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New port: biology/bowtie2.

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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>
This commit is contained in:
Raphael Kubo da Costa 2016-03-23 11:22:39 +00:00
parent 66631eff75
commit bc3c1d13d6
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=411698
6 changed files with 134 additions and 0 deletions
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1
biology/Makefile
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@ -13,6 +13,7 @@
SUBDIR += biojava
SUBDIR += blat
SUBDIR += bowtie
SUBDIR += bowtie2
SUBDIR += bwa
SUBDIR += cd-hit
SUBDIR += cdbfasta

40
biology/bowtie2/Makefile Normal file
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@ -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>

2
biology/bowtie2/distinfo Normal file
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@ -0,0 +1,2 @@
SHA256 (BenLangmead-bowtie2-v2.2.7_GH0.tar.gz) = 54a66a1ce0d1afa75198cc10e9e4e7436cc86cd7d6d93ae41c079462a1c19916
SIZE (BenLangmead-bowtie2-v2.2.7_GH0.tar.gz) = 5813850

22
biology/bowtie2/files/patch-Makefile Normal file
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@ -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

5
biology/bowtie2/pkg-descr Normal file
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@ -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

64
biology/bowtie2/pkg-plist Normal file
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@ -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