From owner-svn-ports-all@freebsd.org Tue Dec 20 17:01:28 2016 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id A28DAC898BD; Tue, 20 Dec 2016 17:01:28 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 555AD1E74; Tue, 20 Dec 2016 17:01:28 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id uBKH1RFd064379; Tue, 20 Dec 2016 17:01:27 GMT (envelope-from jrm@FreeBSD.org) Received: (from jrm@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id uBKH1RCp064377; Tue, 20 Dec 2016 17:01:27 GMT (envelope-from jrm@FreeBSD.org) Message-Id: <201612201701.uBKH1RCp064377@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jrm set sender to jrm@FreeBSD.org using -f From: Joseph Mingrone Date: Tue, 20 Dec 2016 17:01:27 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r429003 - head/biology/bowtie2 X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 20 Dec 2016 17:01:28 -0000 Author: jrm Date: Tue Dec 20 17:01:27 2016 New Revision: 429003 URL: https://svnweb.freebsd.org/changeset/ports/429003 Log: biology/bowtie2: Update to version 2.2.9 - Update license information. - Add python to USES (bowtie2-build bowtie2-inspect need python) - Add DOCS and EXAMPLES options Approved by: AMDmi3 (mentor) swills (mentor) Differential Revision: https://reviews.freebsd.org/D8182 Modified: head/biology/bowtie2/Makefile head/biology/bowtie2/distinfo Modified: head/biology/bowtie2/Makefile ============================================================================== --- head/biology/bowtie2/Makefile Tue Dec 20 16:48:12 2016 (r429002) +++ head/biology/bowtie2/Makefile Tue Dec 20 17:01:27 2016 (r429003) @@ -1,25 +1,28 @@ # Created by: Jason Bacon # $FreeBSD$ -PORTNAME= bowtie2 -PORTVERSION= 2.2.8 +PORTNAME= bowtie2 +PORTVERSION= 2.2.9 DISTVERSIONPREFIX= v -CATEGORIES= biology +CATEGORIES= biology MAINTAINER= bacon4000@gmail.com COMMENT= Ultrafast, memory-efficient short read aligner -LICENSE= GPLv3 +LICENSE= GPLv3+ +LICENSE_FILE= ${WRKSRC}/LICENSE # May also work on other 64-bit platforms, but untested ONLY_FOR_ARCHS= amd64 -USES= gmake perl5 shebangfix +USES= gmake perl5 python shebangfix USE_PERL5= run -SHEBANG_FILES= scripts/*.pl +SHEBANG_FILES= bowtie2-build bowtie2-inspect scripts/*.pl USE_GITHUB= yes GH_ACCOUNT= BenLangmead +OPTIONS_DEFINE= DOCS EXAMPLES + post-install: ${MKDIR} ${STAGEDIR}${DATADIR}/scripts ${INSTALL_PROGRAM} \ @@ -30,11 +33,11 @@ post-install: ${WRKSRC}/scripts/*.sh \ ${WRKSRC}/scripts/*.pl \ ${STAGEDIR}${DATADIR}/scripts - cd ${WRKSRC}/example && ${COPYTREE_SHARE} \ - 'index reads reference' \ - ${STAGEDIR}${EXAMPLESDIR} - cd ${WRKSRC}/doc && ${COPYTREE_SHARE} \ - \* \ - ${STAGEDIR}${DOCSDIR} + +post-install-DOCS-on: + (cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}) + +post-install-EXAMPLES-on: + (cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) .include Modified: head/biology/bowtie2/distinfo ============================================================================== --- head/biology/bowtie2/distinfo Tue Dec 20 16:48:12 2016 (r429002) +++ head/biology/bowtie2/distinfo Tue Dec 20 17:01:27 2016 (r429003) @@ -1,2 +1,3 @@ -SHA256 (BenLangmead-bowtie2-v2.2.8_GH0.tar.gz) = e4795f5779dfdefffcc9c341239c1fb6f7d78e15528c6094d9c580a5c0e87ac1 -SIZE (BenLangmead-bowtie2-v2.2.8_GH0.tar.gz) = 5814699 +TIMESTAMP = 1475861880 +SHA256 (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = af940f77fc36aabea90d3d865724fd7ec7e250788d2d2f793c45c713d16ae5ee +SIZE (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = 5815106