1 files changed, 34 insertions, 0 deletions
diff --git a/sci-biology/RAILS/RAILS-1.5.1.ebuild b/sci-biology/RAILS/RAILS-1.5.1.ebuild
new file mode 100644
index 000000000..df5f0ea4a
--- /dev/null
+++ b/sci-biology/RAILS/RAILS-1.5.1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 2018-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Cobbler and RAILS scaffolding tools acting on SAM streams"
+HOMEPAGE="https://github.com/bcgsc/RAILS"
+SRC_URI="https://github.com/bcgsc/RAILS/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	dev-lang/perl
+	sci-biology/samtools
+	sci-biology/bwa
+"
+# bin/runRAILSminimap.sh calls minimap2 but one can stream the SAM data directly
+BDEPEND=""
+
+src_prepare(){
+	# remove hardcoded PATHs
+	# https://github.com/bcgsc/RAILS/issues/8
+	sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i bin/*.sh || die
+	default
+}
+
+src_install(){
+	dobin bin/*
+	dodoc readme.md paper/paper.pdf
+}