r-epimix: init

BioArchLinux/r-epimix.data/PKGBUILD

@@ -0,0 +1,31 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=EpiMix.data
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Data for the EpiMix package"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-experimenthub
+)
+optdepends=(
+  r-knitr
+  r-rmarkdown
+)
+source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('52c386f6828945121acfca44eabb7827')
+sha256sums=('a591facc097ee811e82d574f3b37ed7bafca8c9c14c9fc75b76499bda4440c97')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-epimix.data/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-epimix.data/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-experimenthub
+update_on:
+- source: rpkgs
+  pkgname: EpiMix.data
+  repo: bioc-data-experiment
+  md5: true
+- alias: r

BioArchLinux/r-epimix/PKGBUILD

@@ -0,0 +1,83 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=EpiMix
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="EpiMix: an integrative tool for the population-level analysis of DNA methylation"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-annotationdbi
+  r-annotationhub
+  r-biobase
+  r-biomart
+  r-data.table
+  r-doparallel
+  r-dosnow
+  r-downloader
+  r-dplyr
+  r-elmer.data
+  r-epimix.data
+  r-experimenthub
+  r-foreach
+  r-genomeinfodb
+  r-genomicfeatures
+  r-genomicranges
+  r-ggplot2
+  r-impute
+  r-iranges
+  r-limma
+  r-plyr
+  r-progress
+  r-r.matlab
+  r-rcolorbrewer
+  r-rcurl
+  r-rlang
+  r-rpmm
+  r-s4vectors
+  r-summarizedexperiment
+  r-tibble
+  r-tidyr
+)
+checkdepends=(
+  r-biocgenerics
+  r-runit
+  r-sesamedata
+)
+optdepends=(
+  r-biocgenerics
+  r-biocstyle
+  r-clusterprofiler
+  r-geoquery
+  r-karyoploter
+  r-knitr
+  r-mirbaseconverter
+  r-multimir
+  r-org.hs.eg.db
+  r-regioner
+  r-runit
+  r-seurat
+  r-survminer
+  r-txdb.hsapiens.ucsc.hg19.knowngene
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('d86305c56618b7f327d0068e09ad6558')
+sha256sums=('014364e942b93938904a3ff958f1540d0e52364ad7bbde9a652a97342d6130fb')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" Rscript --vanilla runTests.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-epimix/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-epimix/lilac.yaml

@@ -0,0 +1,46 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-annotationdbi
+- r-annotationhub
+- r-biobase
+- r-biomart
+- r-data.table
+- r-doparallel
+- r-dosnow
+- r-downloader
+- r-dplyr
+- r-elmer.data
+- r-epimix.data
+- r-experimenthub
+- r-foreach
+- r-genomeinfodb
+- r-genomicfeatures
+- r-genomicranges
+- r-ggplot2
+- r-impute
+- r-iranges
+- r-limma
+- r-plyr
+- r-progress
+- r-r.matlab
+- r-rcolorbrewer
+- r-rcurl
+- r-rlang
+- r-rpmm
+- r-s4vectors
+- r-summarizedexperiment
+- r-tibble
+- r-tidyr
+repo_makedepends:
+- r-biocgenerics
+- r-runit
+- r-sesamedata
+update_on:
+- source: rpkgs
+  pkgname: EpiMix
+  repo: bioc
+  md5: true
+- alias: r