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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.cbcb.umd.edu/software/jellyfish"
SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
# also was bundled in quorum-0.2.1 and MaSuRca-2.1.0
# also bundled in SEECER-0.1.3
LICENSE="GPL-3+ BSD"
SLOT="1"
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 econf ${myconf[@]}
eapply_user
}
src_install(){
default
# install the binary under jellyfish1 name like Debian/Ubuntu to avoid name clash with jellyfish2 and allow simultaneous installs
mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish1 || die
sed -e "s#jellyfish-${PV}#jellyfish1#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-1.1.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"${SLOT}".1 || die
newdoc doc/jellyfish.pdf jellyfish"${SLOT}".pdf
}
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