Attachment 100800 Details for Bug 140147 – velvet-0.7.55.shar

velvet-0.7.55.shar

velvet-0.7.55.shar (text/plain), 10.00 KB, created by Motomichi Matsuzaki on 2009-10-31 18:10:00 UTC

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Creator: Motomichi Matsuzaki

Created: 2009-10-31 18:10:00 UTC

Size: 10.00 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:
>#
>#	velvet
>#	velvet/distinfo
>#	velvet/files
>#	velvet/files/patch-Makefile
>#	velvet/files/patch-src-run.c
>#	velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl
>#	velvet/pkg-descr
>#	velvet/Makefile
>#
>echo c - velvet
>mkdir -p velvet > /dev/null 2>&1
>echo x - velvet/distinfo
>sed 's/^X//' >velvet/distinfo << '567a9516d3c29f0972442a40f735d26a'
>XMD5 (velvet_0.7.55.tgz) = ea99c0b157b4195c313f93bd9f77ecb3
>XSHA256 (velvet_0.7.55.tgz) = 315331f418c2de89c6c871cea3759d947320c0adbc763fea290ec78ece69b614
>XSIZE (velvet_0.7.55.tgz) = 3475289
>567a9516d3c29f0972442a40f735d26a
>echo c - velvet/files
>mkdir -p velvet/files > /dev/null 2>&1
>echo x - velvet/files/patch-Makefile
>sed 's/^X//' >velvet/files/patch-Makefile << '88db4fa29804901c6db62f24845d0ca8'
>X--- Makefile.orig	2009-09-02 22:21:01.000000000 +0900
>X+++ Makefile	2009-10-27 22:05:49.000000000 +0900
>X@@ -1,18 +1,18 @@
>X-CC = gcc
>X-CFLAGS = -Wall
>X+CC ?= gcc
>X+CFLAGS += -Wall
>X DEBUG = -g
>X-LDFLAGS = -lm
>X-OPT = -O3
>X-MAXKMERLENGTH=31
>X-CATEGORIES=2
>X+#LDFLAGS = -lm
>X+#OPT = -O3
>X+MAXKMERLENGTH?=31
>X+CATEGORIES?=2
>X DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
>X 
>X Z_LIB_DIR=third-party/zlib-1.2.3
>X Z_LIB_FILES=$(Z_LIB_DIR)/*.o
>X 
>X # Mac OS users: uncomment the following lines
>X-# Z_LIB_FILES=
>X-# LDFLAGS = -lm -lz
>X+Z_LIB_FILES=
>X+LDFLAGS += -lm -lz
>X # CFLAGS = -Wall -m64
>X 
>X # Sparc/Solaris users: uncomment the following line
>X@@ -32,7 +32,7 @@
>X 	-rm obj/*.o obj/dbg/*.o 
>X 
>X zlib : 
>X-	cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
>X+#	cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
>X 
>X velveth : $(OBJ) 
>X 	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
>88db4fa29804901c6db62f24845d0ca8
>echo x - velvet/files/patch-src-run.c
>sed 's/^X//' >velvet/files/patch-src-run.c << '2af71c099be70a087523b7644892eb3b'
>X--- src/run.c.orig	2009-09-16 20:11:59.000000000 +0900
>X+++ src/run.c	2009-10-27 22:27:27.000000000 +0900
>X@@ -152,7 +152,7 @@
>X 						   double_strand);
>X 
>X 	destroySplayTable(splayTable);
>X-	closedir(dir);
>X+	if (dir) closedir(dir);
>X 	free(filename);
>X 	free(buf);
>X 
>2af71c099be70a087523b7644892eb3b
>echo x - velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl
>sed 's/^X//' >velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl << 'cb4a718353d291773202039bb121c3da'
>X--- contrib/VelvetOptimiser/VelvetOptimiser.pl.orig	2009-09-14 23:44:19.000000000 +0900
>X+++ contrib/VelvetOptimiser/VelvetOptimiser.pl	2009-10-30 22:13:45.000000000 +0900
>X@@ -44,9 +44,10 @@
>X my @hashvals;
>X my %assemblies;
>X my $readfile;
>X+my $MAXKMERLENGTH = %%MAXKMERLENGTH%%;
>X my $logfile = "logfile.txt";
>X my $hashs = 19;
>X-my $hashe = 129;
>X+my $hashe = $MAXKMERLENGTH;
>X my $ass_num = 1;
>X my $interested = 1;
>X 
>X@@ -311,26 +312,26 @@
>X     my $ass = shift;
>X     print STDERR "\tPlease type in the insert length for the short reads: ";
>X     #my $len = <>;
>X-    my $len = "200"; #do not ask for insert size!
>X+    my $len = "auto"; #do not ask for insert size!
>X     chomp($len);
>X-    while($len =~ /\D+/){
