From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 889541381DF for ; Tue, 16 Feb 2016 18:03:49 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 027E2E07A0; Tue, 16 Feb 2016 18:03:47 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 9045DE07A0 for ; Tue, 16 Feb 2016 18:03:45 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C4701340B9C for ; Tue, 16 Feb 2016 18:03:44 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 4EDB6E5F for ; Tue, 16 Feb 2016 18:03:43 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1455645657.fdbb0df35cd149e408bb18fdcfa8debc839c6026.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/phusion2/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/phusion2/metadata.xml sci-biology/phusion2/phusion2-3.0.ebuild X-VCS-Directories: sci-biology/phusion2/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: fdbb0df35cd149e408bb18fdcfa8debc839c6026 X-VCS-Branch: master Date: Tue, 16 Feb 2016 18:03:43 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 909f9b51-84a0-40c4-8a13-61c4ef41bd15 X-Archives-Hash: 979d5c41f1c3645999aa86cb699c2e02 commit: fdbb0df35cd149e408bb18fdcfa8debc839c6026 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Feb 16 18:00:57 2016 +0000 Commit: Martin Mokrejs fold natur cuni 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 @@ + + + + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + + + sci-biology@gentoo.org + Gentoo Biology Project + + 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 +}