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# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=VariantFiltering
_pkgver=1.38.0
pkgname=r-${_pkgname,,}
pkgver=1.38.0
pkgrel=1
pkgdesc='Filtering of coding and non-coding genetic variants'
arch=('x86_64')
url="https://bioconductor.org/packages/${_pkgname}"
license=('Artistic2.0')
depends=(
r
r-annotationdbi
r-biobase
r-biocgenerics
r-biocparallel
r-biostrings
r-bsgenome
r-dt
r-genomeinfodb
r-genomicfeatures
r-genomicranges
r-genomicscores
r-graph
r-gviz
r-iranges
r-rbgl
r-rsamtools
r-s4vectors
r-shiny
r-shinyjs
r-shinythemes
r-shinytree
r-summarizedexperiment
r-variantannotation
r-xvector
)
optdepends=(
r-biocstyle
r-bsgenome.hsapiens.1000genomes.hs37d5
r-mafdb.1kgenomes.phase1.hs37d5
r-org.hs.eg.db
r-phastcons100way.ucsc.hg19
r-polyphen.hsapiens.dbsnp131
r-runit
r-sift.hsapiens.dbsnp137
r-snplocs.hsapiens.dbsnp144.grch37
r-txdb.hsapiens.ucsc.hg19.knowngene
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
sha256sums=('597f0bef39c64106029475bfdfe9748fa794d6b1c1fb49c8c6a8e2df10ea9f05')
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:
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