Generic Makefile

include $(KENT)/src/inc/common.mk

CFLAGS=-I ${KENT}/src/inc -I ${KENT}/src/hg/inc 
L = -lm $(MYSQLLIBS)
MYLIBDIR = $(KENT)/src/lib/$(MACHTYPE)
MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a 

O = $(PROG).o ../lib/bedUtil.o

$(PROG): $O $(MYLIBS) 
        ${CC} ${COPT} ${CFLAGS}  -o $(HOME)/bin/$(MACHTYPE)/$(PROG) $O $(MYLIBS) $L
        strip $(HOME)/bin/$(MACHTYPE)/$(PROG)

clean:
        rm *.o
        rm core

Make sure that the four indented lines are indenten with tabs, otherwise the file will not work.

See also: the newProg command in the kent source tree. It will generate not only a generic Makefile but also the generic structure of a kent source utility.