From b0e2de643849a951ec3ab584e3296c57c05a4f37 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Wed, 29 Nov 2023 13:36:40 +0200
Subject: [PATCH] r-cardelino: init

---
 BioArchLinux/r-cardelino/PKGBUILD   | 54 +++++++++++++++++++++++++++++
 BioArchLinux/r-cardelino/lilac.py   | 17 +++++++++
 BioArchLinux/r-cardelino/lilac.yaml | 24 +++++++++++++
 3 files changed, 95 insertions(+)
 create mode 100644 BioArchLinux/r-cardelino/PKGBUILD
 create mode 100644 BioArchLinux/r-cardelino/lilac.py
 create mode 100644 BioArchLinux/r-cardelino/lilac.yaml

diff --git a/BioArchLinux/r-cardelino/PKGBUILD b/BioArchLinux/r-cardelino/PKGBUILD
new file mode 100644
index 0000000000..4f2f6c45d1
--- /dev/null
+++ b/BioArchLinux/r-cardelino/PKGBUILD
@@ -0,0 +1,54 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=cardelino
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Clone Identification from Single Cell Data"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-combinat
+  r-genomeinfodb
+  r-genomicranges
+  r-ggplot2
+  r-ggtree
+  r-matrixstats
+  r-pheatmap
+  r-s4vectors
+  r-snpstats
+  r-variantannotation
+  r-vcfr
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-foreach
+  r-knitr
+  r-pcamethods
+  r-rmarkdown
+  r-testthat
+  r-vgam
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('363c06547419f29e1cdfe473651e1861')
+sha256sums=('f6ed2a646b833f4a63b0641731ce2c1dbc4718d76d7418c0878acb00561b8d78')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-cardelino/lilac.py b/BioArchLinux/r-cardelino/lilac.py
new file mode 100644
index 0000000000..39dc53390d
--- /dev/null
+++ b/BioArchLinux/r-cardelino/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_needscompilation = True,
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-cardelino/lilac.yaml b/BioArchLinux/r-cardelino/lilac.yaml
new file mode 100644
index 0000000000..3cfd5ae90b
--- /dev/null
+++ b/BioArchLinux/r-cardelino/lilac.yaml
@@ -0,0 +1,24 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-combinat
+- r-genomeinfodb
+- r-genomicranges
+- r-ggplot2
+- r-ggtree
+- r-matrixstats
+- r-pheatmap
+- r-s4vectors
+- r-snpstats
+- r-variantannotation
+- r-vcfr
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: cardelino
+  repo: bioc
+  md5: true
+- alias: r