Attachment 167715 Details for Bug 206939 – Shar archive

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bowtie-shar.txt (text/plain), 7.50 KB, created by Jason W. Bacon on 2016-03-04 15:38:45 UTC

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Creator: Jason W. Bacon

Created: 2016-03-04 15:38:45 UTC

Size: 7.50 KB

patch

obsolete

># This is a shell archive.  Save it in a file, remove anything before
># this line, and then unpack it by entering "sh file".  Note, it may
># create directories; files and directories will be owned by you and
># have default permissions.
>#
># This archive contains:
>#
>#	bowtie
>#	bowtie/files
>#	bowtie/files/patch-Makefile
>#	bowtie/pkg-descr
>#	bowtie/distinfo
>#	bowtie/pkg-plist
>#	bowtie/Makefile
>#
>echo c - bowtie
>mkdir -p bowtie > /dev/null 2>&1
>echo c - bowtie/files
>mkdir -p bowtie/files > /dev/null 2>&1
>echo x - bowtie/files/patch-Makefile
>sed 's/^X//' >bowtie/files/patch-Makefile << 'ae54f0f7b83cbe32d398cbe5cf29d1c7'
>X--- Makefile.orig	2015-06-23 16:32:51 UTC
>X+++ Makefile
>X@@ -8,9 +8,13 @@ bindir = $(prefix)/bin
>X SEQAN_DIR = SeqAn-1.1
>X SEQAN_INC = -I $(SEQAN_DIR)
>X INC = $(SEQAN_INC) -I third_party
>X-CPP = g++
>X-CXX = $(CPP)
>X-CC = gcc
>X+
>X+# Use ?= to allow environment CPP, CC, CXX to take precedence.  This avoids
>X+# the need to modify the Makefile on different platforms.  Package managers
>X+# such as FreeBSD ports, MacPorts, etc. set these variables automatically.
>X+CPP ?= g++
>X+CXX ?= $(CPP)
>X+CC ?= gcc
>X HEADERS = $(wildcard *.h)
>X BOWTIE_MM = 1
>X BOWTIE_SHARED_MEM = 1
>X@@ -90,10 +94,10 @@ PREFETCH_LOCALITY = 2
>X PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
>X 
>X ifeq (1,$(WITH_TBB))
>X-	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
>X+	LIBS = ${LDFLAGS} $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
>X 	EXTRA_FLAGS += -DWITH_TBB
>X else
>X-	LIBS = $(PTHREAD_LIB)
>X+	LIBS = ${LDFLAGS} $(PTHREAD_LIB)
>X endif
>X 
>X SEARCH_LIBS = 
>X@@ -123,7 +127,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
>X VERSION = $(shell cat VERSION)
>X 
>X BITS=32
>X-ifeq (x86_64,$(shell uname -m))
>X+ifeq (amd64,$(shell uname -m))
>X 	BITS=64
>X endif
>X # msys will always be 32 bit so look at the cpu arch instead.
>X@@ -143,8 +147,8 @@ ifeq (32,$(BITS))
>X     $(error bowtie2 compilation requires a 64-bit platform )
>X endif
>X 
>X-DEBUG_FLAGS = -O0 -g3 -m64
>X-RELEASE_FLAGS = -O3 -m64
>X+DEBUG_FLAGS = -O0 -g3
>X+RELEASE_FLAGS = -O
>X NOASSERT_FLAGS = -DNDEBUG
>X FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
>X 
>ae54f0f7b83cbe32d398cbe5cf29d1c7
>echo x - bowtie/pkg-descr
>sed 's/^X//' >bowtie/pkg-descr << '96a57e2251d3f8329edc73be6fcd2adf'
>XBowtie is an ultrafast, memory-efficient short read aligner. It aligns short
>XDNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
