From 5c9d660bc452933079c8e5f74fa004ba23211295 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sun, 15 Oct 2023 13:16:32 +0300
Subject: [PATCH] r-bg2: init

---
 BioArchLinux/r-bg2/PKGBUILD   | 37 +++++++++++++++++++++++++++++++++++
 BioArchLinux/r-bg2/lilac.py   | 17 ++++++++++++++++
 BioArchLinux/r-bg2/lilac.yaml | 14 +++++++++++++
 3 files changed, 68 insertions(+)
 create mode 100644 BioArchLinux/r-bg2/PKGBUILD
 create mode 100644 BioArchLinux/r-bg2/lilac.py
 create mode 100644 BioArchLinux/r-bg2/lilac.yaml

diff --git a/BioArchLinux/r-bg2/PKGBUILD b/BioArchLinux/r-bg2/PKGBUILD
new file mode 100644
index 0000000000..78b677598f
--- /dev/null
+++ b/BioArchLinux/r-bg2/PKGBUILD
@@ -0,0 +1,37 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=BG2
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Performs Bayesian GWAS analysis for non-Gaussian data using BG2"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-caret
+  r-ga
+  r-memoise
+)
+optdepends=(
+  r-biocstyle
+  r-formatr
+  r-knitr
+  r-rmarkdown
+  r-rrblup
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('261572229e90f2182464a60b7e938b5b')
+sha256sums=('e17b5bddb3afe5364045dbc1451f885decc9f229275dc03b91c54a49c99b3e62')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-bg2/lilac.py b/BioArchLinux/r-bg2/lilac.py
new file mode 100644
index 0000000000..c08ad6cea8
--- /dev/null
+++ b/BioArchLinux/r-bg2/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_license = "GPL-3 + file LICENSE",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-bg2/lilac.yaml b/BioArchLinux/r-bg2/lilac.yaml
new file mode 100644
index 0000000000..c9972c2583
--- /dev/null
+++ b/BioArchLinux/r-bg2/lilac.yaml
@@ -0,0 +1,14 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-caret
+- r-ga
+- r-memoise
+update_on:
+- source: rpkgs
+  pkgname: BG2
+  repo: bioc
+  md5: true
+- alias: r