r-raids: init

BioArchLinux/r-raids/PKGBUILD

@@ -0,0 +1,58 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=RAIDS
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Accurate Inference of Genetic Ancestry from Cancer Sequences"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Apache)
+depends=(
+  r-annotationdbi
+  r-annotationfilter
+  r-bsgenome
+  r-ensembldb
+  r-gdsfmt
+  r-genesis
+  r-genomicranges
+  r-iranges
+  r-matrixgenerics
+  r-proc
+  r-rlang
+  r-s4vectors
+  r-snprelate
+  r-variantannotation
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-bsgenome.hsapiens.ucsc.hg38
+  r-ensdb.hsapiens.v86
+  r-genomeinfodb
+  r-knitr
+  r-rmarkdown
+  r-testthat
+  r-withr
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('768d047b002bb44e1178d69233878818')
+sha256sums=('0208eb91f74930bbcebbec4844b708878391831b9097c0080d36cce9c78c5799')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-raids/lilac.py

@@ -0,0 +1,17 @@
+#!/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,
+        expect_license = "Apache License (>= 2)",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-raids/lilac.yaml

@@ -0,0 +1,27 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-annotationdbi
+- r-annotationfilter
+- r-bsgenome
+- r-ensembldb
+- r-gdsfmt
+- r-genesis
+- r-genomicranges
+- r-iranges
+- r-matrixgenerics
+- r-proc
+- r-rlang
+- r-s4vectors
+- r-snprelate
+- r-variantannotation
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: RAIDS
+  repo: bioc
+  md5: true
+- alias: r