diff options
Diffstat (limited to 'sci-biology/SPAdes/SPAdes-3.11.1.ebuild')
-rw-r--r-- | sci-biology/SPAdes/SPAdes-3.11.1.ebuild | 72 |
1 files changed, 72 insertions, 0 deletions
diff --git a/sci-biology/SPAdes/SPAdes-3.11.1.ebuild b/sci-biology/SPAdes/SPAdes-3.11.1.ebuild new file mode 100644 index 000000000..1842fca37 --- /dev/null +++ b/sci-biology/SPAdes/SPAdes-3.11.1.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2018 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://cab.spbu.ru/software/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 -> ${P}_truspades_manual.html" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=" + sys-libs/zlib + app-arch/bzip2 + dev-python/regex" +RDEPEND="${DEPEND}" +# BUG: +# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used, +# not *.so or *.a are even used) +# +# 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, being installed as bwa-spades binary? +# 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 || $(gcc-major-version) -lt 4 ]] ; then + eerror "You need at least sys-devel/gcc-4.7.0" + die "You need at least sys-devel/gcc-4.7.0" + fi + fi + fi +} + +src_compile(){ + PREFIX="${ED}"/usr ./spades_compile.sh || die +} + +src_install(){ + # BUG: move *.py files to standard site-packages/ subdirectories + insinto /usr/share/"${PN}" + dodoc "${DISTDIR}"/${P}_*manual.html +} |