Version 1.6.1

2 files changed, 194 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..6b91bb3ee8b1
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,89 @@
+pkgbase = r-granie
+	pkgdesc = GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
+	pkgver = 1.6.1
+	pkgrel = 1
+	url = https://bioconductor.org/packages/GRaNIE
+	arch = any
+	license = Artistic2.0
+	depends = r-annotationhub
+	depends = r-biomart
+	depends = r-biostrings
+	depends = r-checkmate
+	depends = r-circlize
+	depends = r-colorspace
+	depends = r-complexheatmap
+	depends = r-data.table
+	depends = r-deseq2
+	depends = r-dplyr
+	depends = r-ensembldb
+	depends = r-forcats
+	depends = r-futile.logger
+	depends = r-genomeinfodb
+	depends = r-genomicranges
+	depends = r-ggplot2
+	depends = r-gridextra
+	depends = r-igraph
+	depends = r-limma
+	depends = r-magrittr
+	depends = r-matrixstats
+	depends = r-patchwork
+	depends = r-progress
+	depends = r-rcolorbrewer
+	depends = r-readr
+	depends = r-reshape2
+	depends = r-rlang
+	depends = r-s4vectors
+	depends = r-scales
+	depends = r-stringr
+	depends = r-summarizedexperiment
+	depends = r-tibble
+	depends = r-tidyr
+	depends = r-tidyselect
+	depends = r-topgo
+	depends = r-viridis
+	optdepends = r-biocfilecache
+	optdepends = r-biocparallel
+	optdepends = r-biocstyle
+	optdepends = r-bsgenome.dmelanogaster.ucsc.dm6
+	optdepends = r-bsgenome.hsapiens.ucsc.hg19
+	optdepends = r-bsgenome.hsapiens.ucsc.hg38
+	optdepends = r-bsgenome.mmulatta.ucsc.rhemac10
+	optdepends = r-bsgenome.mmusculus.ucsc.mm10
+	optdepends = r-bsgenome.mmusculus.ucsc.mm9
+	optdepends = r-bsgenome.rnorvegicus.ucsc.rn6
+	optdepends = r-bsgenome.rnorvegicus.ucsc.rn7
+	optdepends = r-chipseeker
+	optdepends = r-clusterprofiler
+	optdepends = r-csaw
+	optdepends = r-dose
+	optdepends = r-edaseq
+	optdepends = r-ihw
+	optdepends = r-jaspar2022
+	optdepends = r-knitr
+	optdepends = r-ldlinkr
+	optdepends = r-motifmatchr
+	optdepends = r-org.dm.eg.db
+	optdepends = r-org.hs.eg.db
+	optdepends = r-org.mm.eg.db
+	optdepends = r-org.mmu.eg.db
+	optdepends = r-org.rn.eg.db
+	optdepends = r-purrr
+	optdepends = r-rbioapi
+	optdepends = r-reactomepa
+	optdepends = r-testthat
+	optdepends = r-tfbstools
+	optdepends = r-txdb.dmelanogaster.ucsc.dm6.ensgene
+	optdepends = r-txdb.hsapiens.ucsc.hg19.knowngene
+	optdepends = r-txdb.hsapiens.ucsc.hg38.knowngene
+	optdepends = r-txdb.mmulatta.ucsc.rhemac10.refgene
+	optdepends = r-txdb.mmusculus.ucsc.mm10.knowngene
+	optdepends = r-txdb.mmusculus.ucsc.mm9.knowngene
+	optdepends = r-txdb.rnorvegicus.ucsc.rn6.refgene
+	optdepends = r-txdb.rnorvegicus.ucsc.rn7.refgene
+	optdepends = r-variancepartition
+	optdepends = r-wgcna
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/GRaNIE_1.6.1.tar.gz
+	md5sums = d9db703063398ccd263ce6b54def9266
+	sha256sums = 681f6cd397a1861871fedcbc84b69e5cfe86db7bb5493bd69d9eb1e2b43d37ed
+
+pkgname = r-granie
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..bdaa88eb2943
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,105 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=GRaNIE
+_pkgver=1.6.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-annotationhub
+  r-biomart
+  r-biostrings
+  r-checkmate
+  r-circlize
+  r-colorspace
+  r-complexheatmap
+  r-data.table
+  r-deseq2
+  r-dplyr
+  r-ensembldb
+  r-forcats
+  r-futile.logger
+  r-genomeinfodb
+  r-genomicranges
+  r-ggplot2
+  r-gridextra
+  r-igraph
+  r-limma
+  r-magrittr
+  r-matrixstats
+  r-patchwork
+  r-progress
+  r-rcolorbrewer
+  r-readr
+  r-reshape2
+  r-rlang
+  r-s4vectors
+  r-scales
+  r-stringr
+  r-summarizedexperiment
+  r-tibble
+  r-tidyr
+  r-tidyselect
+  r-topgo
+  r-viridis
+)
+optdepends=(
+  r-biocfilecache
+  r-biocparallel
+  r-biocstyle
+  r-bsgenome.dmelanogaster.ucsc.dm6
+  r-bsgenome.hsapiens.ucsc.hg19
+  r-bsgenome.hsapiens.ucsc.hg38
+  r-bsgenome.mmulatta.ucsc.rhemac10
+  r-bsgenome.mmusculus.ucsc.mm10
+  r-bsgenome.mmusculus.ucsc.mm9
+  r-bsgenome.rnorvegicus.ucsc.rn6
+  r-bsgenome.rnorvegicus.ucsc.rn7
+  r-chipseeker
+  r-clusterprofiler
+  r-csaw
+  r-dose
+  r-edaseq
+  r-ihw
+  r-jaspar2022
+  r-knitr
+  r-ldlinkr
+  r-motifmatchr
+  r-org.dm.eg.db
+  r-org.hs.eg.db
+  r-org.mm.eg.db
+  r-org.mmu.eg.db
+  r-org.rn.eg.db
+  r-purrr
+  r-rbioapi
+  r-reactomepa
+  r-testthat
+  r-tfbstools
+  r-txdb.dmelanogaster.ucsc.dm6.ensgene
+  r-txdb.hsapiens.ucsc.hg19.knowngene
+  r-txdb.hsapiens.ucsc.hg38.knowngene
+  r-txdb.mmulatta.ucsc.rhemac10.refgene
+  r-txdb.mmusculus.ucsc.mm10.knowngene
+  r-txdb.mmusculus.ucsc.mm9.knowngene
+  r-txdb.rnorvegicus.ucsc.rn6.refgene
+  r-txdb.rnorvegicus.ucsc.rn7.refgene
+  r-variancepartition
+  r-wgcna
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('d9db703063398ccd263ce6b54def9266')
+sha256sums=('681f6cd397a1861871fedcbc84b69e5cfe86db7bb5493bd69d9eb1e2b43d37ed')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}