add r-variantfiltering

2 files changed, 108 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..ef16825fb5fa
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,46 @@
+pkgbase = r-variantfiltering
+	pkgdesc = Filtering of coding and non-coding genetic variants
+	pkgver = 1.32.0
+	pkgrel = 1
+	url = https://bioconductor.org/packages/VariantFiltering
+	arch = x86_64
+	license = Artistic2.0
+	depends = r
+	depends = r-annotationdbi
+	depends = r-biobase
+	depends = r-biocgenerics
+	depends = r-biocparallel
+	depends = r-biostrings
+	depends = r-bsgenome
+	depends = r-dt
+	depends = r-genomeinfodb
+	depends = r-genomicfeatures
+	depends = r-genomicranges
+	depends = r-genomicscores
+	depends = r-graph
+	depends = r-gviz
+	depends = r-iranges
+	depends = r-rbgl
+	depends = r-rsamtools
+	depends = r-s4vectors
+	depends = r-shiny
+	depends = r-shinyjs
+	depends = r-shinythemes
+	depends = r-shinytree
+	depends = r-summarizedexperiment
+	depends = r-variantannotation
+	depends = r-xvector
+	optdepends = r-biocstyle
+	optdepends = r-bsgenome.hsapiens.1000genomes.hs37d5
+	optdepends = r-mafdb.1kgenomes.phase1.hs37d5
+	optdepends = r-org.hs.eg.db
+	optdepends = r-phastcons100way.ucsc.hg19
+	optdepends = r-polyphen.hsapiens.dbsnp131
+	optdepends = r-runit
+	optdepends = r-sift.hsapiens.dbsnp137
+	optdepends = r-snplocs.hsapiens.dbsnp144.grch37
+	optdepends = r-txdb.hsapiens.ucsc.hg19.knowngene
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/VariantFiltering_1.32.0.tar.gz
+	sha256sums = 68f6c040bbc4243d099cac3373398cb1907dd04da9bd8d17e841881931b258ae
+
+pkgname = r-variantfiltering
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..e760277ca04e
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,62 @@
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+
+_pkgname=VariantFiltering
+_pkgver=1.32.0
+pkgname=r-${_pkgname,,}
+pkgver=1.32.0
+pkgrel=1
+pkgdesc='Filtering of coding and non-coding genetic variants'
+arch=('x86_64')
+url="https://bioconductor.org/packages/${_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=('68f6c040bbc4243d099cac3373398cb1907dd04da9bd8d17e841881931b258ae')
+
+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: