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

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     413c2c2dd02a27666281094f516976c8c7f3f357
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 15:20:19 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 15:20:19 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=413c2c2d

sci-biology/SPAdes: new package

Package-Manager: portage-2.2.26

 sci-biology/SPAdes/SPAdes-3.5.0.ebuild | 48 ++++++++++++++++++++++++++++++++++
 sci-biology/SPAdes/metadata.xml        |  9 +++++++
 2 files changed, 57 insertions(+)

diff --git a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild b/sci-biology/SPAdes/SPAdes-3.5.0.ebuild
new file mode 100644
index 0000000..7265909
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.5.0.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} )
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="De novo assembler for smaller genomes (bacteria to fungi)"
+HOMEPAGE="http://bioinf.spbau.ru/en/spades"
+SRC_URI="http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz
+	http://spades.bioinf.spbau.ru/release3.5.0/manual.html"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sys-libs/zlib
+	app-arch/bzip2
+	dev-python/regex
+	dev-libs/boost"
+RDEPEND="${DEPEND}"
+
+pkg_pretend() {
+	if [[ ${MERGE_TYPE} != binary ]]; then
+		if [[ $(tc-getCXX) == *g++ ]] ; then
+			if [[ $(gcc-major-version) == 4 && $(gcc-minor-version) -lt 7 || $(gcc-major-version) -lt 4 ]] ; then
+				eerror "You need at least sys-devel/gcc-4.7.0"
+				die "You need at least sys-devel/gcc-4.7.0"
+			fi
+		fi
+	fi
+}
+
+src_prepare(){
+	insinto /usr/share/doc/SPAdes
+	dodoc "${DISTDIR}"/manual.html
+}
+
+src_compile(){
+	# grr, it actually also installs the files into $PREFIX
+	PREFIX="${D}"/usr ./spades_compile.sh || die
+}
+
+# BUG: contents of "${D}" do not propagate during qmerge?

diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/SPAdes/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>