BGI/SOAPdenovo2/standardPregraph/Makefile

   1 ####################################
   2 #
   3 # Use "make 127mer=1" to make 127mer version
   4 # Use "make 63mer=1" to make 63mer version(default)
   5 #
   6 ###################################
   7
   8 CC=             gcc
   9 GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4)
  10 GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4)
  11 ifdef debug
  12 CFLAGS=         -O0 -g -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
  13 else
  14 CFLAGS=         -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
  15 endif
  16 DFLAGS=
  17 OBJS=           arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
  18                 concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o \
  19                 darray.o dfib.o dfibHeap.o fib.o fibHeap.o \
  20                 hashFunction.o kmer.o lib.o loadGraph.o loadPath.o \
  21                 loadPreGraph.o localAsm.o main.o map.o mem_manager.o \
  22                 newhash.o node2edge.o orderContig.o output_contig.o output_pregraph.o \
  23                 output_scaffold.o pregraph.o prlHashCtg.o prlHashReads.o prlRead2Ctg.o \
  24                 prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o\
  25                 readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \
  26                 cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o
  27 PROG=       SOAPdenovo-63mer
  28 INCLUDES=   -Iinc
  29 SUBDIRS=    .
  30 LIBPATH=    -L/lib64 -L/usr/lib64 -L./inc
  31 LIBS=       -pthread -lz -lm
  32 EXTRA_FLAGS=
  33
  34 BIT_ERR = 0
  35 ifeq (,$(findstring $(shell uname -m), x86_64 ppc64 ia64))
  36 BIT_ERR = 1
  37 endif
  38
  39 ifdef 127mer
  40 CFLAGS += -DMER127
  41 PROG = SOAPdenovo-127mer
  42 else
  43 CFLAGS += -DMER63
  44 PROG = SOAPdenovo-63mer
  45 endif
  46
  47 ifneq (,$(findstring Linux,$(shell uname)))
  48 EXTRA_FLAGS += -Wl,--hash-style=both
  49 LIBS += -lbam -lrt
  50 endif
  51
  52 ifneq (,$(findstring Unix,$(shell uname)))
  53 EXTRA_FLAGS += -Wl,--hash-style=both
  54 LIBS += -lbam -lrt
  55 endif
  56
  57 ifneq (,$(findstring Darwin,$(shell uname)))
  58 LIBS += -lbammac
  59 endif
  60
  61 ifneq (,$(findstring $(shell uname -m), x86_64))
  62 CFLAGS += -m64
  63 endif
  64
  65 ifneq (,$(findstring $(shell uname -m), ia64))
  66 CFLAGS +=
  67 endif
  68
  69 ifneq (,$(findstring $(shell uname -m), ppc64))
  70 CFLAGS += -mpowerpc64
  71 endif
  72
  73 .SUFFIXES:.c .o
  74
  75 .c.o:
  76                 @printf "Compiling $<...                             \r"; \
  77                 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
  78
  79 all:            clean $(OBJS)
  80
  81 #SOAPdenovo
  82
  83 .PHONY:all clean install
  84
  85 envTest:
  86                 @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;'
  87                 @test $(GCCVERSIONMAJOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;'
  88                 @test $(GCCVERSIONMINOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;'
  89
  90 SOAPdenovo:     envTest $(OBJS)
  91                 @printf "Linking...                                                \r"
  92                 @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
  93                 @printf "$(PROG) compilation done.\n";
  94
  95 clean:
  96                 @rm -fr gmon.out *.o a.out *.exe *.dSYM $(PROG) *~ *.a *.so.* *.so *.dylib
  97                 @printf "$(PROG) cleaning done.\n";
  98
  99 install:
 100                 @cp $(PROG) ../bin/
 101                 @printf "$(PROG) installed at ../bin/$(PROG)\n"