commit: 9ce7d7d02ffa5ea884d926a61506108d5db723a5 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon Mar 24 01:14:56 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon Mar 24 01:14:56 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9ce7d7d0
sci-biology/sga: new package; forces its own optimization flags but works fine --- sci-biology/sga/ChangeLog | 10 +++++++++ sci-biology/sga/metadata.xml | 9 ++++++++ sci-biology/sga/sga-9999.ebuild | 47 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 66 insertions(+) diff --git a/sci-biology/sga/ChangeLog b/sci-biology/sga/ChangeLog new file mode 100644 index 0000000..0f7e181 --- /dev/null +++ b/sci-biology/sga/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/sga +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*sga-9999 (24 Mar 2014) + + 24 Mar 2014; Martin Mokrejs <[email protected]> +sga-9999.ebuild, + +metadata.xml: + new package; forces its own optimization flags but works fine + diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/sga/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> diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild new file mode 100644 index 0000000..5393f87 --- /dev/null +++ b/sci-biology/sga/sga-9999.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +[ "$PV" == "9999" ] && inherit git-2 + +DESCRIPTION="String Graph Assembler for short-read assemblies" +HOMEPAGE="https://github.com/jts/sga"; +EGIT_REPO_URI="git://github.com/jts/sga" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="jemalloc python" + +DEPEND="dev-cpp/sparsehash + sci-biology/bamtools + sys-libs/zlib + jemalloc? ( dev-libs/jemalloc ) + python? ( sci-biology/pysam + sci-biology/ruffus )" +RDEPEND="${DEPEND}" + +src_configure(){ + cd src || die + ./autogen.sh + econf --with-bamtools=/usr +} + +src_compile(){ + cd src || die + emake +} + +src_install(){ + cd src || die + dodoc README + emake install DESTDIR="${D}" + insinto /usr/share/sga/examples + doins examples/* + cd .. || + dodoc README.md +}
