanogaster.ucsc.dm3.ensgene"
"r-txdb.hsapiens.ucsc.hg18.knowngene"
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_bcname}_${_bcver}.tar.gz")
b2sums=('9c880a2869e87a9a24ac5afcb2c191dd58308da3f08fe456e30ff93f84693dc5f86754a390ecbeaa87426a8a23f32bcc8ab3b7495ac0ed0c762be6232f004763')
options=(!lto !buildflags staticlibs)
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"
if [[ -f "${_bcname}/LICENSE" ]]; then
install -Dm0644 "${_bcname}/LICENSE" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
fi
}
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