From owner-svn-ports-head@freebsd.org Wed Mar 23 11:22:41 2016 Return-Path: Delivered-To: svn-ports-head@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 1415EADAC09; Wed, 23 Mar 2016 11:22:41 +0000 (UTC) (envelope-from rakuco@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 CB1711ECF; Wed, 23 Mar 2016 11:22:40 +0000 (UTC) (envelope-from rakuco@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id u2NBMeGO025309; Wed, 23 Mar 2016 11:22:40 GMT (envelope-from rakuco@FreeBSD.org) Received: (from rakuco@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u2NBMdrv025303; Wed, 23 Mar 2016 11:22:39 GMT (envelope-from rakuco@FreeBSD.org) Message-Id: <201603231122.u2NBMdrv025303@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: rakuco set sender to rakuco@FreeBSD.org using -f From: Raphael Kubo da Costa Date: Wed, 23 Mar 2016 11:22:39 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r411698 - in head/biology: . bowtie2 bowtie2/files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 23 Mar 2016 11:22:41 -0000 Author: rakuco Date: Wed Mar 23 11:22:39 2016 New Revision: 411698 URL: https://svnweb.freebsd.org/changeset/ports/411698 Log: New port: biology/bowtie2. Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. This is Bowtie version 2, which will need to coexists with Bowtie 1 for the foreseeable future. Both are required by certain genomics pipelines, in some cases (e.g. Trinity) by the same pipeline. WWW: https://github.com/BenLangmead/bowtie2 PR: 207908 Submitted by: Jason Bacon Added: head/biology/bowtie2/ head/biology/bowtie2/Makefile (contents, props changed) head/biology/bowtie2/distinfo (contents, props changed) head/biology/bowtie2/files/ head/biology/bowtie2/files/patch-Makefile (contents, props changed) head/biology/bowtie2/pkg-descr (contents, props changed) head/biology/bowtie2/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Wed Mar 23 11:00:44 2016 (r411697) +++ head/biology/Makefile Wed Mar 23 11:22:39 2016 (r411698) @@ -13,6 +13,7 @@ SUBDIR += biojava SUBDIR += blat SUBDIR += bowtie + SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += cd-hit SUBDIR += cdbfasta Added: head/biology/bowtie2/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie2/Makefile Wed Mar 23 11:22:39 2016 (r411698) @@ -0,0 +1,40 @@ +# Created by: Jason Bacon +# $FreeBSD$ + +PORTNAME= bowtie2 +PORTVERSION= 2.2.7 +DISTVERSIONPREFIX= v +CATEGORIES= biology + +MAINTAINER= bacon4000@gmail.com +COMMENT= Ultrafast, memory-efficient short read aligner + +LICENSE= GPLv3 + +# May also work on other 64-bit platforms, but untested +ONLY_FOR_ARCHS= amd64 +USES= gmake perl5 shebangfix +USE_PERL5= run +SHEBANG_FILES= scripts/*.pl + +USE_GITHUB= yes +GH_ACCOUNT= BenLangmead + +post-install: + ${MKDIR} ${STAGEDIR}${DATADIR}/scripts + ${INSTALL_PROGRAM} \ + ${WRKSRC}/bowtie2*-s \ + ${WRKSRC}/bowtie2*-l \ + ${STAGEDIR}${PREFIX}/bin + ${INSTALL_SCRIPT} \ + ${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} + +.include Added: head/biology/bowtie2/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie2/distinfo Wed Mar 23 11:22:39 2016 (r411698) @@ -0,0 +1,2 @@ +SHA256 (BenLangmead-bowtie2-v2.2.7_GH0.tar.gz) = 54a66a1ce0d1afa75198cc10e9e4e7436cc86cd7d6d93ae41c079462a1c19916 +SIZE (BenLangmead-bowtie2-v2.2.7_GH0.tar.gz) = 5813850 Added: head/biology/bowtie2/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie2/files/patch-Makefile Wed Mar 23 11:22:39 2016 (r411698) @@ -0,0 +1,22 @@ +--- Makefile.orig 2016-02-11 17:20:57 UTC ++++ Makefile +@@ -21,8 +21,8 @@ + # Makefile for bowtie, bowtie2-build, bowtie2-inspect + # + +-prefix = /usr/local +-bindir = $(prefix)/bin ++PREFIX ?