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/userApps/Makefile src/userApps/Makefile
index 11f32a5..080ec50 100644
--- src/userApps/Makefile
+++ src/userApps/Makefile
@@ -1,69 +1,64 @@
 #  Makefile for userApps project
 #  performs the operations of fetching selected directories from
 #  the kent source tree using 'git' and then building the utilities
 #  in the kent source tree.  All build results will be kept locally
 #  in this directory.
 
 export DESTDIR = ${CURDIR}
 export BINDIR = /bin
 export MACHTYPE = local
 export CGI_BIN = ${DESTDIR}/cgi-bin
 export DOCUMENTROOT = ${DESTDIR}/htdocs
 export SCRIPTS = ${DESTDIR}/scripts
-export SAMTABIXDIR = ${DESTDIR}/samtabix
-export USE_SAMTABIX = 1
 export USE_SSL = 1
 export NOSQLTEST = 1
 
 all:  utils
 
 utils: libs
 	cd kent/src && ${MAKE} userApps
 	cd kent/src/parasol && ${MAKE}
 	./kent/src/utils/userApps/mkREADME.sh ${DESTDIR}/${BINDIR} ${CURDIR}/kentUtils.Documentation.txt
 
 libs: installEnvironment
-	cd samtabix && ${MAKE}
 	cd kent/src && ${MAKE} libs
 
 clean:
 	test ! -d kent/src || (cd kent/src && ${MAKE} -i -k clean)
 	rm -f part1Src.zip part2Src.zip part3Src.zip part4Src.zip part5Src.zip
 	rm -f userApps.zip
 
 fetchSource:
 	./fetchKentSource.sh
 	@echo -n "size of fetched kent source tree: "
 	@du -hs kent
 	@echo -n "number of files in kent source tree: "
 	@find ./kent -type f | wc -l
 
 # this installEnvironment will add all the shell environment variables
 # to the kent/src/inc/localEnvironment.mk file which is included
 # from the kent/src/inc/userApps.mk to allow any 'make' to function
 # properly when inside this extracted source tree.  The 'sed' operation
 # removes the '-e' from the echo for systems where the echo command doesn't
 # recognize the '-e' argument
 
 installEnvironment:
 	@test -d kent/src/inc || (echo "ERROR: source has not been fetched yet, try 'make fetchSource' first."; exit 255)
 	@echo -e "export DESTDIR = ${DESTDIR}\n\
 export BINDIR = ${BINDIR}\n\
 export MACHTYPE = ${MACHTYPE}\n\
 export CGI_BIN = ${CGI_BIN}\n\
 export DOCUMENTROOT = ${DOCUMENTROOT}\n\
 export SCRIPTS = ${SCRIPTS}\n\
-export SAMTABIXDIR = ${SAMTABIXDIR}\n\
-export USE_SAMTABIX = 1\n\
 export USE_SSL = 1\n\
 export NOSQLTEST = 1" | sed -e 's/-e //' > kent/src/inc/localEnvironment.mk
 
 update: clean userApps
 	${MAKE} fetchSource
 	${MAKE} utils
 
 userApps:
 	git archive --format=zip -9 \
 	    --remote=git://genome-source.cse.ucsc.edu/kent.git \
 	    HEAD src/userApps > userApps.zip
 	unzip -q -o -d . -j userApps.zip