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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit eutils flag-o-matic autotools
DESCRIPTION="k-mer counter within reads for assemblies"
HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
SRC_URI="https://github.com/gmarcais/Jellyfish/archive/v2.2.6.tar.gz -> ${P}.tar.gz
ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
LICENSE="GPL-3+ BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse"
RDEPEND="dev-lang/yaggo"
DEPEND="${RDEPEND}
virtual/pkgconfig"
S="${WORKDIR}/Jellyfish-${PV}"
src_prepare(){
eautoreconf
default
}
# TODO: enable compilation of Bindings to Ruby, Python and Perl
# '--enable-ruby-binding', '--enable-python-binding' or '--enable-perl-binding', '--enable-swig'
src_configure(){
# --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 ${myconf[@]}
}
src_install(){
default
sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
mkdir -p "${ED}/usr/include/${PN}" || die
mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}/" || die
rm -r "${ED}/usr/include/${P}" || die
}
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