>Xreads per hour.
>X
>XWWW: http://bowtie-bio.sourceforge.net/index.shtml
>96a57e2251d3f8329edc73be6fcd2adf
>echo x - bowtie/distinfo
>sed 's/^X//' >bowtie/distinfo << 'db0a283e9b91fd406319e76b833f116a'
>XSHA256 (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 717145f12d599e9b3672981f5444fbbdb8e02bfde2a80eba577e28baa4125ba7
>XSIZE (BenLangmead-bowtie-v1.1.2_GH0.tar.gz) = 7831346
>db0a283e9b91fd406319e76b833f116a
>echo x - bowtie/pkg-plist
>sed 's/^X//' >bowtie/pkg-plist << 'eb7027b5f7fec6e16f910f7d9a21457d'
>Xbin/bowtie
>Xbin/bowtie-align-l
>Xbin/bowtie-align-s
>Xbin/bowtie-build
>Xbin/bowtie-build-l
>Xbin/bowtie-build-s
>Xbin/bowtie-inspect
>Xbin/bowtie-inspect-l
>Xbin/bowtie-inspect-s
>X%%DATADIR%%/genomes/.cvsignore
>X%%DATADIR%%/genomes/NC_008253.fna
>X%%DATADIR%%/indexes/e_coli.1.ebwt
>X%%DATADIR%%/indexes/e_coli.2.ebwt
>X%%DATADIR%%/indexes/e_coli.3.ebwt
>X%%DATADIR%%/indexes/e_coli.4.ebwt
>X%%DATADIR%%/indexes/e_coli.README
>X%%DATADIR%%/indexes/e_coli.rev.1.ebwt
>X%%DATADIR%%/indexes/e_coli.rev.2.ebwt
>X%%DATADIR%%/reads/e_coli_1000.fa
>X%%DATADIR%%/reads/e_coli_1000.fq
>X%%DATADIR%%/reads/e_coli_1000.raw
>X%%DATADIR%%/reads/e_coli_10000snp.csfasta
>X%%DATADIR%%/reads/e_coli_10000snp.fa
>X%%DATADIR%%/reads/e_coli_10000snp.fq
>X%%DATADIR%%/reads/e_coli_1000_1.fa
>X%%DATADIR%%/reads/e_coli_1000_1.fq
>X%%DATADIR%%/reads/e_coli_1000_2.fa
>X%%DATADIR%%/reads/e_coli_1000_2.fq
>X%%DATADIR%%/scripts/best_verify.pl
>X%%DATADIR%%/scripts/bs_mapability.pl
>X%%DATADIR%%/scripts/build_test.sh
>X%%DATADIR%%/scripts/colorize_fasta.pl
>X%%DATADIR%%/scripts/colorize_fastq.pl
>X%%DATADIR%%/scripts/convert_quals.pl
>X%%DATADIR%%/scripts/fastq_to_tabbed.pl
>X%%DATADIR%%/scripts/gen_2b_occ_lookup.pl
>X%%DATADIR%%/scripts/gen_dnamasks2colormask.pl
>X%%DATADIR%%/scripts/gen_occ_lookup.pl
>X%%DATADIR%%/scripts/gen_solqual_lookup.pl
>X%%DATADIR%%/scripts/infer_fraglen.pl
>X%%DATADIR%%/scripts/make_a_thaliana_tair.sh
>X%%DATADIR%%/scripts/make_b_taurus_UMD3.sh
>X%%DATADIR%%/scripts/make_c_elegans.sh
>X%%DATADIR%%/scripts/make_canFam2.sh
>X%%DATADIR%%/scripts/make_d_melanogaster.sh
>X%%DATADIR%%/scripts/make_e_coli.sh
>X%%DATADIR%%/scripts/make_galGal3.sh
>X%%DATADIR%%/scripts/make_h_sapiens_ncbi36.sh
>X%%DATADIR%%/scripts/make_h_sapiens_ncbi37.sh
>X%%DATADIR%%/scripts/make_hg18.sh
>X%%DATADIR%%/scripts/make_hg19.sh
>X%%DATADIR%%/scripts/make_m_musculus_ncbi37.sh
>X%%DATADIR%%/scripts/make_mm8.sh
>X%%DATADIR%%/scripts/make_mm9.sh
>X%%DATADIR%%/scripts/make_rn4.sh
>X%%DATADIR%%/scripts/make_s_cerevisiae.sh
>X%%DATADIR%%/scripts/mapability.pl
>X%%DATADIR%%/scripts/pe_verify.pl
>X%%DATADIR%%/scripts/reconcile_alignments.pl
>X%%DATADIR%%/scripts/reconcile_alignments_pe.pl
>X%%PORTDOCS%%%%DOCSDIR%%/README
>X%%PORTDOCS%%%%DOCSDIR%%/manual.html
>X%%PORTDOCS%%%%DOCSDIR%%/release.txt
