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# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=4
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/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="+bam debug"
DEPEND="
dev-libs/boost
bam? ( sci-biology/samtools )"
RDEPEND="${DEPEND}
sci-biology/bowtie"
PATCHES=( "${FILESDIR}"/${P}-flags.patch )
src_configure() {
local myeconfargs=( $(use_enable debug) )
autotools-utils_src_configure
}
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