diff --git a/BioArchLinux/r-cytofqc/PKGBUILD b/BioArchLinux/r-cytofqc/PKGBUILD new file mode 100644 index 0000000000..7a4d2f2e83 --- /dev/null +++ b/BioArchLinux/r-cytofqc/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Pekka Ristola + +_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" +} diff --git a/BioArchLinux/r-cytofqc/lilac.py b/BioArchLinux/r-cytofqc/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/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() diff --git a/BioArchLinux/r-cytofqc/lilac.yaml b/BioArchLinux/r-cytofqc/lilac.yaml new file mode 100644 index 0000000000..963b577b04 --- /dev/null +++ b/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