From 275356af4d9f58abd6e8c923cb92a0562ae8b5e3 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Thu, 30 Nov 2023 15:35:42 +0200
Subject: [PATCH] r-dnafusion: init

---
 BioArchLinux/r-dnafusion/PKGBUILD   | 51 +++++++++++++++++++++++++++++
 BioArchLinux/r-dnafusion/lilac.py   | 14 ++++++++
 BioArchLinux/r-dnafusion/lilac.yaml | 23 +++++++++++++
 3 files changed, 88 insertions(+)
 create mode 100644 BioArchLinux/r-dnafusion/PKGBUILD
 create mode 100644 BioArchLinux/r-dnafusion/lilac.py
 create mode 100644 BioArchLinux/r-dnafusion/lilac.yaml

diff --git a/BioArchLinux/r-dnafusion/PKGBUILD b/BioArchLinux/r-dnafusion/PKGBUILD
new file mode 100644
index 0000000000..d6bea8b6e4
--- /dev/null
+++ b/BioArchLinux/r-dnafusion/PKGBUILD
@@ -0,0 +1,51 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=DNAfusion
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Identification of gene fusions using paired-end sequencing"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-bamsignals
+  r-biocbaseutils
+  r-biocgenerics
+  r-genomicalignments
+  r-genomicfeatures
+  r-genomicranges
+  r-iranges
+  r-rsamtools
+  r-s4vectors
+  r-txdb.hsapiens.ucsc.hg38.knowngene
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-knitr
+  r-rmarkdown
+  r-sessioninfo
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('b7ef2bb10bea5334d6d159208c284c16')
+sha256sums=('687e11a620c606ac02e5732f83ebdeb1c8edee1818d9ec38a84431b9d00c221d')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-dnafusion/lilac.py b/BioArchLinux/r-dnafusion/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-dnafusion/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-dnafusion/lilac.yaml b/BioArchLinux/r-dnafusion/lilac.yaml
new file mode 100644
index 0000000000..c90cee3b47
--- /dev/null
+++ b/BioArchLinux/r-dnafusion/lilac.yaml
@@ -0,0 +1,23 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-bamsignals
+- r-biocbaseutils
+- r-biocgenerics
+- r-genomicalignments
+- r-genomicfeatures
+- r-genomicranges
+- r-iranges
+- r-rsamtools
+- r-s4vectors
+- r-txdb.hsapiens.ucsc.hg38.knowngene
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: DNAfusion
+  repo: bioc
+  md5: true
+- alias: r