1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
|
CC = gcc
CFLAGS += -Wall
DEBUG = -g
LIBS = -lm
OPT = -O3
MAXKMERLENGTH=31
CATEGORIES=2
DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
# Mac OS users: uncomment the following lines
# CFLAGS = -Wall -m64
# Sparc/Solaris users: uncomment the following line
# CFLAGS = -Wall -m64
ifdef BIGASSEMBLY
override DEF := $(DEF) -D BIGASSEMBLY
endif
ifdef VBIGASSEMBLY
override DEF := $(DEF) -D BIGASSEMBLY -D VBIGASSEMBLY
endif
ifdef LONGSEQUENCES
override DEF := $(DEF) -D LONGSEQUENCES
endif
# OpenMP
ifdef OPENMP
override CFLAGS := $(CFLAGS) -fopenmp
endif
# Per library coverage
ifdef SINGLE_COV_CAT
override DEF := $(DEF) -D SINGLE_COV_CAT
endif
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
clean : clean-zlib
-rm obj/*.o obj/dbg/*.o ./velvet*
-rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log
-rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log
cleanobj:
-rm obj/*.o obj/dbg/*.o
ifdef BUNDLEDZLIB
Z_LIB_DIR=third-party/zlib-1.2.3
Z_LIB_FILES=$(Z_LIB_DIR)/*.o
override DEF := $(DEF) -D BUNDLEDZLIB
zlib:
cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
clean-zlib :
cd $(Z_LIB_DIR) && make clean
else
Z_LIB_FILES=-lz
zlib :
clean-zlib :
endif
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/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
velvetg : obj
$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.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/scaffold.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/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
debug : override DEF := $(DEF) -D DEBUG
debug : cleanobj obj/dbg
$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
color : override DEF := $(DEF) -D COLOR
color : cleanobj obj_de
$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.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/scaffold.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/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
colordebug : override DEF := $(DEF) -D COLOR -D DEBUG
colordebug : cleanobj obj/dbg_de
$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
objdir:
mkdir -p obj
obj: zlib cleanobj objdir $(OBJ)
obj_de: override DEF := $(DEF) -D COLOR
obj_de: zlib cleanobj objdir $(OBJ)
obj/dbgdir:
mkdir -p obj/dbg
obj/dbg: override DEF := $(DEF) -D DEBUG
obj/dbg: zlib cleanobj obj/dbgdir $(OBJDBG)
obj/dbg_de: override DEF := $(DEF) -D COLOR -D DEBUG
obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
obj/%.o: src/%.c
$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@
obj/dbg/%.o: src/%.c
$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@
doc: Manual.pdf
Manual.pdf: doc/manual_src/Manual.tex doc/manual_src/Columbus_manual.tex
cd doc/manual_src; pdflatex Manual.tex; pdflatex Manual.tex; mv Manual.pdf ../..; pdflatex Columbus_manual.tex; mv Columbus_manual.pdf ../..
test: velvetg velveth
cd tests && ./run-tests.sh
|