[gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/

[Martin Mokrejs]

commit:     4dd7fc5f1806465684c1101c88021ab3e1993fa2
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan  9 22:03:02 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan  9 22:03:02 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4dd7fc5f

sci-biology/SPAdes: version bump

Try to follow the upstream's approach to compile and install
the tool. src_compile() therefore does also src_install()
into a DESTDIR.

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-biology/SPAdes/SPAdes-3.11.1.ebuild | 72 +++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)

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
+}