Date: Thu, 2 Jun 2011 11:55:17 GMT From: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/157527: [maintainer update] biology/velvet to 1.1.04 Message-ID: <201106021155.p52BtH5q086644@red.freebsd.org> Resent-Message-ID: <201106021200.p52C0QFL064833@freefall.freebsd.org>
next in thread | raw e-mail | index | archive | help
>Number: 157527 >Category: ports >Synopsis: [maintainer update] biology/velvet to 1.1.04 >Confidential: no >Severity: non-critical >Priority: medium >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Thu Jun 02 12:00:26 UTC 2011 >Closed-Date: >Last-Modified: >Originator: Motomichi Matsuzaki >Release: >Organization: >Environment: >Description: Removed files: files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl files/patch-src-run.c >How-To-Repeat: >Fix: Patch attached with submission follows: diff -ruN velvet.orig/Makefile velvet/Makefile --- velvet.orig/Makefile 2009-11-07 10:23:58.000000000 +0900 +++ velvet/Makefile 2011-06-02 20:40:20.000000000 +0900 @@ -6,7 +6,7 @@ # PORTNAME= velvet -PORTVERSION= 0.7.55 +PORTVERSION= 1.1.04 CATEGORIES= biology MASTER_SITES= http://www.ebi.ac.uk/~zerbino/velvet/ DISTNAME= ${PORTNAME}_${PORTVERSION} @@ -19,28 +19,34 @@ ALL_TARGET= default MAXKMERLENGTH?= 31 -MAKE_ENV+= MAXKMERLENGTH=${MAXKMERLENGTH} +VELVET_CATEGORIES?= 2 +MAKE_ENV+= MAXKMERLENGTH=${MAXKMERLENGTH} CATEGORIES=${VELVET_CATEGORIES} USE_PERL5_RUN= yes BINARIES= velvetg velveth -SCRIPTS= contrib/VelvetOptimiser/VelvetOptimiser.pl \ +SCRIPTS= shuffleSequences_fasta.pl shuffleSequences_fastq.pl \ + contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl \ contrib/afg_handling/asmbly_splitter.pl \ contrib/afg_handling/snp_view.pl \ + contrib/columbus_scripts/enlarge_exons.pl \ + contrib/columbus_scripts/gff2fasta.pl \ + contrib/columbus_scripts/merge_gtf_exons.pl \ contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl \ - contrib/fasta2agp/fasta2agp.pl \ contrib/extractContigReads/extractContigReads.pl \ + contrib/fasta2agp/fasta2agp.pl \ contrib/observed-insert-length.pl/observed-insert-length.pl \ - contrib/shuffleSequences_fasta/shuffleSequences_fasta.pl -PERLMOD_DIRS= contrib/VelvetOptimiser/VelvetOpt -PERLMOD_FILES= contrib/VelvetOptimiser/VelvetOpt/Assembly.pm \ - contrib/VelvetOptimiser/VelvetOpt/Utils.pm \ - contrib/VelvetOptimiser/VelvetOpt/gwrap.pm \ - contrib/VelvetOptimiser/VelvetOpt/hwrap.pm + contrib/select_paired/select_paired.pl \ + contrib/show_repeats/show_repeats.pl +PERLMOD_DIRS= contrib/VelvetOptimiser-2.1.7/VelvetOpt +PERLMOD_FILES= contrib/VelvetOptimiser-2.1.7/VelvetOpt/Assembly.pm \ + contrib/VelvetOptimiser-2.1.7/VelvetOpt/Utils.pm \ + contrib/VelvetOptimiser-2.1.7/VelvetOpt/gwrap.pm \ + contrib/VelvetOptimiser-2.1.7/VelvetOpt/hwrap.pm .if !defined(WITHOUT_PYTHON) USE_PYTHON= yes -SCRIPTS+= contrib/layout/graph2.py +SCRIPTS+= contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py .endif .for f in ${BINARIES} ${SCRIPTS} @@ -53,19 +59,16 @@ PLIST_FILES+= %%SITE_PERL%%/${f:H:T}/${f:T} .endfor -PORTDOCS= ChangeLog Manual.pdf +PORTDOCS= ChangeLog Manual.pdf Columbus_manual.pdf post-patch: .for f in ${SCRIPTS} ${REINPLACE_CMD} -e s,#!/usr/bin/perl,${PERL}, ${WRKSRC}/${f} .endfor .if !defined(WITHOUT_PYTHON) - (IFS=''; ${REINPLACE_CMD} -e `${ECHO} '1i\'; ${ECHO} '#!${PYTHON_CMD}'` ${WRKSRC}/contrib/layout/graph2.py) + ${REINPLACE_CMD} -e s,#!