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# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit eutils flag-o-matic
DESCRIPTION="k-mer counter within reads for assemblies"
HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
LICENSE="GPL-3+ BSD"
SLOT="2"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse"
DEPEND=""
DEPEND="${RDEPEND}
virtual/pkgconfig"
src_prepare(){
# --with-sse enable SSE
# --with-half enable half float (16 bits)
# --with-int128 enable int128
local myconf
use cpu_flags_x86_sse && myconf+=( --with-sse )
econf ${myconf[@]}
eapply_user
}
src_install(){
default
mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
done
mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
rm -r "${ED}/usr/include/${P}" || die
mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
}
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