diff --git a/BioArchLinux/r-cytopipeline/PKGBUILD b/BioArchLinux/r-cytopipeline/PKGBUILD new file mode 100644 index 0000000000..3c4ddf3228 --- /dev/null +++ b/BioArchLinux/r-cytopipeline/PKGBUILD @@ -0,0 +1,55 @@ +# Maintainer: Pekka Ristola + +_pkgname=CytoPipeline +_pkgver=1.0.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Automation and visualization of flow cytometry data analysis pipelines" +arch=(any) +url="https://bioconductor.org/packages/${_pkgname}" +license=(GPL3) +depends=( + r-biocfilecache + r-biocparallel + r-diagram + r-flowai + r-flowcore + r-ggcyto + r-ggplot2 + r-jsonlite + r-peacoqc + r-rlang + r-scales + r-withr +) +checkdepends=( + r-testthat + r-vdiffr +) +optdepends=( + r-biocstyle + r-diffviewer + r-knitr + r-rmarkdown + r-testthat + r-vdiffr +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('03008ccf1f86b39cc48a5f9fa82ae3a2') +sha256sums=('145a7860d3d62ba50957fa3b05a1aa3f3b79ac0d2808369e2833e1833476e176') + +build() { + mkdir -p build + R CMD INSTALL "$_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-cytopipeline/lilac.py b/BioArchLinux/r-cytopipeline/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-cytopipeline/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-cytopipeline/lilac.yaml b/BioArchLinux/r-cytopipeline/lilac.yaml new file mode 100644 index 0000000000..5046b3f1cd --- /dev/null +++ b/BioArchLinux/r-cytopipeline/lilac.yaml @@ -0,0 +1,26 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-biocfilecache +- r-biocparallel +- r-diagram +- r-flowai +- r-flowcore +- r-ggcyto +- r-ggplot2 +- r-jsonlite +- r-peacoqc +- r-rlang +- r-scales +- r-withr +repo_makedepends: +- r-testthat +- r-vdiffr +update_on: +- source: rpkgs + pkgname: CytoPipeline + repo: bioc + md5: true +- alias: r