/usr/bin/python,${PYTHON_CMD}, ${WRKSRC}/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py .endif -post-build: - ${REINPLACE_CMD} -e s,%%MAXKMERLENGTH%%,${MAXKMERLENGTH},g ${WRKSRC}/contrib/VelvetOptimiser/VelvetOptimiser.pl - do-install: .for f in ${BINARIES} ${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin diff -ruN velvet.orig/distinfo velvet/distinfo --- velvet.orig/distinfo 2011-03-19 21:29:39.000000000 +0900 +++ velvet/distinfo 2011-06-02 19:02:13.000000000 +0900 @@ -1,2 +1,2 @@ -SHA256 (velvet_0.7.55.tgz) = 315331f418c2de89c6c871cea3759d947320c0adbc763fea290ec78ece69b614 -SIZE (velvet_0.7.55.tgz) = 3475289 +SHA256 (velvet_1.1.04.tgz) = 7ae9855c3eabd1d222815a7132cdc9eeb387d83132390d020fc78491e6dcc9d6 +SIZE (velvet_1.1.04.tgz) = 7744134 diff -ruN velvet.orig/files/patch-Makefile velvet/files/patch-Makefile --- velvet.orig/files/patch-Makefile 2009-11-07 10:23:59.000000000 +0900 +++ velvet/files/patch-Makefile 2011-06-02 20:28:10.000000000 +0900 @@ -1,5 +1,5 @@ ---- Makefile.orig 2009-09-02 22:21:01.000000000 +0900 -+++ Makefile 2009-10-27 22:05:49.000000000 +0900 +--- Makefile.orig 2011-03-30 14:34:09.000000000 +0900 ++++ Makefile 2011-06-02 20:28:04.000000000 +0900 @@ -1,18 +1,18 @@ -CC = gcc -CFLAGS = -Wall @@ -27,12 +27,21 @@ # CFLAGS = -Wall -m64 # Sparc/Solaris users: uncomment the following line -@@ -32,7 +32,7 @@ +@@ -35,7 +35,7 @@ + OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/scaffold.o obj/kmerOccurenceTable.o obj/allocArray.o + OBJDBG = $(subst obj,obj/dbg,$(OBJ)) + +-default : cleanobj zlib obj velveth velvetg doc ++default : cleanobj zlib obj velveth velvetg + + clean : + -rm obj/*.o obj/dbg/*.o ./velvet* +@@ -47,7 +47,7 @@ -rm obj/*.o obj/dbg/*.o zlib : - cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o +# cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o - velveth : $(OBJ) - $(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) + velveth : obj + $(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/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES) diff -ruN velvet.orig/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl --- velvet.orig/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl 2009-11-07 10:23:59.000000000 +0900 +++ velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl 1970-01-01 09:00:00.000000000 +0900 @@ -1,92 +0,0 @@ ---- contrib/VelvetOptimiser/VelvetOptimiser.pl.orig 2009-09-14 23:44:19.000000000 +0900 -+++ contrib/VelvetOptimiser/VelvetOptimiser.pl 2009-10-30 22:13:45.000000000 +0900 -@@ -44,9 +44,10 @@ - my @hashvals; - my %assemblies; - my $readfile; -+my $MAXKMERLENGTH = %%MAXKMERLENGTH%%; - my $logfile = "logfile.txt"; - my $hashs = 19; --my $hashe = 129; -+my $hashe = $MAXKMERLENGTH; - my $ass_num = 1; - my $interested = 1; - -@@ -311,26 +312,26 @@ - my $ass = shift; - print STDERR "\tPlease type in the insert length for the short reads: "; - #my $len = <>; -- my $len = "200"; #do not ask for insert size! -+ my $len = "auto"; #do not ask for insert size! - chomp($len); -- while($len =~ /\D+/){ -- print STDERR "\tThe length needs to be a number, please re-enter: "; -- $len = <>; -- chomp($len); -- } -+ #while($len =~ /\D+/){ -+ # print STDERR "\tThe length needs to be a number, please re-enter: "; -+ # $len = <>; -+ # chomp($len); -+ #} - print STDERR strftime("%b %e %H:%M:%S", localtime), " Running assembly with short insert length $len\n"; - print OUT strftime("%b %e %H:%M:%S", localtime), " Running assembly with short insert length $len\n"; - - #re-write the pstringg with the new velvetg command.. -- my $vg = $ass->{pstringg}; -- if($vg =~ /ins_length /){ -- $vg =~ s/ins_length\s+\d+/ins_length $len/; -- } -- else { -- $vg .