1 files changed, 54 insertions, 0 deletions
diff --git a/sci-biology/stacks/stacks-2.60.ebuild b/sci-biology/stacks/stacks-2.60.ebuild
new file mode 100644
index 000000000..4de3f8da8
--- /dev/null
+++ b/sci-biology/stacks/stacks-2.60.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-module webapp autotools
+
+DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics"
+HOMEPAGE="http://creskolab.uoregon.edu/stacks"
+SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
+
+LICENSE="GPL-3"
+KEYWORDS="~amd64"
+
+RESTRICT="test"
+
+DEPEND="
+	>=sci-libs/htslib-1.3.1:0
+	dev-cpp/sparsehash
+	sci-biology/samtools:*
+	sci-biology/bamtools
+	sci-biology/gmap
+"
+
+RDEPEND="${DEPEND}
+	dev-lang/perl
+	>=dev-lang/php-5:*
+	dev-perl/DBD-mysql
+"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-make-install.patch"
+)
+
+src_prepare(){
+	default
+	#mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
+	if [ -z "$mycppflags" ]; then mycppflags="."; fi
+	sed -e "s#-I./htslib/htslib#-I/usr/include/bam -I${mycppflags}#" -i configure.ac || die
+	eautoreconf
+}
+
+src_configure() {
+	econf
+	sed -e 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' -i Makefile || die
+}
+
+src_install() {
+	webapp_src_preinst
+	DESTDIR="${ED}" default
+	DESTDIR="${ED}" perl-module_src_install
+	dodir /usr/share/webapps/${PN}/${PV}
+	webapp_src_install
+}