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/hgBeacon/makefile src/hg/hgBeacon/makefile
index 884f99d..bac897c 100644
--- src/hg/hgBeacon/makefile
+++ src/hg/hgBeacon/makefile
@@ -1,40 +1,41 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 #cannot use common include rules, don't know how to overwrite :: targets
 #include ../../inc/cgi_build_rules.mk
 
 ifeq (${CGI_BIN_USER},)
     CGI_BIN_USER=${CGI_BIN}-${USER}
 endif
 
 ifeq (${CGI_BIN_BETA},)
     CGI_BIN_BETA=${CGI_BIN}-beta
 endif
 
 PATH:=$(PATH):/cluster/software/bin
 
 my::
 	rm -f ${CGI_BIN_USER}/hgBeacon
 	cp -p hgBeacon ${CGI_BIN_USER}/
 	mkdir -p ${CGI_BIN_USER}/beacon2
 	ln -sf ${CGI_BIN_USER}/hgBeacon ${CGI_BIN_USER}/beacon2/info
 	ln -sf ${CGI_BIN_USER}/hgBeacon ${CGI_BIN_USER}/beacon2/query
 help:
 	cp help.txt /gbdb/hg19/beacon/
 
 beta::
 	rm -f ${CGI_BIN_BETA}/hgBeacon
 	cp -p hgBeacon ${CGI_BIN_BETA}/
 
 alpha::
 	rm -f ${CGI_BIN}/hgBeacon
 	cp -p hgBeacon ${CGI_BIN}/
 	cp testBeacon ${DESTBINDIR}/
 lint:
 	pylint -E --rcfile=pylint.rc hgBeacon
 clean::
 
 compile::
 
 install::