From a097bb88b212429b8cd517e5c95fa5e64838637a Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 28 Nov 2023 15:35:27 +0200
Subject: [PATCH] r-sarc: init

---
 BioArchLinux/r-sarc/PKGBUILD   | 63 ++++++++++++++++++++++++++++++++++
 BioArchLinux/r-sarc/lilac.py   | 14 ++++++++
 BioArchLinux/r-sarc/lilac.yaml | 32 +++++++++++++++++
 3 files changed, 109 insertions(+)
 create mode 100644 BioArchLinux/r-sarc/PKGBUILD
 create mode 100644 BioArchLinux/r-sarc/lilac.py
 create mode 100644 BioArchLinux/r-sarc/lilac.yaml

diff --git a/BioArchLinux/r-sarc/PKGBUILD b/BioArchLinux/r-sarc/PKGBUILD
new file mode 100644
index 0000000000..27a79e989c
--- /dev/null
+++ b/BioArchLinux/r-sarc/PKGBUILD
@@ -0,0 +1,63 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=SARC
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Statistical Analysis of Regions with CNVs"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-data.table
+  r-desctools
+  r-genomicfeatures
+  r-genomicranges
+  r-ggplot2
+  r-gridextra
+  r-gtable
+  r-iranges
+  r-metap
+  r-multtest
+  r-plotly
+  r-plyranges
+  r-raggedexperiment
+  r-rcolorbrewer
+  r-reshape2
+  r-scales
+  r-tidyverse
+)
+checkdepends=(
+  r-homo.sapiens
+  r-testthat
+  r-txdb.hsapiens.ucsc.hg38.knowngene
+)
+optdepends=(
+  r-genomicalignments
+  r-homo.sapiens
+  r-kableextra
+  r-knitr
+  r-mus.musculus
+  r-testthat
+  r-txdb.hsapiens.ucsc.hg38.knowngene
+  r-txdb.mmusculus.ucsc.mm10.knowngene
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('b3ccd1bbc820bc93c4b13ec4e3ec9705')
+sha256sums=('5f032cedb91ca13f975da592479c83ff79c87c3ba5dd4472c1c7df0b9cec7a10')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-sarc/lilac.py b/BioArchLinux/r-sarc/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-sarc/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-sarc/lilac.yaml b/BioArchLinux/r-sarc/lilac.yaml
new file mode 100644
index 0000000000..ca7ce46bb1
--- /dev/null
+++ b/BioArchLinux/r-sarc/lilac.yaml
@@ -0,0 +1,32 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-data.table
+- r-desctools
+- r-genomicfeatures
+- r-genomicranges
+- r-ggplot2
+- r-gridextra
+- r-gtable
+- r-iranges
+- r-metap
+- r-multtest
+- r-plotly
+- r-plyranges
+- r-raggedexperiment
+- r-rcolorbrewer
+- r-reshape2
+- r-scales
+- r-tidyverse
+repo_makedepends:
+- r-homo.sapiens
+- r-testthat
+- r-txdb.hsapiens.ucsc.hg38.knowngene
+update_on:
+- source: rpkgs
+  pkgname: SARC
+  repo: bioc
+  md5: true
+- alias: r