r-resolve: init

BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/PKGBUILD

@@ -0,0 +1,27 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=BSgenome.Hsapiens.1000genomes.hs37d5
+_pkgver=0.99.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="1000genomes Reference Genome Sequence (hs37d5)"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-bsgenome
+)
+source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('164e1692d38fefa499c2c8ac5fc22793')
+sha256sums=('591fb6b984d10c56d6c6efdabcd694414c1a89f7e2c27405f77ceb8a5d79e0b1')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-bsgenome.hsapiens.1000genomes.hs37d5/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-bsgenome.hsapiens.1000genomes.hs37d5/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-bsgenome
+update_on:
+- source: rpkgs
+  pkgname: BSgenome.Hsapiens.1000genomes.hs37d5
+  repo: bioc-data-annotation
+  md5: true
+- alias: r

BioArchLinux/r-resolve/PKGBUILD

@@ -0,0 +1,55 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=RESOLVE
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Apache)
+depends=(
+  r-biostrings
+  r-bsgenome
+  r-bsgenome.hsapiens.1000genomes.hs37d5
+  r-data.table
+  r-genomeinfodb
+  r-genomicranges
+  r-ggplot2
+  r-glmnet
+  r-gridextra
+  r-iranges
+  r-lsa
+  r-mutationalpatterns
+  r-nnls
+  r-reshape2
+  r-s4vectors
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocgenerics
+  r-biocstyle
+  r-knitr
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('3dd3a656ed19f5faa759f4b37c459f53')
+sha256sums=('3fe1a6d0171af5d2ecd111a4bdb690e466081a16d930587eedacba7fb16af3d7')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-resolve/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 = "file LICENSE",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-resolve/lilac.yaml

@@ -0,0 +1,28 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biostrings
+- r-bsgenome
+- r-bsgenome.hsapiens.1000genomes.hs37d5
+- r-data.table
+- r-genomeinfodb
+- r-genomicranges
+- r-ggplot2
+- r-glmnet
+- r-gridextra
+- r-iranges
+- r-lsa
+- r-mutationalpatterns
+- r-nnls
+- r-reshape2
+- r-s4vectors
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: RESOLVE
+  repo: bioc
+  md5: true
+- alias: r