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/phyloGif/makefile src/hg/phyloGif/makefile
index 5a6a64f..58c1849 100644
--- src/hg/phyloGif/makefile
+++ src/hg/phyloGif/makefile
@@ -1,32 +1,33 @@
+kentSrc = ../..
 include ../../inc/common.mk
 
 L += $(MYSQLLIBS) -lm
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a
 
 A = phyloGif
 
 O = ${A}.o
 
 include ../../inc/cgi_build_rules.mk
 
 my:: compile
 	if [ -d "${BINDIR}" ] && [ ! ${CGI_BIN}-${USER}/$A -ef ${DESTDIR}${BINDIR}/$A ] ; then \
 	    cp ${CGI_BIN}-${USER}/$A ${DESTDIR}${BINDIR}/; \
 	fi
 
 compile: $O
 	${CC} $O ${MYLIBS} ${L}
 	mv ${AOUT} $A${EXE}
 	chmod a+rx $A${EXE}
 
 test: compile
 	${DESTDIR}${BINDIR}/phyloGif -phyloGif_tree=17way.nh > test.gif
 	file test.gif
 
 testWeb: compile
 	wget -O testWeb.gif 'http://hgwdev.cse.ucsc.edu/cgi-bin/phyloGif?phyloGif_tree=(A:0.1,B:0.1);'
 	file testWeb.gif
 
 clean::
 	rm -f test.gif testWeb.gif