>X-        print STDERR "\tThe length needs to be a number, please re-enter: ";
>X-        $len = <>;
>X-        chomp($len);
>X-    }
>X+    #while($len =~ /\D+/){
>X+    #    print STDERR "\tThe length needs to be a number, please re-enter: ";
>X+    #    $len = <>;
>X+    #    chomp($len);
>X+    #}
>X     print STDERR strftime("%b %e %H:%M:%S", localtime), " Running assembly with short insert length $len\n";
>X     print OUT strftime("%b %e %H:%M:%S", localtime), " Running assembly with short insert length $len\n";
>X 
>X     #re-write the pstringg with the new velvetg command..
>X-    my $vg = $ass->{pstringg};
>X-    if($vg =~ /ins_length /){
>X-        $vg =~ s/ins_length\s+\d+/ins_length $len/;
>X-    }
>X-    else {
>X-        $vg .= " -ins_length $len";
>X-    }
>X+    #my $vg = $ass->{pstringg};
>X+    #if($vg =~ /ins_length /){
>X+    #    $vg =~ s/ins_length\s+\d+/ins_length $len/;
>X+    #}
>X+    #else {
>X+    #    $vg .= " -ins_length $len";
>X+    #}
>X 
>X-    $ass->{pstringg} = $vg;
>X+    #$ass->{pstringg} = $vg;
>X     my $worked = VelvetOpt::gwrap::objectVelvetg($ass);
>X     if($worked){
>X         $ass->getAssemblyDetails();
>X@@ -347,8 +348,8 @@
>X my $usage = "\nVelvetOptimiser.pl: A script to run the Velvet assembler and optimise its output. Simon Gladman - CSIRO 2008, 2009.\n\n";
>X $usage .= "Usage: VelvetOptimiser.pl <-f 'velveth parameters'> [-s <hash start>] [-e <hash end>] [-a <yes>]\n\n";
>X $usage .= "Where:\t<-f 'velveth parameters'> is the parameter line normally passed to velveth in quotes.\n";
>X-$usage .= "\t-s <hash start> The hash value you want velvet to start looking from. Default: 19. MUST BE ODD > 0 & <=31!\n";
>X-$usage .= "\t-e <hash end> The hash value you want velvet to stop looking at. Default: 31. MUST BE ODD AND > START & <= 31!\n";
>X+$usage .= "\t-s <hash start> The hash value you want velvet to start looking from. Default: 19. MUST BE ODD > 0 & <=$MAXKMERLENGTH!\n";
>X+$usage .= "\t-e <hash end> The hash value you want velvet to stop looking at. Default: $MAXKMERLENGTH. MUST BE ODD AND > START & <= $MAXKMERLENGTH!\n";
>X $usage .= "\t-a <yes> The final optimised assembly will include read tracking and amos file outputs (however, intermediate assemblies won't.)\n";
>X $usage .= "\nIf the optimizer requires an insert length for some paired end data, it will ask for it when it gets to the optimization step.\n";
>X 
>X@@ -390,9 +391,9 @@
>X     $hashs = $opts{'s'};
>X        print STDERR "\n\t\t's-Param' is >$hashs<\n";
>X     unless($hashs =~ /^\d+$/){ die "\tFatal error! Start hash not a number!\n$usage";}
>X-    if($hashs > 129){
>X-        print STDERR "\tStart hash value too high.  New start hash value is 129.\n";
>X-        $hashs = 129;
>X+    if($hashs > $MAXKMERLENGTH){
>X+        print STDERR "\tStart hash value too high.  New start hash value is $MAXKMERLENGTH.\n";
>X+        $hashs = $MAXKMERLENGTH;
>X     }
>X     if(!&isOdd($hashs)){
>X         $hashs = $hashs - 1;
>X@@ -404,9 +405,9 @@
>X if($opts{'e'}){
>X     $hashe = $opts{'e'};
>X     unless($hashe =~ /^\d+$/){ die "\tFatal error! End hash not a number!\n$usage";}
>X-    if($hashe > 129 || $hashe < 1){
>X-        print STDERR "\tEnd hash value not in workable range.  New end hash value is 129.\n";
>X-        $hashe = 129;
>X+    if($hashe > $MAXKMERLENGTH || $hashe < 1){
>X+        print STDERR "\tEnd hash value not in workable range.  New end hash value is $MAXKMERLENGTH.\n";
>X+        $hashe = $MAXKMERLENGTH;
>X     }
>X     if($hashe < $hashs){
