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# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=4
inherit eutils toolchain-funcs flag-o-matic
MY_P=${PN}_${PV}
DESCRIPTION="A sequence assembler for very short reads"
HOMEPAGE="https://www.ebi.ac.uk/~zerbino/velvet/"
SRC_URI="https://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
LICENSE="GPL-2"
SLOT="0"
IUSE="-doc"
KEYWORDS="amd64 x86"
RDEPEND="sys-libs/zlib"
DEPEND="${RDEPEND}
doc? ( virtual/latex-base )"
S="${WORKDIR}"/${MY_P}
src_prepare() {
# necessary?
# append-flags -O3 # as recommended by upstream
epatch "${FILESDIR}"/${P}-gentoo-r1.diff
use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
}
src_compile() {
tc-export CC
MAKE_XOPTS=""
if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi
if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi
emake -j1 $MAKE_XOPTS || die
emake -j1 $MAKE_XOPTS color || die
}
src_install() {
dobin velvet{g,h,g_de,h_de} || die
insinto /usr/share/${PN}
doins -r contrib || die
dodoc Manual.pdf CREDITS.txt ChangeLog || die
}
pkg_postinst() {
elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual,"
elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your"
elog "environment or /etc/portage/make.conf, then re-emerge the package. For example:"
elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
}
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