r-cytopipeline: init

BioArchLinux/r-cytopipeline/PKGBUILD

@@ -0,0 +1,55 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_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"
+}

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()

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