diff options
| -rw-r--r-- | sci-biology/phusion/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-biology/phusion/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/phusion/metadata.xml | 9 | ||||
| -rw-r--r-- | sci-biology/phusion/phusion-2.1c.ebuild | 42 |
4 files changed, 62 insertions, 0 deletions
diff --git a/sci-biology/phusion/ChangeLog b/sci-biology/phusion/ChangeLog new file mode 100644 index 000000000..b82964513 --- /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 <mmokrejs@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/Manifest b/sci-biology/phusion/Manifest new file mode 100644 index 000000000..ded1cc97c --- /dev/null +++ b/sci-biology/phusion/Manifest @@ -0,0 +1 @@ +DIST phusion_pipeline_v2.1c.tar.gz 12029104 SHA256 d6cd98d9194faf91c3b497c569529f0b0af8b2fa7bf083d24a5c946fd2804457 SHA512 b5ed5b2b893fa3d4cdbb6ae96acf515894b1df65ba2536f3a47829f383eca1e157f1b7b117e0d1bf0f763328e8bc2ffddac9a570dbec757c057040c3fb66a765 WHIRLPOOL 76d21eb6ab558395ac7b18043b4e4e31d1b2a6f02779f09fcbc2e2591a304738af5ab9abe042d3a982f73fd04cf32c1125d8798f3e04ab6fb67fcaa7c2b6e642 diff --git a/sci-biology/phusion/metadata.xml b/sci-biology/phusion/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /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>mmokrejs@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 000000000..14fde04dc --- /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/* +} |