commit: c0c2589594db6900b277d68628ece4d62254e1ae Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Mar 30 20:22:23 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Mar 30 20:22:23 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c0c25895
sci-biology/arachne: new package; does not compile (upstream contacted) and the LICENSE is not exactly MIT? Package-Manager: portage-2.2.28 sci-biology/arachne/arachne-46233.ebuild | 41 ++++++++++++++++++++++++++++++++ sci-biology/arachne/metadata.xml | 12 ++++++++++ 2 files changed, 53 insertions(+) diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild new file mode 100644 index 0000000..71fc0b8 --- /dev/null +++ b/sci-biology/arachne/arachne-46233.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="Whole genome shotgun assembler for Sanger read lengths (overlap-layout-contig)" +HOMEPAGE="https://www.broadinstitute.org/crd/wiki + http://genome.cshlp.org/content/12/1/177.abstract"; +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"; + +LICENSE="MIT" # not exactly MIT ... hence no KEYWORDS +SLOT="0" +KEYWORDS="" +IUSE="doc openmp" + +DEPEND="dev-libs/xerces-c + doc? ( virtual/latex-base app-text/dvipsk )" +RDEPEND="${DEPEND}" + +# needs >=g++-4.7 but does not compile with 5.3.0 + +# --disable-openmp to disable requirement for OpenMP-capable compiler +src_configure() { + local myconf=() + use openmp || myconf+=( --disable-openmp ) + econf ${myconf[@]} +} + +# set the following environment variables +# http://www.broadinstitute.org/crd/wiki/index.php/Setup +# +# ARACHNE_PRE +# ARACHNE_BIN_DIR +# ARACHNE_PRETTY_HELP + +pkg_postinst(){ + einfo "Please add these to your ~/.bashrc" + einfo "limit stacksize 100000" + einfo "limit datasize unlimited" +} diff --git a/sci-biology/arachne/metadata.xml b/sci-biology/arachne/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/arachne/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata>
