5 files changed, 35 insertions, 126 deletions

diff --git a/biology/velvet/Makefile b/biology/velvet/Makefile
index 5fcdca3ac0a5..6808c05340c1 100644
--- a/biology/velvet/Makefile
+++ b/biology/velvet/Makefile
@@ -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 @@ USE_GMAKE=	yes
 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} ${SCRIPTS}
@@ -53,19 +59,16 @@ PLIST_DIRS+=	%%SITE_PERL%%/${d:T}
 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 --git a/biology/velvet/distinfo b/biology/velvet/distinfo
index 693ef3a5a527..a8b66154a0e2 100644
--- a/biology/velvet/distinfo
+++ b/biology/velvet/distinfo
@@ -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 --git a/biology/velvet/files/patch-Makefile b/biology/velvet/files/patch-Makefile
index 554927aa6fd8..cdff89aaf6bf 100644
--- a/biology/velvet/files/patch-Makefile
+++ b/biology/velvet/files/patch-Makefile
@@ -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 --git a/biology/velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl b/biology/velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl
deleted file mode 100644
index 90bd168cc57e..000000000000
--- a/biology/velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl
+++ /dev/null
@@ -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 --git a/biology/velvet/files/patch-src-run.c b/biology/velvet/files/patch-src-run.c
deleted file mode 100644
index 7ecd02708351..000000000000
--- a/biology/velvet/files/patch-src-run.c
+++ /dev/null
@@ -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);
-