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/hgGeneRing/makefile src/hg/hgGeneRing/makefile
index 32a03c2..d3d2805 100644
--- src/hg/hgGeneRing/makefile
+++ src/hg/hgGeneRing/makefile
@@ -1,41 +1,42 @@
+kentSrc = ../..
 
 include ../../inc/common.mk
 
 #make COPT= alpha  
 #(to disable gcc optimization which is messing up RL right now)
 
 A = hgGeneRing
 
 L += $(MYSQLLIBS) -lm -lcrypt
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS = $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a 
 
 O = $A.o
 
 include ../../inc/cgi_build_rules.mk
 
 mgsc: compile
 	mv $A ${CGI_BIN}/$A
 
 compile: $O interaction.o
 	${CC} $O interaction.o ${MYLIBS} ${L}
 	mv ${AOUT} $A${EXE}
 	chmod a+rx $A
 
 $O: $A.c
 
 interaction.c interaction.h: interaction.as
 	autoSql interaction.as interaction -dbLink
 
 interaction.o: interaction.c interaction.h 
 
 backup: clean
 	date +%Y-%m-%d-%H-%M | gawk '{printf("zip -r $(A)%s.zip *\n",$$1);}' > tempX
 	chmod 755 tempX
 	./tempX
 	rm tempX 
 	scp *.zip screech:/scratch/backups/
 	rm *.zip
 
 push:
 	scp $(APACHE)/cgi-bin/$(A) hgwbeta:$(APACHE)/cgi-bin/