r-ataccogaps: init

BioArchLinux/r-ataccogaps/PKGBUILD

@@ -0,0 +1,52 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=ATACCoGAPS
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Analysis Tools for scATACseq Data with CoGAPS"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-bsgenome.hsapiens.ucsc.hg19
+  r-bsgenome.mmusculus.ucsc.mm10
+  r-chromvar
+  r-cogaps
+  r-dplyr
+  r-fgsea
+  r-geneoverlap
+  r-genomicfeatures
+  r-genomicranges
+  r-gplots
+  r-gtools
+  r-homo.sapiens
+  r-iranges
+  r-jaspar2016
+  r-motifmatchr
+  r-msigdbr
+  r-mus.musculus
+  r-projectr
+  r-rgreat
+  r-stringr
+  r-tfbstools
+  r-tidyverse
+)
+optdepends=(
+  r-knitr
+  r-viridis
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('f8cf8dd559b05caf23934090510297de')
+sha256sums=('caaeb2de0ecf051edce19095d387547617d7d500ed606205293b029d364c2aed')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-ataccogaps/lilac.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-ataccogaps/lilac.yaml

@@ -0,0 +1,33 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-bsgenome.hsapiens.ucsc.hg19
+- r-bsgenome.mmusculus.ucsc.mm10
+- r-chromvar
+- r-cogaps
+- r-dplyr
+- r-fgsea
+- r-geneoverlap
+- r-genomicfeatures
+- r-genomicranges
+- r-gplots
+- r-gtools
+- r-homo.sapiens
+- r-iranges
+- r-jaspar2016
+- r-motifmatchr
+- r-msigdbr
+- r-mus.musculus
+- r-projectr
+- r-rgreat
+- r-stringr
+- r-tfbstools
+- r-tidyverse
+update_on:
+- source: rpkgs
+  pkgname: ATACCoGAPS
+  repo: bioc
+  md5: true
+- alias: r

BioArchLinux/r-jaspar2016/PKGBUILD

@@ -0,0 +1,27 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=JASPAR2016
+_pkgver=1.30.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Data package for JASPAR 2016"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL2)
+depends=(
+  r
+)
+source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('2976e4678291944f664396385049180b')
+sha256sums=('fefe5f2854ac17a1f9995578d1ab9f22c2cb24a2d90b599064d85b795c12dd37')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-jaspar2016/lilac.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-jaspar2016/lilac.yaml

@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+update_on:
+- source: rpkgs
+  pkgname: JASPAR2016
+  repo: bioc-data-experiment
+  md5: true
+- alias: r