0829e45130c304f0a15c2f24e84ea22fe59984df
hiram
  Mon May 20 13:59:50 2013 -0700
get stringify built before everything else refs #9104
diff --git src/utils/makefile src/utils/makefile
index 9baed70..b27bb0e 100644
--- src/utils/makefile
+++ src/utils/makefile
@@ -1,192 +1,192 @@
 # Build all directories in utils
 
 include ../inc/common.mk
 
 # all: builds all utilities here
 
 all:    
 	@for D in $(USE_DIRS) x; do \
 	  if test "$$D" != "x" ; then \
 	    ( cd $$D && echo $$D && $(MAKE) ) ;\
 	    x=$$? ; if [ $$x -ne 0 ]; then exit $$x ; fi \
 	    fi ;\
 	done
 
 # userApps: builds on user application specific programs
 
-userApps: $(UTILS_APPLIST:%=%.uApp)
+userApps: $(UTILS_APPLIST:%=%.userApps)
 
-%.uApp:
+%.userApps:
 	( cd $* && echo $* && $(MAKE) )
 
 scripts:
 	@for F in ${SCRIPT_FILES}; do \
 	    chmod +x $$F; \
 	    rm -f ${SCRIPTS}/$${F}; \
 	    echo cp -p $$F ${SCRIPTS}; \
 	    cp -p $$F ${SCRIPTS}; \
 	 done
 	chmod +x genePredToBed/genePredToBed;
 	rm -f ${SCRIPTS}/genePredToBed;
 	echo cp -p genePredToBed/genePredToBed ${SCRIPTS};
 	@cp -p genePredToBed/genePredToBed ${SCRIPTS};
 
 alpha: scripts all
 
 test:
 	cd faToTwoBit && ${MAKE} test
 	cd twoBitToFa && ${MAKE} test
 	cd twoBitInfo && ${MAKE} test
 	cd pslLiftSubrangeBlat && ${MAKE} test
 	cd bedGeneParts && ${MAKE} test
 
 clean:
 	@for D in $(USE_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
 	touch non-empty-rm.o
 	- find . -name \*.o -print | xargs rm
 
 SCRIPT_FILES = \
         agpToLift \
         bedCollapse.pl \
         iSync \
         lodToBedScore \
 	mkMafFrames.pl
 
 # List of directories to build
 USE_DIRS = $(DIRS) $(UTILS_APPLIST) $(UCSC_DIRS)
 
 UCSC_DIRS = \
 	aNotB
 
 UTILS_APPLIST = \
 	bedClip \
 	bedGraphToBigWig \
 	bedToBigBed \
 	bigBedNamedItems \
 	bigBedSummary \
 	bigBedToBed \
 	bigWigAverageOverBed  \
 	bigWigInfo \
 	bigWigMerge \
 	bigWigSummary \
 	bigWigToBedGraph \
 	bigWigToWig\
 	faCount \
 	faFrag \
 	faOneRecord \
 	faPolyASizes \
 	faRandomize \
 	faSize \
 	faSomeRecords \
 	faToNib \
 	faToTwoBit \
 	htmlCheck \
 	nibFrag \
 	nibSize \
 	paraFetch \
 	paraSync \
 	sizeof \
 	stringify \
 	textHistogram \
 	twoBitDup \
 	twoBitInfo \
 	twoBitToFa \
 	wigCorrelate \
 	wigToBigWig
 
 DIRS = \
 	addCols \
 	ave \
 	aveCols \
 	bedCommonRegions \
 	bedGeneParts \
 	bedPileUps \
 	bedRemoveOverlap \
 	bedRestrictToPositions \
 	calc \
 	catDir \
 	catUncomment \
 	ccCp \
 	chopFaLines \
 	colTransform \
 	countChars \
 	convolve \
 	detab \
 	endsInLf \
 	fastqToFa \
 	faAlign \
 	faCmp \
 	faFilterN \
 	faFilter \
 	faFlyBaseToUcsc \
 	faGapLocs \
 	faGapSizes \
 	faNcbiToUcsc \
 	faNoise \
 	faRc \
 	faSimplify \
 	faSplit \
 	faToFastq \
 	faToTab \
 	faTrans \
 	faTrimPolyA \
 	faTrimRead \
 	findMotif \
 	fixCr \
 	gapSplit \
 	gffPeek \
 	git-reports \
 	gitTools \
 	headRest \
 	htmlPics \
 	jkUniq \
 	lineCount \
 	newProg \
 	nt4Frag \
 	pslLiftSubrangeBlat \
 	pslToPslx \
 	pslToXa \
 	randomLines \
 	raSqlQuery \
 	raToTab \
 	raToLines \
 	rmFaDups \
 	rowsToCols \
 	scaffoldFaToAgp \
 	scrambleFa \
 	spacedToTab \
 	splitFile \
 	splitFileByColumn \
 	subChar \
 	subColumn \
 	subs \
 	tableSum \
 	tailLines \
 	textHist2 \
 	tickToDate \
 	timing \
 	toLower \
 	toUpper \
 	udcCleanup \
 	undupFa \
 	upper \
 	venn \
 	verticalSplitSqlTable \
 	weedLines \
 	wigTestMaker \
 	wordLine
 
 BAD_DIRS= \
 	ccCpLock \
 	est2genomeToPsl \
 	geneStarts \
 	jimgrep \
 	jkShell \
 	dnsInfo \
 	wigAsciiToBinary \
 	cCp