From ae48f5535197bacecee93ca8e55d552754f3765d Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Thu, 30 Nov 2023 17:58:17 +0200
Subject: [PATCH] r-epistasisga: init

---
 BioArchLinux/r-epistasisga/PKGBUILD   | 57 +++++++++++++++++++++++++++
 BioArchLinux/r-epistasisga/lilac.py   | 14 +++++++
 BioArchLinux/r-epistasisga/lilac.yaml | 32 +++++++++++++++
 3 files changed, 103 insertions(+)
 create mode 100644 BioArchLinux/r-epistasisga/PKGBUILD
 create mode 100644 BioArchLinux/r-epistasisga/lilac.py
 create mode 100644 BioArchLinux/r-epistasisga/lilac.yaml

diff --git a/BioArchLinux/r-epistasisga/PKGBUILD b/BioArchLinux/r-epistasisga/PKGBUILD
new file mode 100644
index 0000000000..fc629d1be2
--- /dev/null
+++ b/BioArchLinux/r-epistasisga/PKGBUILD
@@ -0,0 +1,57 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=epistasisGA
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="An R package to identify multi-snp effects in nuclear family studies using the GADGETS method"
+arch=(x86_64)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  blas
+  lapack
+  r-batchtools
+  r-bigmemory
+  r-biocparallel
+  r-data.table
+  r-ggplot2
+  r-igraph
+  r-matrixstats
+  r-qgraph
+)
+makedepends=(
+  r-bh
+  r-rcpp
+  r-rcpparmadillo
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-kableextra
+  r-knitr
+  r-magrittr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('79635d9683f002813e51fa3c17e49b39')
+sha256sums=('214867cd3357037f6c094be7ef2dda4c7fb5653a84fd86b2c8354b06882ad836')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-epistasisga/lilac.py b/BioArchLinux/r-epistasisga/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-epistasisga/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-epistasisga/lilac.yaml b/BioArchLinux/r-epistasisga/lilac.yaml
new file mode 100644
index 0000000000..112ad04776
--- /dev/null
+++ b/BioArchLinux/r-epistasisga/lilac.yaml
@@ -0,0 +1,32 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-batchtools
+- r-bigmemory
+- r-biocparallel
+- r-data.table
+- r-ggplot2
+- r-igraph
+- r-matrixstats
+- r-qgraph
+repo_makedepends:
+- r-bh
+- r-rcpp
+- r-rcpparmadillo
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: epistasisGA
+  repo: bioc
+  md5: true
+- alias: r
+- source: alpmfiles
+  pkgname: blas
+  filename: usr/lib/libblas\.so\.([^.]+)
+  repo: extra
+- source: alpmfiles
+  pkgname: lapack
+  filename: usr/lib/liblapack\.so\.([^.]+)
+  repo: extra