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# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=MAGAR
_pkgver=1.14.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-argparse
r-bigstatsr
r-crlmm
r-data.table
r-doparallel
r-ff
r-hdf5array
r-igraph
r-impute
r-jsonlite
r-plyr
r-reshape2
r-rjson
r-rnbeads
r-rnbeads.hg19
r-rnbeads.hg38
r-snpstats
r-upsetr
)
optdepends=(
r-biocgenerics
r-biocmanager
r-devtools
r-gridextra
r-jaspar2018
r-knitr
r-lola
r-qqman
r-rmarkdown
r-rmutil
r-runit
r-seqlogo
r-tfbstools
r-venndiagram
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('a54d3ada0dda135fabf355780623abe0')
b2sums=('5b929ec4754187fa9273949ee0c6300098de9e80c90e0fd1900108e39fb50fd7fd082c0b7004bf2b585331e42956d01b54bcc6fdf1cefdf7e1639903bb35b636')
build() {
mkdir build
R CMD INSTALL -l build "$_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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