11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/hg/cgiExample/makefile src/hg/cgiExample/makefile
index 3ed4177..91b71ea 100644
--- src/hg/cgiExample/makefile
+++ src/hg/cgiExample/makefile
@@ -1,19 +1,20 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 JKSRCDIR = /projects/compbiousr/kent/src
 JKLIBDIR = $(JKSRCDIR)/lib/$(MACHTYPE)
 
 L += $(MYSQLLIBS) -lm 
 MYLIBS =  $(JKLIBDIR)/jkhgap.a $(JKLIBDIR)/jkweb.a
 
 O = cgiExample.o
 
 cgiExample: $O 
 	${CC} ${COPT} ${CFLAGS} $O $(MYLIBS) $L
 	mv ${AOUT} cgiExample
 	${STRIP} cgiExample${EXE}
 	chmod a+rx cgiExample
 	mv cgiExample /usr/local/apache/cgi-bin
 
 clean::
 	rm -f ${O}