From 6d66c7cab4c96e65fddb3eb2e7376587d8b3abc0 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sun, 22 Oct 2023 14:52:52 +0300
Subject: [PATCH] r-hicool: init

---
 BioArchLinux/r-hicool/PKGBUILD   | 53 ++++++++++++++++++++++++++++++++
 BioArchLinux/r-hicool/lilac.py   | 14 +++++++++
 BioArchLinux/r-hicool/lilac.yaml | 26 ++++++++++++++++
 3 files changed, 93 insertions(+)
 create mode 100644 BioArchLinux/r-hicool/PKGBUILD
 create mode 100644 BioArchLinux/r-hicool/lilac.py
 create mode 100644 BioArchLinux/r-hicool/lilac.yaml

diff --git a/BioArchLinux/r-hicool/PKGBUILD b/BioArchLinux/r-hicool/PKGBUILD
new file mode 100644
index 0000000000..578632a9a7
--- /dev/null
+++ b/BioArchLinux/r-hicool/PKGBUILD
@@ -0,0 +1,53 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=HiCool
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="HiCool"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(MIT)
+depends=(
+  r-basilisk
+  r-biocio
+  r-dplyr
+  r-genomicranges
+  r-hicexperiment
+  r-interactionset
+  r-iranges
+  r-plotly
+  r-reticulate
+  r-rmarkdown
+  r-rmdformats
+  r-s4vectors
+  r-sessioninfo
+  r-stringr
+  r-vroom
+)
+optdepends=(
+  r-annotationhub
+  r-biocfilecache
+  r-biocstyle
+  r-hicontacts
+  r-hicontactsdata
+  r-knitr
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('85a6824de7561e4879ae698959606ae3')
+sha256sums=('d44d599c72556a83602fcdb85c1fca32a1d2b4e2b449bf14808697b5e2bd2283')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}
diff --git a/BioArchLinux/r-hicool/lilac.py b/BioArchLinux/r-hicool/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-hicool/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-hicool/lilac.yaml b/BioArchLinux/r-hicool/lilac.yaml
new file mode 100644
index 0000000000..cc4262a02d
--- /dev/null
+++ b/BioArchLinux/r-hicool/lilac.yaml
@@ -0,0 +1,26 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-basilisk
+- r-biocio
+- r-dplyr
+- r-genomicranges
+- r-hicexperiment
+- r-interactionset
+- r-iranges
+- r-plotly
+- r-reticulate
+- r-rmarkdown
+- r-rmdformats
+- r-s4vectors
+- r-sessioninfo
+- r-stringr
+- r-vroom
+update_on:
+- source: rpkgs
+  pkgname: HiCool
+  repo: bioc
+  md5: true
+- alias: r