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Update to 1.2.10.

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PR:		191129
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
This commit is contained in:
Raphael Kubo da Costa 2014-06-17 21:39:44 +00:00
parent 53828d5f20
commit fa8c84c90c
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=358183
3 changed files with 23 additions and 35 deletions
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18
biology/velvet/Makefile
View file

@ -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

4
biology/velvet/distinfo
View file

@ -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

36
biology/velvet/files/patch-Makefile
View file

@ -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)