1 files changed, 40 insertions, 0 deletions
diff --git a/sci-biology/tophat/tophat-2.0.8.ebuild b/sci-biology/tophat/tophat-2.0.8.ebuild
new file mode 100644
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@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.8.ebuild,v 1.1 2013/03/13 16:33:37 jlec Exp $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+
+DEPEND="
+	dev-libs/boost
+	sci-biology/samtools
+	sci-biology/seqan"
+RDEPEND="${DEPEND}
+	sci-biology/bowtie"
+
+PATCHES=( "${FILESDIR}"/${P}-flags.patch )
+
+src_prepare() {
+	rm -rf src/SeqAn* || die
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	local myeconfargs=(
+		--disable-optim
+		$(use_enable debug)
+	)
+	autotools-utils_src_configure
+}