diff options
author | Raphael Kubo da Costa <rakuco@FreeBSD.org> | 2016-03-05 13:21:26 +0000 |
---|---|---|
committer | Raphael Kubo da Costa <rakuco@FreeBSD.org> | 2016-03-05 13:21:26 +0000 |
commit | b8b592e17b9bf7e474749fb68e65037aef758f37 (patch) | |
tree | 0f050240f1953bfefabe392e91ec8c244425a70a /biology | |
parent | Update to 0.04 (diff) |
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 <bacon4000@gmail.com>
Notes
Notes:
svn path=/head/; revision=410180
Diffstat (limited to 'biology')
-rw-r--r-- | biology/Makefile | 1 | ||||
-rw-r--r-- | biology/bowtie/Makefile | 45 | ||||
-rw-r--r-- | biology/bowtie/distinfo | 2 | ||||
-rw-r--r-- | biology/bowtie/files/patch-Makefile | 52 | ||||
-rw-r--r-- | biology/bowtie/pkg-descr | 5 | ||||
-rw-r--r-- | biology/bowtie/pkg-plist | 89 |
6 files changed, 194 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index c2c7b80c4489..25eb27f25ddd 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -12,6 +12,7 @@ SUBDIR += biococoa SUBDIR += biojava SUBDIR += blat + SUBDIR += bowtie SUBDIR += bwa SUBDIR += cd-hit SUBDIR += cdbfasta diff --git a/biology/bowtie/Makefile b/biology/bowtie/Makefile new file mode 100644 index 000000000000..5f3e404bf3ac --- /dev/null +++ b/biology/bowtie/Makefile @@ -0,0 +1,45 @@ +# Created by: Jason Bacon <bacon4000@gmail.com> +# $FreeBSD$ + +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 <bsd.port.mk> diff --git a/biology/bowtie/distinfo b/biology/bowtie/distinfo new file mode 100644 index 000000000000..ffacca889d6c --- /dev/null +++ b/biology/bowtie/distinfo @@ -0,0 +1,2 @@ +SHA256 (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 717145f12d599e9b3672981f5444fbbdb8e02bfde2a80eba577e28baa4125ba7 +SIZE (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 7831346 diff --git a/biology/bowtie/files/patch-Makefile b/biology/bowtie/files/patch-Makefile new file mode 100644 index 000000000000..8f3a35cf59f5 --- /dev/null +++ b/biology/bowtie/files/patch-Makefile @@ -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 + diff --git a/biology/bowtie/pkg-descr b/biology/bowtie/pkg-descr new file mode 100644 index 000000000000..03d1a2c4269f --- /dev/null +++ b/biology/bowtie/pkg-descr @@ -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 diff --git a/biology/bowtie/pkg-plist b/biology/bowtie/pkg-plist new file mode 100644 index 000000000000..e0e8c2056459 --- /dev/null +++ b/biology/bowtie/pkg-plist @@ -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 |