= /usr/local ++bindir = $(PREFIX)/bin + + INC = + GCC_PREFIX = $(shell dirname `which gcc`) +@@ -169,7 +169,7 @@ SSE_FLAG=-msse2 + + DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) + DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" +-RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 ++RELEASE_FLAGS = $(CXXFLAGS) $(SSE_FLAG) -funroll-loops + RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" + NOASSERT_FLAGS = -DNDEBUG + FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE Added: head/biology/bowtie2/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie2/pkg-descr Wed Mar 23 11:22:39 2016 (r411698) @@ -0,0 +1,5 @@ +Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short +DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp +reads per hour. + +WWW: https://github.com/BenLangmead/bowtie2 Added: head/biology/bowtie2/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie2/pkg-plist Wed Mar 23 11:22:39 2016 (r411698) @@ -0,0 +1,64 @@ +bin/bowtie2 +bin/bowtie2-align-l +bin/bowtie2-align-s +bin/bowtie2-build +bin/bowtie2-build-l +bin/bowtie2-build-s +bin/bowtie2-inspect +bin/bowtie2-inspect-l +bin/bowtie2-inspect-s +%%DATADIR%%/scripts/convert_quals.pl +%%DATADIR%%/scripts/gen_2b_occ_lookup.pl +%%DATADIR%%/scripts/gen_occ_lookup.pl +%%DATADIR%%/scripts/gen_solqual_lookup.pl +%%DATADIR%%/scripts/infer_fraglen.pl +%%DATADIR%%/scripts/make_a_thaliana_tair.sh +%%DATADIR%%/scripts/make_b_taurus_UMD3.sh +%%DATADIR%%/scripts/make_c_elegans.sh +%%DATADIR%%/scripts/make_canFam2.sh +%%DATADIR%%/scripts/make_d_melanogaster.sh +%%DATADIR%%/scripts/make_e_coli.sh +%%DATADIR%%/scripts/make_h_sapiens_ncbi36.sh +%%DATADIR%%/scripts/make_h_sapiens_ncbi37.sh +%%DATADIR%%/scripts/make_hg18.sh +%%DATADIR%%/scripts/make_hg19.sh +%%DATADIR%%/scripts/make_m_musculus_ncbi37.sh +%%DATADIR%%/scripts/make_mm10.sh +%%DATADIR%%/scripts/make_mm9.sh +%%DATADIR%%/scripts/make_rn4.sh +%%DATADIR%%/scripts/make_s_cerevisiae.sh +%%PORTDOCS%%%%DOCSDIR%%/README +%%PORTDOCS%%%%DOCSDIR%%/images/bowtie_logo.png +%%PORTDOCS%%%%DOCSDIR%%/images/osi-certified.gif +%%PORTDOCS%%%%DOCSDIR%%/images/sflogo.png +%%PORTDOCS%%%%DOCSDIR%%/images/university.small.horizontal.white.png +%%PORTDOCS%%%%DOCSDIR%%/manual.html +%%PORTDOCS%%%%DOCSDIR%%/release.txt +%%PORTDOCS%%%%DOCSDIR%%/strip_markdown.pl +%%PORTDOCS%%%%DOCSDIR%%/style.css +%%PORTDOCS%%%%DOCSDIR%%/website/faq.shtml +%%PORTDOCS%%%%DOCSDIR%%/website/faq.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/foot.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/index.html +%%PORTDOCS%%%%DOCSDIR%%/website/index.shtml +%%PORTDOCS%%%%DOCSDIR%%/website/manual.shtml +%%PORTDOCS%%%%DOCSDIR%%/website/manual.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/news.shtml +%%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml +%%PORTDOCS%%%%DOCSDIR%%/website/push.sh +%%PORTDOCS%%%%DOCSDIR%%/website/push_images.sh +%%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/top.ssi +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.1.bt2 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.2.bt2 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.3.bt2 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.4.bt2 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.1.bt2 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.2.bt2 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/longreads.fq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_1.fq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_2.fq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/simulate.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reference/lambda_virus.fa