= " -ins_length $len"; -- } -+ #my $vg = $ass->{pstringg}; -+ #if($vg =~ /ins_length /){ -+ # $vg =~ s/ins_length\s+\d+/ins_length $len/; -+ #} -+ #else { -+ # $vg .= " -ins_length $len"; -+ #} - -- $ass->{pstringg} = $vg; -+ #$ass->{pstringg} = $vg; - my $worked = VelvetOpt::gwrap::objectVelvetg($ass); - if($worked){ - $ass->getAssemblyDetails(); -@@ -347,8 +348,8 @@ - my $usage = "\nVelvetOptimiser.pl: A script to run the Velvet assembler and optimise its output. Simon Gladman - CSIRO 2008, 2009.\n\n"; - $usage .= "Usage: VelvetOptimiser.pl <-f 'velveth parameters'> [-s <hash start>] [-e <hash end>] [-a <yes>]\n\n"; - $usage .= "Where:\t<-f 'velveth parameters'> is the parameter line normally passed to velveth in quotes.\n"; --$usage .= "\t-s <hash start> The hash value you want velvet to start looking from. Default: 19. MUST BE ODD > 0 & <=31!\n"; --$usage .= "\t-e <hash end> The hash value you want velvet to stop looking at. Default: 31. MUST BE ODD AND > START & <= 31!\n"; -+$usage .= "\t-s <hash start> The hash value you want velvet to start looking from. Default: 19. MUST BE ODD > 0 & <=$MAXKMERLENGTH!\n"; -+$usage .= "\t-e <hash end> The hash value you want velvet to stop looking at. Default: $MAXKMERLENGTH. MUST BE ODD AND > START & <= $MAXKMERLENGTH!\n"; - $usage .= "\t-a <yes> The final optimised assembly will include read tracking and amos file outputs (however, intermediate assemblies won't.)\n"; - $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"; - -@@ -390,9 +391,9 @@ - $hashs = $opts{'s'}; - print STDERR "\n\t\t's-Param' is >$hashs<\n"; - unless($hashs =~ /^\d+$/){ die "\tFatal error! Start hash not a number!\n$usage";} -- if($hashs > 129){ -- print STDERR "\tStart hash value too high. New start hash value is 129.\n"; -- $hashs = 129; -+ if($hashs > $MAXKMERLENGTH){ -+ print STDERR "\tStart hash value too high. New start hash value is $MAXKMERLENGTH.\n"; -+ $hashs = $MAXKMERLENGTH; - } - if(!&isOdd($hashs)){ - $hashs = $hashs - 1; -@@ -404,9 +405,9 @@ - if($opts{'e'}){ - $hashe = $opts{'e'}; - unless($hashe =~ /^\d+$/){ die "\tFatal error! End hash not a number!\n$usage";} -- if($hashe > 129 || $hashe < 1){ -- print STDERR "\tEnd hash value not in workable range. New end hash value is 129.\n"; -- $hashe = 129; -+ if($hashe > $MAXKMERLENGTH || $hashe < 1){ -+ print STDERR "\tEnd hash value not in workable range. New end hash value is $MAXKMERLENGTH.\n"; -+ $hashe = $MAXKMERLENGTH; - } - if($hashe < $hashs){ - print STDERR "\tEnd hash value lower than start hash value. New end hash value = $hashs.\n"; diff -ruN velvet.orig/files/patch-src-run.c velvet/files/patch-src-run.c --- velvet.orig/files/patch-src-run.c 2009-11-07 10:23:59.000000000 +0900 +++ velvet/files/patch-src-run.c 1970-01-01 09:00:00.000000000 +0900 @@ -1,11 +0,0 @@ ---- src/run.c.orig 2009-09-16 20:11:59.000000000 +0900 -+++ src/run.c 2009-10-27 22:27:27.000000000 +0900 -@@ -152,7 +152,7 @@ - double_strand); - - destroySplayTable(splayTable); -- closedir(dir); -+ if (dir) closedir(dir); - free(filename); - free(buf); - >Release-Note: >Audit-Trail: >Unformatted:
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201106021155.p52BtH5q086644>