d56a210fa7491258be90208f4f3afc2ace9ad0b7
max
  Thu Jul 31 14:27:58 2014 -0700
changing cscope target again for older versions
diff --git src/makefile src/makefile
index 7090314..4d41ed1 100644
--- src/makefile
+++ src/makefile
@@ -1,183 +1,183 @@
 include inc/localEnvironment.mk
 include inc/common.mk
 
 all: utils cgi blatSuite
 
 alpha: clean
 	${MAKE} utils-alpha cgi-alpha blatSuite
 
 beta: check-beta clean cgi-beta
 
 # do a git update and clean
 update:
 	git pull
 	${MAKE} clean
 
 topLibs:
 	@MACHTYPE=${MACHTYPE} ./machTest.sh
 	cd lib && ${MAKE}
 	cd jkOwnLib && ${MAKE}
 	cd parasol/lib && ${MAKE}
 
 hgLib:
 	@./hg/sqlEnvTest.sh
 	cd hg/lib && ${MAKE}
 
 libs: topLibs hgLib
 
 cgi: libs
 	cd hg && ${MAKE} cgi
 
 cgi-alpha: libs
 	cd hg && ${MAKE} alpha
 
 cgi-beta: check-beta libs
 	cd hg && ${MAKE} beta
 
 check-beta:
 	# this will fail if we are not in a beta checkout:
 	git branch | egrep 'v[0-9]+_branch' > /dev/null	
 
 blatSuite: topLibs hgLib
 	cd blat && ${MAKE}
 	cd gfClient && ${MAKE}
 	cd gfServer && ${MAKE}
 	cd webBlat && ${MAKE}
 	cd hg/pslPretty && ${MAKE}
 	cd hg/pslReps && ${MAKE}
 	cd hg/pslSort && ${MAKE}
 	cd utils/nibFrag && ${MAKE}
 	cd utils/faToNib && ${MAKE}
 	cd utils/faToTwoBit && ${MAKE}
 	cd utils/twoBitToFa && ${MAKE}
 	cd utils/twoBitInfo && ${MAKE}
 	cd isPcr && ${MAKE}
 	cd blatz && ${MAKE}
 
 # all of these application makefiles have been updated to include use
 #	of DESTDIR and BINDIR
 
 BLAT_APPLIST = blat gfClient gfServer
 
 userApps: topLibs hgLib destBin
 	cd utils/stringify && echo utils/stringify && ${MAKE}
 	cd utils && echo utils && ${MAKE} userAppsB
 	cd hg && echo hg && ${MAKE} userApps
 	cd hg/utils && echo hg/utils && ${MAKE} userApps
 	cd hg/makeDb && echo hg/makeDb && ${MAKE} userApps
 	cd ameme && echo ameme && ${MAKE}
 	cd index/ixIxx && echo index/ixIxx && ${MAKE}
 	@for P in ${BLAT_APPLIST}; do \
 	    ( cd $${P} && echo $${P} && ${MAKE} ) ; \
 	done
 	cd utils/userApps && echo utils/userApps && ${MAKE}
 
 destBin:
 	${MKDIR} ${DESTBINDIR}
 
 clean:
 	@for D in ${DIRS} x; do \
             if test "$$D" != "x" ; then \
                 ( cd $$D && echo $$D && ${MAKE} clean ) ;\
                 x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
             fi ;\
 	done
 	cd parasol && ${MAKE} clean
 	cd lib && ${MAKE} clean 
 	cd hg && ${MAKE} clean
 	cd hg && ${MAKE} clean_utils
 	cd jkOwnLib && ${MAKE} clean
 	cd utils && ${MAKE} clean
 	cd webBlat && ${MAKE} clean
 	cd isPcr && ${MAKE} clean
 	touch non-empty-rm.o
 	- find . -name \*.o -print | xargs rm
 	rm -f tags TAGS
 
 testDirs = lib utils blat gfServer hg
 test:: $(testDirs:%=%.test)
 %.test:
 	cd $* && ${MAKE} test
 
 LIB_TAGS_IN = lib/*.[hc] */lib/*.[hc] */*/lib/*.[hc] */*/*/lib/*.[hc] jkOwnLib/*.c inc/*.h hg/inc/*.h hg/encode3/encodeDataWarehouse/lib/*.c hg/encode3/encodeDataWarehouse/inc/*.h hg/encode3/eap/inc/*.h
 
 # build tags for libraries
 .PHONY: tags
 tags:
 	ctags ${LIB_TAGS_IN}
 
 cscope: 
-	find `pwd` -name '*.c' -o -name '*.h' > cscope.files
-	cscope -Rb
+	find `pwd` -name '*.c' -o -name '*.h' > sourceFiles
+	cscope -Rb `cat sourceFiles`
 # build emacs tags for libraries
 .PHONY: etags
 etags:
 	etags ${LIB_TAGS_IN}
 
 # build tags for all files
 .PHONY: tags-all
 tags-all:
 	find . -name '*.[ch]' | ctags -L -
 
 # build emacs tags for all files
 .PHONY: etags-all
 etags-all:
 	find . -name '*.[ch]' | etags -
 
 utils: libs destBin
 	${MKDIR} ${SCRIPTS}
 	cd parasol && ${MAKE}
 	@for D in ${DIRS} x; do \
             if test "$$D" != "x" ; then \
                 ( cd $$D && echo $$D && ${MAKE} ) ;\
                 x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
             fi ;\
 	done
 	cd utils && ${MAKE}
 	cd hg && ${MAKE} utils
 
 utils-alpha: libs
 	${MKDIR} ${SCRIPTS}
 	cd parasol && ${MAKE}
 	@for D in ${DIRS} x; do \
             if test "$$D" != "x" ; then \
                 ( cd $$D && echo $$D && ${MAKE} ) ;\
                 x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
             fi ;\
 	done
 	cd utils && ${MAKE} alpha
 	cd hg && ${MAKE} utils
 
 DIRS = ameme blat index dnaDust protDust weblet aladdin primeMate fuse meta
 
 ##  cellar archive for obsolete programs
 
 cellarDirs = cdnaAli getgene idbQuery reformat scanIntrons tracks wormAli \
 	xenoAli
 
 buildCellar: $(cellarDirs:%=%.cellar)
 
 %.cellar: libs destBin
 	cd $* && echo $* && $(MAKE)
 
 cleanCellar: $(cellarDirs:%=%.cellarClean)
 %.cellarClean:
 	cd $* && echo $* && $(MAKE) clean
 
 ## top level target for everything html related
 DOCS_LIST = hg/htdocs hg/js hg/htdocs/style
 doc: ${DOCS_LIST:%=%.docuser}
 %.docuser:
 	cd $* && $(MAKE)
 
 doc-alpha: ${DOCS_LIST:%=%.docalpha}
 %.docalpha:
 	cd $* && $(MAKE) alpha
 
 doc-beta: ${DOCS_LIST:%=%.docbeta}
 %.docbeta:
 	cd $* && $(MAKE) beta
 
 doc-install: ${DOCS_LIST:%=%.docinstall}
 %.docinstall:
 	cd $* && $(MAKE) install