1 files changed, 40 insertions, 0 deletions
diff --git a/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild
new file mode 100644
index 000000000000..36322f463de6
--- /dev/null
+++ b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
+
+DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq"
+HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
+SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="Artistic"
+IUSE="debug"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	>=sci-biology/samtools-0.1.18
+	<sci-biology/samtools-1
+	<dev-libs/boost-1.56:="
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-autotools.patch
+	"${FILESDIR}"/${P}-boost.patch
+	"${FILESDIR}"/${P}-gcc-4.7.patch
+	)
+
+src_configure() {
+	local myeconfargs=(
+		--disable-optim
+		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/"
+		--with-bam="${EPREFIX}/usr/"
+		$(use_enable debug)
+	)
+	autotools-utils_src_configure
+}