From f6ceab09f1f3515969c482a13a5baaeded68286c Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 28 Nov 2023 15:34:08 +0200
Subject: [PATCH] r-rvisdiff: init

---
 BioArchLinux/r-rvisdiff/PKGBUILD   | 38 ++++++++++++++++++++++++++++++
 BioArchLinux/r-rvisdiff/lilac.py   | 14 +++++++++++
 BioArchLinux/r-rvisdiff/lilac.yaml | 12 ++++++++++
 3 files changed, 64 insertions(+)
 create mode 100644 BioArchLinux/r-rvisdiff/PKGBUILD
 create mode 100644 BioArchLinux/r-rvisdiff/lilac.py
 create mode 100644 BioArchLinux/r-rvisdiff/lilac.yaml

diff --git a/BioArchLinux/r-rvisdiff/PKGBUILD b/BioArchLinux/r-rvisdiff/PKGBUILD
new file mode 100644
index 0000000000..96ddafd755
--- /dev/null
+++ b/BioArchLinux/r-rvisdiff/PKGBUILD
@@ -0,0 +1,38 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=Rvisdiff
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Interactive Graphs for Differential Expression"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL)
+depends=(
+  r-edger
+)
+optdepends=(
+  r-airway
+  r-biocmanager
+  r-biocstyle
+  r-deseq2
+  r-knitr
+  r-limma
+  r-matrixtests
+  r-rmarkdown
+  r-summarizedexperiment
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('3e3b8ccc9cb71388e2e7c17d60995cbe')
+sha256sums=('76a2afecab601bcbfbc0764f6ffaea20593a3cffadc2151d4846482caffd24ea')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}
diff --git a/BioArchLinux/r-rvisdiff/lilac.py b/BioArchLinux/r-rvisdiff/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-rvisdiff/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-rvisdiff/lilac.yaml b/BioArchLinux/r-rvisdiff/lilac.yaml
new file mode 100644
index 0000000000..d20e9e2fba
--- /dev/null
+++ b/BioArchLinux/r-rvisdiff/lilac.yaml
@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-edger
+update_on:
+- source: rpkgs
+  pkgname: Rvisdiff
+  repo: bioc
+  md5: true
+- alias: r