
#Makefile for CMfinder
#Dec, 2004
#
BINDIR      = ../bin

CC = gcc	# GNU cc, if you have it...
#CFLAGS =  -g -O2    # most machines
CFLAGS = -g -DDEBUG

SHELL  = /bin/sh
LIBS   = -lm 

AR     = ar rcv 
RANLIB = ranlib

# Where the build arena is (module .h and .o files)
#
SQUIDLIBS   = -lsquid
SQUIDLIBDIR = -L../squid
SQUIDINCDIR = -I../squid

EASELLIBS   = -leasel
EASELLIBDIR = -L../easel
EASELINCDIR = -I../easel

INFLIBS   = -linfernal
INFLIBDIR = -L../infernal
INFINCDIR = -I../infernal

PROGS = candf cands canda cmfinder summarize diff_motif extend_motif

VIENNALIBS   = -lvienna
VIENNALIBDIR = -L../vienna
VIENNAINCDIR = -I../vienna

all : $(PROGS)

MYOBJS  = cand.o automaker.o match_constr.o 

$(PROGS): %: %.o $(MYOBJS) 	
	$(CC) $(CFLAGS) $(MDEFS) $(VIENNALIBDIR)  $(INFLIBDIR)   -o $@ $@.o $(MYOBJS) $(LIBS) $(VIENNALIBS)  $(INFLIBS)


install: $(PROGS)
	cp $(PROGS) $(BINDIR)/

clean:
	-rm -f core.* *.o *~ *.Addrs *.Counts *.pixie Makefile.bak core $(PROGS) TAGS

.c.o:
	$(CC) $(CFLAGS) $(MDEFS)  $(SQUIDINCDIR) $(EASELINCDIR) $(INFINCDIR) $(VIENNAINCDIR)   -c $<		

