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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
PYTHON_COMPAT=( python{2_7,3_{4,5}} )
inherit eutils toolchain-funcs
DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
HOMEPAGE="http://bioinf.spbau.ru/en/spades"
SRC_URI="
http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz
http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html
http://spades.bioinf.spbau.ru/release${PV}/dipspades_manual.html -> ${P}_dipspades_manual.html
http://spades.bioinf.spbau.ru/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
http://spades.bioinf.spbau.ru/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND="
sys-libs/zlib
app-arch/bzip2
dev-python/regex
dev-libs/boost"
RDEPEND="${DEPEND}"
# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their
# existing packages
# nlopt
# llvm
# python_libs
# bamtools
# ConsensusCore
# ssw
# jemalloc
# htrie
# getopt_pp
# cppformat
# cityhash
# samtools
# bwa
# BUG: "${S}"/ext/tools/ contains even two version of bwa
# bwa-0.7.12
# bwa-0.6.2
pkg_pretend() {
if [[ ${MERGE_TYPE} != binary ]]; then
if [[ $(tc-getCXX) == *g++ ]] ; then
if [[ $(gcc-major-version) == 4 && $(gcc-minor-version) -lt 7 || $(gcc-major-version) -lt 4 ]] ; then
eerror "You need at least sys-devel/gcc-4.7.0"
die "You need at least sys-devel/gcc-4.7.0"
fi
fi
fi
}
src_prepare(){
# https://github.com/Homebrew/homebrew-science/pull/5616
epatch "${FILESDIR}"/"${P}"-fix-missing-include.patch
cp -p spades_compile.sh spades_install.sh || die
sed -e 's/make install/#make install/;s/cd $PREFIX/#cd $PREFIX/' -i spades_compile.sh || die
default
}
src_compile(){
mkdir build_spades || die
cd build_spades || die
cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="${ED}/usr" $* "${S}/src" || die
}
src_install(){
cd build_spades || die
emake install PREFIX="${ED}"/usr
# BUG: move *.py files to standard site-packages/ subdirectories
insinto /usr/share/"${PN}"
dodoc "${DISTDIR}"/${P}_*manual.html
}
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