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# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=MAGAR
_pkgver=1.12.0
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}_${_pkgver}.tar.gz")
md5sums=('8be03f80b6556ec3a2e79c29a0cbc114')
b2sums=('7533aa381e4c74936a34311d67dfc662f298ed6bfb588b266c0bfaa904e0a31a32777a49211c01affdc1900217af7d48de1873b9f17afe60fe92a8b16ec98cee')
build() {
mkdir build
R CMD INSTALL -l build "$_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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