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/protein/makefile src/hg/protein/makefile
index bfcb7e9..e732425 100644
--- src/hg/protein/makefile
+++ src/hg/protein/makefile
@@ -1,75 +1,76 @@
+kentSrc = ../..
 # Build all directories in utils
 
 include ../../inc/common.mk
 
 DIRS = \
 	blastRecipBest \
 	gadPos \
 	hmmPfamToTab \
 	kgAliasM \
 	kgAliasP \
 	kgAliasKgXref \
 	kgAliasRefseq \
 	kgProtAlias \
 	kgProtAliasNCBI \
 	kgBestMrna2 \
 	kgBestRef2 \
 	kgCheck \
 	kgGetCds \
 	kgGetPep \
 	kgPepMrna \
 	kgPick \
 	kgPutBack \
 	kgXref \
 	kgXref2 \
 	pbCalDist \
 	pbCalDistGlobal \
 	pbCalPi \
 	pbCalResStd \
 	pbCalResStdGlobal \
 	pbHgnc \
 	pfamXref \
 	rmKGPepMrna \
 	scopCollapse \
 	spDbAddVarSplice \
 	spOrganism \
 	spTest \
 	spToDb \
 	spLoadPsiBlast \
 	spLoadRankProp \
 	spToProteinsVar \
 	spToSpXref2 \
 	spXref3 \
 	spm3 \
 	spm6 \
 	spm7 \
 	spToProteins
 USE_DIRS = $(DIRS)
 
 TEST_DIRS = \
 	spToDb
 
 all::    utils
 
 utils: $(USE_DIRS:%=%.utils)
 
 %.utils:
 	(cd $* && echo $* && $(MAKE))
 
 test::	${TEST_DIRS:%=%.test}
 %.test:
 	(cd $* && ${MAKE} test)
 
 # List of directories to build
 
 clean: $(USE_DIRS:%=%.clean)
 
 %.clean:
 	(cd $* && $(MAKE) clean)
 
 
 # no makefile for:
 #       pfamXref
 #	spXref2