From owner-freebsd-ports-bugs@FreeBSD.ORG Sat Oct 31 18:10:01 2009 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 6B3F0106568F for ; Sat, 31 Oct 2009 18:10:01 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 2BFD48FC1E for ; Sat, 31 Oct 2009 18:10:01 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.3/8.14.3) with ESMTP id n9VIA16r037527 for ; Sat, 31 Oct 2009 18:10:01 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.3/8.14.3/Submit) id n9VIA1du037526; Sat, 31 Oct 2009 18:10:01 GMT (envelope-from gnats) Resent-Date: Sat, 31 Oct 2009 18:10:01 GMT Resent-Message-Id: <200910311810.n9VIA1du037526@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Motomichi Matsuzaki Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id E89361065695 for ; Sat, 31 Oct 2009 18:02:48 +0000 (UTC) (envelope-from mzaki@z800.mzaki.org) Received: from z800.mzaki.org (ip80.nphys.m.u-tokyo.ac.jp [133.11.187.80]) by mx1.freebsd.org (Postfix) with ESMTP id 4154A8FC13 for ; Sat, 31 Oct 2009 18:02:47 +0000 (UTC) Received: from z800.mzaki.org (localhost [127.0.0.1]) by z800.mzaki.org (8.14.3/8.14.3) with ESMTP id n9VHpGwS074742; Sun, 1 Nov 2009 02:51:16 +0900 (JST) (envelope-from mzaki@z800.mzaki.org) Received: (from mzaki@localhost) by z800.mzaki.org (8.14.3/8.14.3/Submit) id n9VHpGAq074741; Sun, 1 Nov 2009 02:51:16 +0900 (JST) (envelope-from mzaki) Message-Id: <200910311751.n9VHpGAq074741@z800.mzaki.org> Date: Sun, 1 Nov 2009 02:51:16 +0900 (JST) From: Motomichi Matsuzaki To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Cc: Motomichi Matsuzaki Subject: ports/140147: [NEW PORT] biology/velvet: Sequence assembler for very short reads X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 31 Oct 2009 18:10:01 -0000 >Number: 140147 >Category: ports >Synopsis: [NEW PORT] biology/velvet: Sequence assembler for very short reads >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Sat Oct 31 18:10:00 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Motomichi Matsuzaki >Release: FreeBSD 8.0-RC1 amd64 >Organization: >Environment: System: FreeBSD z800.m.u-tokyo.ac.jp 8.0-RC1 FreeBSD 8.0-RC1 #0: Tue Oct 13 19:07:49 JST 2009 >Description: Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) WWW: http://www.ebi.ac.uk/~zerbino/velvet/ Generated with FreeBSD Port Tools 0.99 >How-To-Repeat: >Fix: --- velvet-0.7.55.shar begins here --- # 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 ] [-e ] [-a ]\n\n"; X $usage .= "Where:\t<-f 'velveth parameters'> is the parameter line normally passed to velveth in quotes.\n"; X-$usage .= "\t-s The hash value you want velvet to start looking from. Default: 19. MUST BE ODD > 0 & <=31!\n"; X-$usage .= "\t-e The hash value you want velvet to stop looking at. Default: 31. MUST BE ODD AND > START & <= 31!\n"; X+$usage .= "\t-s The hash value you want velvet to start looking from. Default: 19. MUST BE ODD > 0 & <=$MAXKMERLENGTH!\n"; X+$usage .= "\t-e The hash value you want velvet to stop looking at. Default: $MAXKMERLENGTH. MUST BE ODD AND > START & <= $MAXKMERLENGTH!\n"; X $usage .= "\t-a 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 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 95306d57571d7991bbc7b0899257a2cd exit --- velvet-0.7.55.shar ends here --- >Release-Note: >Audit-Trail: >Unformatted: