Makefile

   1 CC=                     gcc
   2 CFLAGS=         -g -Wall -O2 -fPIC #-m64 #-arch ppc
   3 DFLAGS=         -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE
   4 LOBJS=          bgzf.o kstring.o knetfile.o index.o bedidx.o
   5 AOBJS=          main.o
   6 PROG=           tabix bgzip
   7 INCLUDES=
   8 SUBDIRS=        .
   9 LIBPATH=
  10 LIBCURSES=
  11
  12 .SUFFIXES:.c .o
  13
  14 .c.o:
  15                 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
  16
  17 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
  18                 @target=`echo $@ | sed s/-recur//`; \
  19                 wdir=`pwd`; \
  20                 list='$(SUBDIRS)'; for subdir in $$list; do \
  21                         cd $$subdir; \
  22                         $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
  23                                 INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
  24                         cd $$wdir; \
  25                 done;
  26
  27 all:$(PROG)
  28
  29 lib:libtabix.a
  30
  31 libtabix.so.1:$(LOBJS)
  32                 $(CC) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
  33
  34 libtabix.1.dylib:$(LOBJS)
  35                 libtool -dynamic $(LOBJS) -o $@ -lc -lz
  36
  37 libtabix.a:$(LOBJS)
  38                 $(AR) -csru $@ $(LOBJS)
  39
  40 tabix:lib $(AOBJS)
  41                 $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. -ltabix -lm $(LIBPATH) -lz
  42
  43 bgzip:bgzip.o bgzf.o knetfile.o
  44                 $(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
  45
  46 TabixReader.class:TabixReader.java
  47                 javac -cp .:sam.jar TabixReader.java
  48
  49 kstring.o:kstring.h
  50 knetfile.o:knetfile.h
  51 bgzf.o:bgzf.h knetfile.h
  52 index.o:bgzf.h tabix.h khash.h ksort.h kstring.h
  53 main.o:tabix.h kstring.h bgzf.h
  54 bgzip.o:bgzf.h
  55 bedidx.o:kseq.h khash.h
  56
  57 tabix.pdf:tabix.tex
  58                 pdflatex tabix.tex
  59
  60 cleanlocal:
  61                 rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log tabix.pdf *.class libtabix.*.dylib libtabix.so*
  62
  63 clean:cleanlocal-recur