| # Copyright 1999-2014 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| EAPI="2" |
| |
| inherit 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/${P}.tar.gz" |
| |
| LICENSE="Artistic" |
| SLOT="0" |
| IUSE="" |
| KEYWORDS="amd64 x86" |
| |
| DEPEND="" |
| RDEPEND="sci-biology/bowtie" |
| |
| src_prepare() { |
| # fix missing includes |
| sed -i '/#include <string>/ a #include <stdio.h>' "${S}/src/gff_juncs.cpp" || die |
| sed -i \ |
| -e '/#include <stdio.h>/ a #include <unistd.h>' \ |
| "${S}/src/prep_reads.cpp" \ |
| "${S}/src/extract_reads.cpp" || die |
| # fix parallel make race |
| sed -i -e 's/\$(top_builddir)\/src\///g' src/Makefile.am || die |
| # remove broken arch-dependent CFLAGS setting |
| perl -i -ne 'print unless /case "\${host_cpu}-\${host_os}" in/../^esac/' configure.ac || die |
| eautoreconf |
| } |
| |
| src_install() { |
| einstall || die |
| dodoc AUTHORS NEWS THANKS |
| } |
