commit: a73a521f084a0e830acc97812812a694a7fe3e00 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat May 2 15:09:00 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sat May 2 15:09:00 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a73a521f
sci-biology/phusion: clarified missing LICENSE, have asked upstream for clarification Package-Manager: portage-2.2.18 sci-biology/phusion/ChangeLog | 10 ++++++++ sci-biology/phusion/metadata.xml | 9 +++++++ sci-biology/phusion/phusion-2.1c.ebuild | 42 +++++++++++++++++++++++++++++++++ 3 files changed, 61 insertions(+) diff --git a/sci-biology/phusion/ChangeLog b/sci-biology/phusion/ChangeLog new file mode 100644 index 0000000..b829645 --- /dev/null +++ b/sci-biology/phusion/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/phusion +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*phusion-2.1c (02 May 2015) + + 02 May 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> +metadata.xml, + +phusion-2.1c.ebuild: + sci-biology/phusion: clarified missing LICENSE, have asked upstream for + clarification diff --git a/sci-biology/phusion/metadata.xml b/sci-biology/phusion/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/phusion/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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/phusion/phusion-2.1c.ebuild b/sci-biology/phusion/phusion-2.1c.ebuild new file mode 100644 index 0000000..14fde04 --- /dev/null +++ b/sci-biology/phusion/phusion-2.1c.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +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="ftp://ftp.sanger.ac.uk/pub/resources/software/phusion/phusion_pipeline_v2.1c.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" +RDEPEND="${DEPEND} + sci-biology/phrap + dev-lang/perl" + +# contains bundled ssaha +# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq + +S="${WORKDIR}"/"phusion_pipeline_v2.1c" + +src_prepare(){ + cp -pf /usr/bin/phrap src/phrap/phrap.manylong || die +} + +src_compile(){ + tcsh install.csh || csh install.csh || die +} + +src_install(){ + dobin bin/* + dodoc README.1st releaseNote_v2.1c doc/* +}
