commit: fdbb0df35cd149e408bb18fdcfa8debc839c6026 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Feb 16 18:00:57 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Feb 16 18:00:57 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fdbb0df3
sci-biology/phusion2: renamed a package; version bump; note that upstream sourceforge site contains additional components of the bundle Package-Manager: portage-2.2.26 sci-biology/phusion2/metadata.xml | 12 ++++++++++ sci-biology/phusion2/phusion2-3.0.ebuild | 40 ++++++++++++++++++++++++++++++++ 2 files changed, 52 insertions(+) diff --git a/sci-biology/phusion2/metadata.xml b/sci-biology/phusion2/metadata.xml new file mode 100644 index 0000000..1699e58 --- /dev/null +++ b/sci-biology/phusion2/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> diff --git a/sci-biology/phusion2/phusion2-3.0.ebuild b/sci-biology/phusion2/phusion2-3.0.ebuild new file mode 100644 index 0000000..5f2d7ca --- /dev/null +++ b/sci-biology/phusion2/phusion2-3.0.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)" +HOMEPAGE="http://www.sanger.ac.uk/resources/software/phusion/"; +SRC_URI="http://downloads.sourceforge.net/project/${PN}/${P}.tar.gz"; + +LICENSE="all-rights-reserved" # temporarily placed value +# from http://genome.cshlp.org/content/13/1/81.full +# Availability +# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors. +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="app-shells/tcsh + sys-cluster/openmpi" +RDEPEND="${DEPEND} + sci-biology/phrap + dev-lang/perl" + +# contains bundled ssaha +# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq + +S="${WORKDIR}" + +src_prepare(){ + rm -f phusion2 *.o + sed -e 's/^CFLAGS =/# CFLAGS =/' -i Makefile || die +} + +src_install(){ + dobin ctgreads.pl phusion2 + dodoc how_to_make_mates +}