>X         print STDERR "\tEnd hash value lower than start hash value.  New end hash value = $hashs.\n";
>cb4a718353d291773202039bb121c3da
>echo x - velvet/pkg-descr
>sed 's/^X//' >velvet/pkg-descr << '5e38a15ab18c8781d890dde239e06856'
>XVelvet is a de novo genomic assembler specially designed for short read
>Xsequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
>Xand Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).
>X
>XCitation:
>X
>XVelvet: algorithms for de novo short read assembly using de Bruijn graphs.
>XD.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)
>X
>XWWW: http://www.ebi.ac.uk/~zerbino/velvet/
>5e38a15ab18c8781d890dde239e06856
>echo x - velvet/Makefile
>sed 's/^X//' >velvet/Makefile << '95306d57571d7991bbc7b0899257a2cd'
>X# New ports collection makefile for:	velvet
>X# Date created:		27 Oct 2009
>X# Whom:			Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
>X#
>X# $FreeBSD$
>X#
>X
>XPORTNAME=	velvet
>XPORTVERSION=	0.7.55
>XCATEGORIES=	biology
>XMASTER_SITES=	http://www.ebi.ac.uk/~zerbino/velvet/
>XDISTNAME=	${PORTNAME}_${PORTVERSION}
>XEXTRACT_SUFX=	.tgz
>X
>XMAINTAINER=	mzaki@m.u-tokyo.ac.jp
>XCOMMENT=	Sequence assembler for very short reads
>X
>XUSE_GMAKE=	yes
>XALL_TARGET=	default
>X
>XMAXKMERLENGTH?=	31
>XMAKE_ENV+=	MAXKMERLENGTH=${MAXKMERLENGTH}
>X
>XUSE_PERL5_RUN=	yes
>X
>XBINARIES=	velvetg velveth
>XSCRIPTS=	contrib/VelvetOptimiser/VelvetOptimiser.pl \
>X		contrib/afg_handling/asmbly_splitter.pl \
>X		contrib/afg_handling/snp_view.pl \
>X		contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl \
>X		contrib/fasta2agp/fasta2agp.pl \
>X		contrib/extractContigReads/extractContigReads.pl \
>X		contrib/observed-insert-length.pl/observed-insert-length.pl \
>X		contrib/shuffleSequences_fasta/shuffleSequences_fasta.pl
>XPERLMOD_DIRS=	contrib/VelvetOptimiser/VelvetOpt
>XPERLMOD_FILES=	contrib/VelvetOptimiser/VelvetOpt/Assembly.pm \
>X		contrib/VelvetOptimiser/VelvetOpt/Utils.pm \
>X		contrib/VelvetOptimiser/VelvetOpt/gwrap.pm \
>X		contrib/VelvetOptimiser/VelvetOpt/hwrap.pm
>X
>X.if !defined(WITHOUT_PYTHON)
>XUSE_PYTHON=	yes
>XSCRIPTS+=	contrib/layout/graph2.py
>X.endif
>X
>X.for f in ${BINARIES} ${SCRIPTS}
>XPLIST_FILES+=	bin/${f:T}
>X.endfor
>X.for d in ${PERLMOD_DIRS}
>XPLIST_DIRS+=	%%SITE_PERL%%/${d:T}
>X.endfor
>X.for f in ${PERLMOD_FILES}
>XPLIST_FILES+=	%%SITE_PERL%%/${f:H:T}/${f:T}
>X.endfor
>X
>XPORTDOCS=	ChangeLog Manual.pdf
>X
>Xpost-patch:
>X.for f in ${SCRIPTS}
>X	${REINPLACE_CMD} -e s,#!/usr/bin/perl,${PERL}, ${WRKSRC}/${f}
>X.endfor
>X.if !defined(WITHOUT_PYTHON)
>X	(IFS=''; ${REINPLACE_CMD} -e `${ECHO} '1i\'; ${ECHO} '#!${PYTHON_CMD}'` ${WRKSRC}/contrib/layout/graph2.py)
>X.endif
>X
>Xpost-build:
>X	${REINPLACE_CMD} -e s,%%MAXKMERLENGTH%%,${MAXKMERLENGTH},g ${WRKSRC}/contrib/VelvetOptimiser/VelvetOptimiser.pl
>X
>Xdo-install:
>X.for f in ${BINARIES}
>X	${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
>X.endfor
>X.for f in ${SCRIPTS}
>X	${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/bin/${f:T}
>X.endfor
>X.for d in ${PERLMOD_DIRS}
>X	${MKDIR} ${PREFIX}/${SITE_PERL_REL}/${d:T}
>X.endfor
>X.for f in ${PERLMOD_FILES}
>X	${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/${SITE_PERL_REL}/${f:H:T}/${f:T}
>X.endfor
>X.if !defined(NOPORTDOCS)
>X	${MKDIR} ${DOCSDIR}
>X.for f in ${PORTDOCS}
>X	${INSTALL_MAN} ${WRKSRC}/${f} ${DOCSDIR}
>X.endfor
>X.endif
>X
>X.include <bsd.port.mk>
>95306d57571d7991bbc7b0899257a2cd
>exit

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Attachments on bug 140147: 100800