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# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=VariantAnnotation
_pkgver=1.52.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Annotation of Genetic Variants"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
bzip2
curl
r-annotationdbi
r-biobase
r-biocgenerics
r-biostrings
r-bsgenome
r-dbi
r-genomeinfodb
r-genomicfeatures
r-genomicranges
r-iranges
r-matrixgenerics
r-rsamtools
r-rtracklayer
r-s4vectors
r-summarizedexperiment
r-xvector
r-zlibbioc
xz
zlib
)
makedepends=(
r-rhtslib
)
optdepends=(
r-annotationhub
r-biocstyle
r-bsgenome.hsapiens.ucsc.hg19
r-ggplot2
r-httr
r-jsonlite
r-knitr
r-magick
r-polyphen.hsapiens.dbsnp131
r-rjsoncons
r-runit
r-sift.hsapiens.dbsnp132
r-sift.hsapiens.dbsnp137
r-snplocs.hsapiens.dbsnp144.grch37
r-snpstats
r-txdb.hsapiens.ucsc.hg19.knowngene
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('dd78ea409fc16978cf2d87763e3b808e')
b2sums=('5cf75fb8b5c99a38ee9af06ed6d63ef396ab6e75911f3914905b7d4c518d9e7d2a45458017064aa2c992b28641037c8c752b26ad6dd073d1ddee9da1b0250fdb')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
package() {
install -d "$pkgdir/usr/lib/R/library"
cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
}
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