add r-musicatk

2 files changed, 156 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..b77f10b7d011
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,70 @@
+pkgbase = r-musicatk
+	pkgdesc = Mutational Signature Comprehensive Analysis Toolkit
+	pkgver = 1.6.0
+	pkgrel = 1
+	url = https://bioconductor.org/packages/musicatk
+	arch = any
+	license = LGPL
+	depends = r
+	depends = r-biostrings
+	depends = r-bsgenome
+	depends = r-bsgenome.hsapiens.ucsc.hg19
+	depends = r-bsgenome.hsapiens.ucsc.hg38
+	depends = r-bsgenome.mmusculus.ucsc.mm10
+	depends = r-bsgenome.mmusculus.ucsc.mm9
+	depends = r-complexheatmap
+	depends = r-cowplot
+	depends = r-data.table
+	depends = r-decomptumor2sig
+	depends = r-deconstructsigs
+	depends = r-dplyr
+	depends = r-factoextra
+	depends = r-genomeinfodb
+	depends = r-genomicfeatures
+	depends = r-genomicranges
+	depends = r-ggplot2
+	depends = r-ggrepel
+	depends = r-gridextra
+	depends = r-gtools
+	depends = r-iranges
+	depends = r-maftools
+	depends = r-magrittr
+	depends = r-matrixtests
+	depends = r-mcmcprecision
+	depends = r-nmf
+	depends = r-philentropy
+	depends = r-plotly
+	depends = r-rlang
+	depends = r-s4vectors
+	depends = r-shiny
+	depends = r-shinyalert
+	depends = r-shinybs
+	depends = r-shinybusy
+	depends = r-shinydashboard
+	depends = r-shinyjqui
+	depends = r-shinyjs
+	depends = r-sortable
+	depends = r-stringi
+	depends = r-stringr
+	depends = r-summarizedexperiment
+	depends = r-tcgabiolinks
+	depends = r-tibble
+	depends = r-tidyr
+	depends = r-topicmodels
+	depends = r-txdb.hsapiens.ucsc.hg19.knowngene
+	depends = r-txdb.hsapiens.ucsc.hg38.knowngene
+	depends = r-uwot
+	depends = r-variantannotation
+	depends = r-withr
+	optdepends = r-biocstyle
+	optdepends = r-covr
+	optdepends = r-knitr
+	optdepends = r-qpdf
+	optdepends = r-rmarkdown
+	optdepends = r-survival
+	optdepends = r-testthat
+	optdepends = r-xvector
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/musicatk_1.6.0.tar.gz
+	sha256sums = df0038f6b34d4cc3bac381bcdf4358889da241fe8a72b8fa1f4855c6bd0064c8
+
+pkgname = r-musicatk
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..39b6150b39f5
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,86 @@
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+
+_pkgname=musicatk
+_pkgver=1.6.0
+pkgname=r-${_pkgname,,}
+pkgver=1.6.0
+pkgrel=1
+pkgdesc='Mutational Signature Comprehensive Analysis Toolkit'
+arch=('any')
+url="https://bioconductor.org/packages/${_pkgname}"
+license=('LGPL')
+depends=(
+  r
+  r-biostrings
+  r-bsgenome
+  r-bsgenome.hsapiens.ucsc.hg19
+  r-bsgenome.hsapiens.ucsc.hg38
+  r-bsgenome.mmusculus.ucsc.mm10
+  r-bsgenome.mmusculus.ucsc.mm9
+  r-complexheatmap
+  r-cowplot
+  r-data.table
+  r-decomptumor2sig
+  r-deconstructsigs
+  r-dplyr
+  r-factoextra
+  r-genomeinfodb
+  r-genomicfeatures
+  r-genomicranges
+  r-ggplot2
+  r-ggrepel
+  r-gridextra
+  r-gtools
+  r-iranges
+  r-maftools
+  r-magrittr
+  r-matrixtests
+  r-mcmcprecision
+  r-nmf
+  r-philentropy
+  r-plotly
+  r-rlang
+  r-s4vectors
+  r-shiny
+  r-shinyalert
+  r-shinybs
+  r-shinybusy
+  r-shinydashboard
+  r-shinyjqui
+  r-shinyjs
+  r-sortable
+  r-stringi
+  r-stringr
+  r-summarizedexperiment
+  r-tcgabiolinks
+  r-tibble
+  r-tidyr
+  r-topicmodels
+  r-txdb.hsapiens.ucsc.hg19.knowngene
+  r-txdb.hsapiens.ucsc.hg38.knowngene
+  r-uwot
+  r-variantannotation
+  r-withr
+)
+optdepends=(
+  r-biocstyle
+  r-covr
+  r-knitr
+  r-qpdf
+  r-rmarkdown
+  r-survival
+  r-testthat
+  r-xvector
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('df0038f6b34d4cc3bac381bcdf4358889da241fe8a72b8fa1f4855c6bd0064c8')
+
+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: