svn commit: r358183 - in head/biology/velvet: . files
Raphael Kubo da Costa
rakuco at FreeBSD.org
Tue Jun 17 21:39:45 UTC 2014
Author: rakuco
Date: Tue Jun 17 21:39:44 2014
New Revision: 358183
URL: http://svnweb.freebsd.org/changeset/ports/358183
QAT: https://qat.redports.org/buildarchive/r358183/
Log:
Update to 1.2.10.
PR: 191129
Submitted by: mzaki at m.u-tokyo.ac.jp (maintainer)
Modified:
head/biology/velvet/Makefile
head/biology/velvet/distinfo
head/biology/velvet/files/patch-Makefile
Modified: head/biology/velvet/Makefile
==============================================================================
--- head/biology/velvet/Makefile Tue Jun 17 21:36:06 2014 (r358182)
+++ head/biology/velvet/Makefile Tue Jun 17 21:39:44 2014 (r358183)
@@ -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 shuff
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
Modified: head/biology/velvet/distinfo
==============================================================================
--- head/biology/velvet/distinfo Tue Jun 17 21:36:06 2014 (r358182)
+++ head/biology/velvet/distinfo Tue Jun 17 21:39:44 2014 (r358183)
@@ -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
Modified: head/biology/velvet/files/patch-Makefile
==============================================================================
--- head/biology/velvet/files/patch-Makefile Tue Jun 17 21:36:06 2014 (r358182)
+++ head/biology/velvet/files/patch-Makefile Tue Jun 17 21:39:44 2014 (r358183)
@@ -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)
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