3 files changed, 23 insertions, 35 deletions

diff --git a/biology/velvet/Makefile b/biology/velvet/Makefile
index 9b514578d4f4..d52a55ba354d 100644
--- a/biology/velvet/Makefile
+++ b/biology/velvet/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	velvet
-PORTVERSION=	1.1.04
+PORTVERSION=	1.2.10
 CATEGORIES=	biology
 MASTER_SITES=	http://www.ebi.ac.uk/~zerbino/velvet/
 DISTNAME=	${PORTNAME}_${PORTVERSION}
@@ -21,8 +21,9 @@ USES=		perl5 gmake
 USE_PERL5=	run
 
 BINARIES=	velvetg velveth
-SCRIPTS=	shuffleSequences_fasta.pl shuffleSequences_fastq.pl \
-		contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl \
+SCRIPTS=	contrib/shuffleSequences_fasta/shuffleSequences_fasta.pl \
+		contrib/shuffleSequences_fasta/shuffleSequences_fastq.pl \
+		contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl \
 		contrib/afg_handling/asmbly_splitter.pl \
 		contrib/afg_handling/snp_view.pl \
 		contrib/columbus_scripts/enlarge_exons.pl \
@@ -32,13 +33,14 @@ SCRIPTS=	shuffleSequences_fasta.pl shuffleSequences_fastq.pl \
 		contrib/extractContigReads/extractContigReads.pl \
 		contrib/fasta2agp/fasta2agp.pl \
 		contrib/observed-insert-length.pl/observed-insert-length.pl \
+		contrib/read_prepare/pe_read_prepare.0.1.pl \
 		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
+PERLMOD_DIRS=	contrib/VelvetOptimiser-2.2.4/VelvetOpt
+PERLMOD_FILES=	contrib/VelvetOptimiser-2.2.4/VelvetOpt/Assembly.pm \
+		contrib/VelvetOptimiser-2.2.4/VelvetOpt/Utils.pm \
+		contrib/VelvetOptimiser-2.2.4/VelvetOpt/gwrap.pm \
+		contrib/VelvetOptimiser-2.2.4/VelvetOpt/hwrap.pm
 
 .if !defined(WITHOUT_PYTHON)
 USE_PYTHON=	yes
diff --git a/biology/velvet/distinfo b/biology/velvet/distinfo
index a8b66154a0e2..4cde54526810 100644
--- a/biology/velvet/distinfo
+++ b/biology/velvet/distinfo
@@ -1,2 +1,2 @@
-SHA256 (velvet_1.1.04.tgz) = 7ae9855c3eabd1d222815a7132cdc9eeb387d83132390d020fc78491e6dcc9d6
-SIZE (velvet_1.1.04.tgz) = 7744134
+SHA256 (velvet_1.2.10.tgz) = 884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640
+SIZE (velvet_1.2.10.tgz) = 18818559
diff --git a/biology/velvet/files/patch-Makefile b/biology/velvet/files/patch-Makefile
index cdff89aaf6bf..fd3536304593 100644
--- a/biology/velvet/files/patch-Makefile
+++ b/biology/velvet/files/patch-Makefile
@@ -1,47 +1,33 @@
---- Makefile.orig	2011-03-30 14:34:09.000000000 +0900
-+++ Makefile	2011-06-02 20:28:04.000000000 +0900
-@@ -1,18 +1,18 @@
+--- Makefile.orig	2013-10-18 01:03:39.000000000 +0900
++++ Makefile	2014-06-17 21:34:34.000000000 +0900
+@@ -1,15 +1,15 @@
 -CC = gcc
 -CFLAGS = -Wall
 +CC ?= gcc
 +CFLAGS += -Wall
  DEBUG = -g
--LDFLAGS = -lm
+ LIBS = -lm
 -OPT = -O3
 -MAXKMERLENGTH=31
 -CATEGORIES=2
-+#LDFLAGS = -lm
 +#OPT = -O3
 +MAXKMERLENGTH?=31
 +CATEGORIES?=2
  DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
- 
- Z_LIB_DIR=third-party/zlib-1.2.3
- Z_LIB_FILES=$(Z_LIB_DIR)/*.o
+ PDFLATEX_VERSION := $(shell pdflatex --version 2> /dev/null)
  
  # Mac OS users: uncomment the following lines
--# Z_LIB_FILES=
--# LDFLAGS = -lm -lz
-+Z_LIB_FILES=
-+LDFLAGS += -lm -lz
- # CFLAGS = -Wall -m64
+-CFLAGS = -Wall -m64
++#CFLAGS = -Wall -m64
  
  # Sparc/Solaris users: uncomment the following line
-@@ -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
+ # CFLAGS = -Wall -m64
+@@ -40,7 +40,7 @@
+ 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/binarySequences.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 obj/autoOpen.o
  OBJDBG = $(subst obj,obj/dbg,$(OBJ))
  
 -default : cleanobj zlib obj velveth velvetg doc
 +default : cleanobj zlib obj velveth velvetg
  
- clean :
+ clean : clean-zlib
  	-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/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)