diff options
author | Raphael Kubo da Costa <rakuco@FreeBSD.org> | 2016-03-23 11:22:39 +0000 |
---|---|---|
committer | Raphael Kubo da Costa <rakuco@FreeBSD.org> | 2016-03-23 11:22:39 +0000 |
commit | bc3c1d13d61545e1c2da83a8ad636f16036c6cba (patch) | |
tree | 0e3904a8d452b2322757fa1730f4be8a34411db4 /biology | |
parent | New port: biology/slclust. (diff) |
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 <bacon4000@gmail.com>
Notes
Notes:
svn path=/head/; revision=411698
Diffstat (limited to 'biology')
-rw-r--r-- | biology/Makefile | 1 | ||||
-rw-r--r-- | biology/bowtie2/Makefile | 40 | ||||
-rw-r--r-- | biology/bowtie2/distinfo | 2 | ||||
-rw-r--r-- | biology/bowtie2/files/patch-Makefile | 22 | ||||
-rw-r--r-- | biology/bowtie2/pkg-descr | 5 | ||||
-rw-r--r-- | biology/bowtie2/pkg-plist | 64 |
6 files changed, 134 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index bf13346a0bf9..1f9a2d813665 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -13,6 +13,7 @@ SUBDIR += biojava SUBDIR += blat SUBDIR += bowtie + SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += cd-hit SUBDIR += cdbfasta diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile new file mode 100644 index 000000000000..9a37e9cb81b4 --- /dev/null +++ b/biology/bowtie2/Makefile @@ -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 <bsd.port.mk> diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo new file mode 100644 index 000000000000..a77e0bcf15e3 --- /dev/null +++ b/biology/bowtie2/distinfo @@ -0,0 +1,2 @@ +SHA256 (BenLangmead-bowtie2-v2.2.7_GH0.tar.gz) = 54a66a1ce0d1afa75198cc10e9e4e7436cc86cd7d6d93ae41c079462a1c19916 +SIZE (BenLangmead-bowtie2-v2.2.7_GH0.tar.gz) = 5813850 diff --git a/biology/bowtie2/files/patch-Makefile b/biology/bowtie2/files/patch-Makefile new file mode 100644 index 000000000000..be8a43586cec --- /dev/null +++ b/biology/bowtie2/files/patch-Makefile @@ -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 diff --git a/biology/bowtie2/pkg-descr b/biology/bowtie2/pkg-descr new file mode 100644 index 000000000000..05ac47289c51 --- /dev/null +++ b/biology/bowtie2/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: https://github.com/BenLangmead/bowtie2 diff --git a/biology/bowtie2/pkg-plist b/biology/bowtie2/pkg-plist new file mode 100644 index 000000000000..aeb30e8203aa --- /dev/null +++ b/biology/bowtie2/pkg-plist @@ -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 |