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	RELEASE_7_4_0:1.1
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1.2
date	2011.06.09.16.33.21;	author jlaffaye;	state Exp;
branches;
next	1.1;

1.1
date	2009.11.07.01.23.59;	author amdmi3;	state Exp;
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desc
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1.2
log
@Update to 1.1.04

PR:		ports/157527
Submitted by:	Motomichi Matsuzaki <mzaki@@m.u-tokyo.ac.jp>
Approved by:	bapt (mentor)
@
text
@--- 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
+CC ?= gcc
+CFLAGS += -Wall
 DEBUG = -g
-LDFLAGS = -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
 
 # Mac OS users: uncomment the following lines
-# Z_LIB_FILES=
-# LDFLAGS = -lm -lz
+Z_LIB_FILES=
+LDFLAGS += -lm -lz
 # 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
 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/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)
@


1.1
log
@Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).

Citation:

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)

WWW: http://www.ebi.ac.uk/~zerbino/velvet/

PR:		140147
Submitted by:	Motomichi Matsuzaki <mzaki@@m.u-tokyo.ac.jp>
@
text
@d1 2
a2 2
--- Makefile.orig	2009-09-02 22:21:01.000000000 +0900
+++ Makefile	2009-10-27 22:05:49.000000000 +0900
d30 10
a39 1
@@@@ -32,7 +32,7 @@@@
d46 2
a47 2
 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)
@

