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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=IsoformSwitchAnalyzeR
_pkgver=2.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=1
pkgdesc="Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-2.0-or-later')
depends=(
r-biobase
r-biocgenerics
r-biocparallel
r-biostrings
r-bsgenome
r-dbi
r-dexseq
r-dplyr
r-edger
r-futile.logger
r-genomeinfodb
r-genomicranges
r-ggplot2
r-gridextra
r-iranges
r-limma
r-magrittr
r-pfamanalyzer
r-plyr
r-pwalign
r-rcolorbrewer
r-rcurl
r-readr
r-reshape2
r-rtracklayer
r-s4vectors
r-saturn
r-stringr
r-summarizedexperiment
r-sva
r-tibble
r-tidyr
r-tximeta
r-tximport
r-venndiagram
r-xvector
)
optdepends=(
r-bsgenome.hsapiens.ucsc.hg19
r-knitr
r-rmarkdown
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('38363ce3a91427e534ea9b1c06ff3fd7')
b2sums=('cc6f0b7bf43f9387d16a4caca7503999301f5c7872d09e0f9539f46aa27567622c9a11c388a0b46e9dc2bc8bd13a2e4ee7ebb8822161b8661df160e87b6e9710')
build() {
mkdir build
R CMD INSTALL -l build "$_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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