From owner-svn-ports-all@freebsd.org Sat Mar 5 13:21:28 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 75F1BA099A8; Sat, 5 Mar 2016 13:21:28 +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 51483977; Sat, 5 Mar 2016 13:21:28 +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 u25DLRDF023864; Sat, 5 Mar 2016 13:21:27 GMT (envelope-from rakuco@FreeBSD.org) Received: (from rakuco@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u25DLQGO023857; Sat, 5 Mar 2016 13:21:26 GMT (envelope-from rakuco@FreeBSD.org) Message-Id: <201603051321.u25DLQGO023857@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: rakuco set sender to rakuco@FreeBSD.org using -f From: Raphael Kubo da Costa Date: Sat, 5 Mar 2016 13:21:26 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r410180 - in head/biology: . bowtie bowtie/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-all@freebsd.org X-Mailman-Version: 2.1.21 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: Sat, 05 Mar 2016 13:21:28 -0000 Author: rakuco Date: Sat Mar 5 13:21:26 2016 New Revision: 410180 URL: https://svnweb.freebsd.org/changeset/ports/410180 Log: New port: biology/bowtie. 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: http://bowtie-bio.sourceforge.net/index.shtml PR: 206939 Submitted by: Jason Bacon Added: head/biology/bowtie/ head/biology/bowtie/Makefile (contents, props changed) head/biology/bowtie/distinfo (contents, props changed) head/biology/bowtie/files/ head/biology/bowtie/files/patch-Makefile (contents, props changed) head/biology/bowtie/pkg-descr (contents, props changed) head/biology/bowtie/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat Mar 5 13:19:33 2016 (r410179) +++ head/biology/Makefile Sat Mar 5 13:21:26 2016 (r410180) @@ -12,6 +12,7 @@ SUBDIR += biococoa SUBDIR += biojava SUBDIR += blat + SUBDIR += bowtie SUBDIR += bwa SUBDIR += cd-hit SUBDIR += cdbfasta Added: head/biology/bowtie/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie/Makefile Sat Mar 5 13:21:26 2016 (r410180) @@ -0,0 +1,45 @@ +# Created by: Jason Bacon +# $FreeBSD$ + +PORTNAME= bowtie +PORTVERSION= 1.1.2 +DISTVERSIONPREFIX= v +CATEGORIES= biology + +MAINTAINER= bacon4000@gmail.com +COMMENT= Ultrafast, memory-efficient short read aligner + +LICENSE= ART10 + +# May also work on other 64-bit platforms, but untested +ONLY_FOR_ARCHS= amd64 +# FIXME: bowtie-align intermittently dumps core when compiled with clang +# GCC 4.2 does not provide good performance +USE_GCC= yes +USES= gmake perl5 shebangfix +USE_PERL5= run +SHEBANG_FILES= scripts/*.pl + +USE_GITHUB= yes +GH_ACCOUNT= BenLangmead + +post-install: + ${MKDIR} ${STAGEDIR}${DATADIR}/scripts + ${INSTALL_SCRIPT} \ + ${WRKSRC}/bowtie \ + ${WRKSRC}/bowtie-build \ + ${WRKSRC}/bowtie-inspect \ + ${STAGEDIR}${PREFIX}/bin + ${INSTALL_SCRIPT} \ + ${WRKSRC}/scripts/*.sh \ + ${WRKSRC}/scripts/*.pl \ + ${STAGEDIR}${DATADIR}/scripts + cd ${WRKSRC} && ${COPYTREE_SHARE} \ + 'genomes indexes reads' \ + ${STAGEDIR}${DATADIR} + cd ${WRKSRC}/doc && ${COPYTREE_SHARE} \ + \* \ + ${STAGEDIR}${DOCSDIR} + ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*-[sl] + +.include Added: head/biology/bowtie/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie/distinfo Sat Mar 5 13:21:26 2016 (r410180) @@ -0,0 +1,2 @@ +SHA256 (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 717145f12d599e9b3672981f5444fbbdb8e02bfde2a80eba577e28baa4125ba7 +SIZE (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 7831346 Added: head/biology/bowtie/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie/files/patch-Makefile Sat Mar 5 13:21:26 2016 (r410180) @@ -0,0 +1,52 @@ +--- Makefile.orig 2015-06-23 16:32:51 UTC ++++ Makefile +@@ -8,9 +8,13 @@ bindir = $(prefix)/bin + SEQAN_DIR = SeqAn-1.1 + SEQAN_INC = -I $(SEQAN_DIR) + INC = $(SEQAN_INC) -I third_party +-CPP = g++ +-CXX = $(CPP) +-CC = gcc ++ ++# Use ?= to allow environment CPP, CC, CXX to take precedence. This avoids ++# the need to modify the Makefile on different platforms. Package managers ++# such as FreeBSD ports, MacPorts, etc. set these variables automatically. ++CPP ?= g++ ++CXX ?= $(CPP) ++CC ?