97a41387e5a5dafe84e94c34640ec494d2f316ea
hiram
  Thu May 23 14:19:32 2013 -0700
approaching something useful refs #9104
diff --git src/makefile src/makefile
index adce4cb..85602d3 100644
--- src/makefile
+++ src/makefile
@@ -1,182 +1,183 @@
 include inc/common.mk
 
 
 all: utils cgi blatSuite
 
 alpha: clean utils-alpha cgi-alpha blatSuite
 
 beta: check-beta clean cgi-beta
 
 # do a git update and clean
 update:
 	git pull
 	${MAKE} clean
 
 topLibs:
 	@./machTest.sh
 	cd lib && ${MAKE}
 	cd jkOwnLib && ${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
 
 HG_APPLIST = bedSort liftUp liftOver bedItemOverlapCount encode/validateFiles \
 	 featureBits ratStuff/mafsInRegion ratStuff/mafSpeciesSubset \
 	 pslCDnaFilter genePredToGtf pslPretty pslReps pslSort 
 
 
 HG_UTILS_APPLIST = bedExtendRanges gff3ToGenePred gtfToGenePred \
 	hubCheck overlapSelect makeTableList pslMap
 
 HG_HGWIGGLE_APP = hgWiggle
 
 HG_LOAD_APPLIST = hgGcPercent
 
 BLAT_APPLIST = blat gfClient gfServer
 
-userApps: topLibs hgLib
+userApps: topLibs hgLib destBin
 	cd utils/stringify && echo utils/stringify && ${MAKE}
 	cd utils && echo utils && ${MAKE} userAppsB
 	@for P in ${HG_APPLIST}; do \
 	    ( cd hg/$${P} && echo hg/$${P} && ${MAKE} ) ; \
 	done
 	@for P in ${HG_UTILS_APPLIST}; do \
 	    ( cd hg/utils/$${P} && echo hg/utils/$${P} && ${MAKE} ) ; \
 	done
 	@for P in ${HG_HGWIGGLE_APP}; do \
 	    ( cd hg/makeDb/hgLoadWiggle && echo hg/makeDb/hgLoadWiggle && ${MAKE} $${P} ) ; \
 	done
 	@for P in ${HG_LOAD_APPLIST}; do \
 	    ( cd hg/makeDb/$${P} && echo hg/makeDb/$${P} && ${MAKE} $${P} ) ; \
 	done
 	@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 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 blat gfServer hg
 test:: $(testDirs:%=%.test)
 %.test:
 	cd $* && ${MAKE} test
 
 LIB_TAGS_IN = lib/*.[hc] */lib/*.[hc] */*/lib/*.[hc] jkOwnLib/*.c inc/*.h hg/inc/*.h hg/encode3/encodeDataWarehouse/lib/*.c hg/encode3/encodeDataWarehouse/inc/*.h
 
 # build tags for libraries
 .PHONY: tags
 tags:
 	ctags ${LIB_TAGS_IN}
 
 # 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
+utils: libs destBin
 	${MKDIR} ${SCRIPTS}
-	${MKDIR} ${DESTDIR}${BINDIR}
 	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
 	@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: libs
-	${MKDIR} ${DESTDIR}${BINDIR}
+buildCellar: libs destBin
 	@for D in ${cellarDirs} x; do \
             if test "$$D" != "x" ; then \
                 ( cd $$D && echo $$D && ${MAKE} ) ;\
                 x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
             fi ;\
 	done
 
 cleanCellar:
 	@for D in ${cellarDirs} x; do \
             if test "$$D" != "x" ; then \
                 ( cd $$D && echo $$D && ${MAKE} clean ) ;\
                 x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
             fi ;\
 	done