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diff --git a/sci-biology/tophat/tophat-2.0.0.ebuild b/sci-biology/tophat/tophat-2.0.0.ebuild
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+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.0.ebuild,v 1.1 2012/04/15 21:21:30 weaver Exp $
+
+EAPI=4
+
+inherit flag-o-matic autotools
+
+DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
+HOMEPAGE="http://tophat.cbcb.umd.edu/"
+SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE="+bam"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="bam? ( sci-biology/samtools )"
+RDEPEND="${DEPEND}
+	sci-biology/bowtie"
+
+MAKEOPTS="${MAKEOPTS} -j1"
+
+src_prepare() {
+	filter-ldflags -Wl,--as-needed
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		$(use_with bam) || die
+}
+
+src_install() {
+	einstall || die
+	dodoc AUTHORS NEWS THANKS
+}