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65 lines
1.3 KiB
Bash
65 lines
1.3 KiB
Bash
# system requirements: systemPipeR can be used to run externalcommand-line software (e.g. short read aligners), but thecorresponding tool needs to be installed on a system.
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# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
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_pkgname=systemPipeR
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_pkgver=2.0.5
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pkgname=r-${_pkgname,,}
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pkgver=${_pkgver//[:-]/.}
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pkgrel=1
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pkgdesc='systemPipeR: NGS workflow and report generation environment'
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arch=('any')
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url="https://bioconductor.org/packages/${_pkgname}"
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license=('Artistic2.0')
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depends=(
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r
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r-biocgenerics
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r-biostrings
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r-crayon
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r-genomicranges
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r-ggplot2
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r-htmlwidgets
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r-magrittr
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r-rsamtools
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r-s4vectors
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r-shortread
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r-stringr
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r-summarizedexperiment
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r-yaml
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)
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optdepends=(
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r-annotate
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r-annotationdbi
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r-batchtools
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r-biocstyle
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r-deseq2
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r-dplyr
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r-dt
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r-edger
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r-genomeinfodb
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r-genomicalignments
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r-genomicfeatures
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r-go.db
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r-grid
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r-iranges
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r-kableextra
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r-knitr
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r-limma
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r-rjson
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r-rmarkdown
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r-rtracklayer
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r-systempiperdata
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r-testthat
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r-variantannotation
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)
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source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
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sha256sums=('a')
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build() {
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R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
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}
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package() {
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install -dm0755 "${pkgdir}/usr/lib/R/library"
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cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
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}
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# vim:set ts=2 sw=2 et:
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