From ba7c3d5224ef3d33ffeb29144ab604122591e3e9 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sun, 22 Oct 2023 16:50:26 +0300
Subject: [PATCH] r-intomics: init

---
 BioArchLinux/r-intomics/PKGBUILD   | 56 ++++++++++++++++++++++++++++++
 BioArchLinux/r-intomics/lilac.py   | 14 ++++++++
 BioArchLinux/r-intomics/lilac.yaml | 27 ++++++++++++++
 3 files changed, 97 insertions(+)
 create mode 100644 BioArchLinux/r-intomics/PKGBUILD
 create mode 100644 BioArchLinux/r-intomics/lilac.py
 create mode 100644 BioArchLinux/r-intomics/lilac.yaml

diff --git a/BioArchLinux/r-intomics/PKGBUILD b/BioArchLinux/r-intomics/PKGBUILD
new file mode 100644
index 0000000000..f1fc1d82fb
--- /dev/null
+++ b/BioArchLinux/r-intomics/PKGBUILD
@@ -0,0 +1,56 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=IntOMICS
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Integrative analysis of multi-omics data to infer regulatory networks"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-bestnormalize
+  r-bnlearn
+  r-bnstruct
+  r-cowplot
+  r-ggplot2
+  r-ggraph
+  r-gplots
+  r-igraph
+  r-matrixstats
+  r-numbers
+  r-rcolorbrewer
+  r-rlang
+  r-summarizedexperiment
+)
+checkdepends=(
+  r-multiassayexperiment
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-curatedtcgadata
+  r-knitr
+  r-rmarkdown
+  r-tcgautils
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('eec7530ce0fd9941c0cfe06c864e7511')
+sha256sums=('370511a058607140956106269f754afc533bd869b6f9574833b5ba74f4defd80')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-intomics/lilac.py b/BioArchLinux/r-intomics/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-intomics/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-intomics/lilac.yaml b/BioArchLinux/r-intomics/lilac.yaml
new file mode 100644
index 0000000000..a86da511b4
--- /dev/null
+++ b/BioArchLinux/r-intomics/lilac.yaml
@@ -0,0 +1,27 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-bestnormalize
+- r-bnlearn
+- r-bnstruct
+- r-cowplot
+- r-ggplot2
+- r-ggraph
+- r-gplots
+- r-igraph
+- r-matrixstats
+- r-numbers
+- r-rcolorbrewer
+- r-rlang
+- r-summarizedexperiment
+repo_makedepends:
+- r-multiassayexperiment
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: IntOMICS
+  repo: bioc
+  md5: true
+- alias: r