>X%%PORTDOCS%%%%DOCSDIR%%/strip_markdown.pl
>X%%PORTDOCS%%%%DOCSDIR%%/style.css
>X%%PORTDOCS%%%%DOCSDIR%%/website/css/style.css
>X%%PORTDOCS%%%%DOCSDIR%%/website/foot.ssi
>X%%PORTDOCS%%%%DOCSDIR%%/website/images/bowtie_logo.png
>X%%PORTDOCS%%%%DOCSDIR%%/website/images/osi-certified.gif
>X%%PORTDOCS%%%%DOCSDIR%%/website/images/sflogo.png
>X%%PORTDOCS%%%%DOCSDIR%%/website/images/university.small.horizontal.white.png
>X%%PORTDOCS%%%%DOCSDIR%%/website/index.html
>X%%PORTDOCS%%%%DOCSDIR%%/website/index.shtml
>X%%PORTDOCS%%%%DOCSDIR%%/website/latest-version.txt
>X%%PORTDOCS%%%%DOCSDIR%%/website/manual.html
>X%%PORTDOCS%%%%DOCSDIR%%/website/manual.shtml
>X%%PORTDOCS%%%%DOCSDIR%%/website/manual.ssi
>X%%PORTDOCS%%%%DOCSDIR%%/website/md5s.shtml
>X%%PORTDOCS%%%%DOCSDIR%%/website/md5s.ssi
>X%%PORTDOCS%%%%DOCSDIR%%/website/news.shtml
>X%%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi
>X%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml
>X%%PORTDOCS%%%%DOCSDIR%%/website/other_tools.ssi
>X%%PORTDOCS%%%%DOCSDIR%%/website/push_langmead.sh
>X%%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi
>X%%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi
>X%%PORTDOCS%%%%DOCSDIR%%/website/top.ssi
>X%%PORTDOCS%%%%DOCSDIR%%/website/tutorial.html
>X%%PORTDOCS%%%%DOCSDIR%%/website/tutorial.shtml
>eb7027b5f7fec6e16f910f7d9a21457d
>echo x - bowtie/Makefile
>sed 's/^X//' >bowtie/Makefile << '8ad548654a900b2c4ec05592f8a52392'
>X# Created by: Jason Bacon <bacon4000@gmail.com>
>X# $FreeBSD$
>X
>XPORTNAME=		bowtie
>XPORTVERSION=		1.1.2
>XDISTVERSIONPREFIX=	v
>XCATEGORIES=		biology
>X
>XMAINTAINER=	bacon4000@gmail.com
>XCOMMENT=	Ultrafast, memory-efficient short read aligner
>X
>XLICENSE=	ART10
>X
>X# May also work on other 64-bit platforms, but untested
>XONLY_FOR_ARCHS=	amd64
>X# FIXME: bowtie-align intermittently dumps core when compiled with clang
>X# GCC 4.2 does not provide good performance
>XUSE_GCC=	yes
>XUSES=		gmake perl5 shebangfix
>XUSE_PERL5=	run
>XSHEBANG_FILES=	scripts/*.pl
>X
>XUSE_GITHUB=	yes
>XGH_ACCOUNT=	BenLangmead
>X
>Xpost-install:
>X	${MKDIR} ${STAGEDIR}${DATADIR}/scripts
>X	${INSTALL_SCRIPT} \
>X		${WRKSRC}/bowtie \
>X		${WRKSRC}/bowtie-build \
>X		${WRKSRC}/bowtie-inspect \
>X		${STAGEDIR}${PREFIX}/bin
>X	${INSTALL_SCRIPT} \
>X		${WRKSRC}/scripts/*.sh \
>X		${WRKSRC}/scripts/*.pl \
>X		${STAGEDIR}${DATADIR}/scripts
>X	cd ${WRKSRC} && ${COPYTREE_SHARE} \
>X		'genomes indexes reads' \
>X		${STAGEDIR}${DATADIR}
>X	cd ${WRKSRC}/doc && ${COPYTREE_SHARE} \
>X		\* \
>X		${STAGEDIR}${DOCSDIR}
>X	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*-[sl]
>X
>X.include <bsd.port.mk>
>8ad548654a900b2c4ec05592f8a52392
>exit
>

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Attachments on bug 206939: 166589 | 166590 | 166591 | 167715 | 167716 | 167717