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>[email protected]</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