= gcc + HEADERS = $(wildcard *.h) + BOWTIE_MM = 1 + BOWTIE_SHARED_MEM = 1 +@@ -90,10 +94,10 @@ PREFETCH_LOCALITY = 2 + PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY) + + ifeq (1,$(WITH_TBB)) +- LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy ++ LIBS = ${LDFLAGS} $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy + EXTRA_FLAGS += -DWITH_TBB + else +- LIBS = $(PTHREAD_LIB) ++ LIBS = ${LDFLAGS} $(PTHREAD_LIB) + endif + + SEARCH_LIBS = +@@ -123,7 +127,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p + VERSION = $(shell cat VERSION) + + BITS=32 +-ifeq (x86_64,$(shell uname -m)) ++ifeq (amd64,$(shell uname -m)) + BITS=64 + endif + # msys will always be 32 bit so look at the cpu arch instead. +@@ -143,8 +147,8 @@ ifeq (32,$(BITS)) + $(error bowtie2 compilation requires a 64-bit platform ) + endif + +-DEBUG_FLAGS = -O0 -g3 -m64 +-RELEASE_FLAGS = -O3 -m64 ++DEBUG_FLAGS = -O0 -g3 ++RELEASE_FLAGS = -O + NOASSERT_FLAGS = -DNDEBUG + FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE + Added: head/biology/bowtie/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie/pkg-descr Sat Mar 5 13:21:26 2016 (r410180) @@ -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: http://bowtie-bio.sourceforge.net/index.shtml Added: head/biology/bowtie/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie/pkg-plist Sat Mar 5 13:21:26 2016 (r410180) @@ -0,0 +1,89 @@ +bin/bowtie +bin/bowtie-align-l +bin/bowtie-align-s +bin/bowtie-build +bin/bowtie-build-l +bin/bowtie-build-s +bin/bowtie-inspect +bin/bowtie-inspect-l +bin/bowtie-inspect-s +%%DATADIR%%/genomes/.cvsignore +%%DATADIR%%/genomes/NC_008253.fna +%%DATADIR%%/indexes/e_coli.1.ebwt +%%DATADIR%%/indexes/e_coli.2.ebwt +%%DATADIR%%/indexes/e_coli.3.ebwt +%%DATADIR%%/indexes/e_coli.4.ebwt +%%DATADIR%%/indexes/e_coli.README +%%DATADIR%%/indexes/e_coli.rev.1.ebwt +%%DATADIR%%/indexes/e_coli.rev.2.ebwt +%%DATADIR%%/reads/e_coli_1000.fa +%%DATADIR%%/reads/e_coli_1000.fq +%%DATADIR%%/reads/e_coli_1000.raw +%%DATADIR%%/reads/e_coli_10000snp.csfasta +%%DATADIR%%/reads/e_coli_10000snp.fa +%%DATADIR%%/reads/e_coli_10000snp.fq +%%DATADIR%%/reads/e_coli_1000_1.fa +%%DATADIR%%/reads/e_coli_1000_1.fq +%%DATADIR%%/reads/e_coli_1000_2.fa +%%DATADIR%%/reads/e_coli_1000_2.fq +%%DATADIR%%/scripts/best_verify.pl +%%DATADIR%%/scripts/bs_mapability.pl +%%DATADIR%%/scripts/build_test.sh +%%DATADIR%%/scripts/colorize_fasta.pl +%%DATADIR%%/scripts/colorize_fastq.pl +%%DATADIR%%/scripts/convert_quals.pl +%%DATADIR%%/scripts/fastq_to_tabbed.pl +%%DATADIR%%/scripts/gen_2b_occ_lookup.pl +%%DATADIR%%/scripts/gen_dnamasks2colormask.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_galGal3.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_mm8.sh +%%DATADIR%%/scripts/make_mm9.sh +%%DATADIR%%/scripts/make_rn4.sh +%%DATADIR%%/scripts/make_s_cerevisiae.sh +%%DATADIR%%/scripts/mapability.pl +%%DATADIR%%/scripts/pe_verify.pl +%%DATADIR%%/scripts/reconcile_alignments.pl +%%DATADIR%%/scripts/reconcile_alignments_pe.pl +%%PORTDOCS%%%%DOCSDIR%%/README +%%PORTDOCS%%%%DOCSDIR%%/manual.html +%%PORTDOCS%%%%DOCSDIR%%/release.txt +%%PORTDOCS%%%%DOCSDIR%%/strip_markdown.pl +%%PORTDOCS%%%%DOCSDIR%%/style.css +%%PORTDOCS%%%%DOCSDIR%%/website/css/style.css +%%PORTDOCS%%%%DOCSDIR%%/website/foot.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/images/bowtie_logo.png +%%PORTDOCS%%%%DOCSDIR%%/website/images/osi-certified.gif +%%PORTDOCS%%%%DOCSDIR%%/website/images/sflogo.png +%%PORTDOCS%%%%DOCSDIR%%/website/images/university.small.horizontal.white.png +%%PORTDOCS%%%%DOCSDIR%%/website/index.html +%%PORTDOCS%%%%DOCSDIR%%/website/index.shtml +%%PORTDOCS%%%%DOCSDIR%%/website/latest-version.txt +%%PORTDOCS%%%%DOCSDIR%%/website/manual.html +%%PORTDOCS%%%%DOCSDIR%%/website/manual.shtml +%%PORTDOCS%%%%DOCSDIR%%/website/manual.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/md5s.shtml +%%PORTDOCS%%%%DOCSDIR%%/website/md5s.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/news.shtml +%%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml +%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/push_langmead.sh +%%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/top.ssi +%%PORTDOCS%%%%DOCSDIR%%/website/tutorial.html +%%PORTDOCS%%%%DOCSDIR%%/website/tutorial.shtml