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# 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
}
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