r-cytofqc: init

BioArchLinux/r-cytofqc/PKGBUILD

@@ -0,0 +1,55 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=cytofQC
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Labels normalized cells for CyTOF data and assigns probabilities for each label"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-catalyst
+  r-e1071
+  r-eztune
+  r-flowcore
+  r-gbm
+  r-ggplot2
+  r-hrbrthemes
+  r-matrixstats
+  r-randomforest
+  r-rmarkdown
+  r-s4vectors
+  r-singlecellexperiment
+  r-ssc
+  r-summarizedexperiment
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-gridextra
+  r-knitr
+  r-rcolorbrewer
+  r-testthat
+  r-uwot
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('d0505813678c5c80055b22702fd6efc1')
+sha256sums=('2815ba1264e0a4b6e5db5d94cd3bbc97b353e0790c639a97e3f1af04d5b34e47')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-cytofqc/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-cytofqc/lilac.yaml

@@ -0,0 +1,27 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-catalyst
+- r-e1071
+- r-eztune
+- r-flowcore
+- r-gbm
+- r-ggplot2
+- r-hrbrthemes
+- r-matrixstats
+- r-randomforest
+- r-rmarkdown
+- r-s4vectors
+- r-singlecellexperiment
+- r-ssc
+- r-summarizedexperiment
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: cytofQC
+  repo: bioc
+  md5: true
+- alias: r