| # Copyright 1999-2014 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| EAPI=5 |
| |
| AUTOTOOLS_AUTORECONF=yes |
| PYTHON_COMPAT=( python2_7 ) |
| |
| inherit autotools-utils python-single-r1 |
| |
| DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" |
| HOMEPAGE="http://tophat.cbcb.umd.edu/" |
| SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz" |
| |
| LICENSE="Artistic" |
| SLOT="0" |
| KEYWORDS="~amd64 ~x86" |
| IUSE="debug" |
| |
| DEPEND=" |
| dev-libs/boost |
| sci-biology/samtools |
| ~sci-biology/seqan-1.3.1" |
| RDEPEND="${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 |
| $(use_enable debug) |
| ) |
| autotools-utils_src_configure |
| } |
| |
| src_install() { |
| autotools-utils_src_install |
| python_fix_shebang "${ED}"/usr/bin/tophat |
| } |
