dc2a1aed940aee3152f6778d8e380b699792f426
hiram
  Thu May 23 15:09:51 2013 -0700
updating list of userApps in src/utils refs #9104
diff --git src/utils/makefile src/utils/makefile
index 92c991b..5b65c99 100644
--- src/utils/makefile
+++ src/utils/makefile
@@ -1,159 +1,158 @@
 # Build all directories in utils
 
 include ../inc/common.mk
 
 # note: lists such as the following need to be defined *before*
 # they are used in the wildcard target rules.  An oddity of gnu make
 
 # define the list of user applications to build
 
 UTILS_APPLIST = \
+	ave \
 	bedClip \
 	bedGraphToBigWig \
 	bedToBigBed \
+	bigBedInfo \
 	bigBedNamedItems \
 	bigBedSummary \
 	bigBedToBed \
+	bedCommonRegions \
+	bedGeneParts \
+	bedPileUps \
+	bedRemoveOverlap \
+	bedRestrictToPositions \
 	bigWigAverageOverBed  \
 	bigWigInfo \
 	bigWigMerge \
 	bigWigSummary \
 	bigWigToBedGraph \
 	bigWigToWig \
+	calc \
+	catDir \
+	catUncomment \
+	chopFaLines \
+	colTransform \
+	countChars \
+	fastqToFa \
+	faCmp \
 	faCount \
+	faFilterN \
+	faFilter \
 	faFrag \
 	faOneRecord \
 	faPolyASizes \
 	faRandomize \
+	faRc \
 	faSize \
 	faSomeRecords \
-	faToNib \
+	faSplit \
+	faToFastq \
+	faToTab \
 	faToTwoBit \
+	faTrans \
+	findMotif \
+	headRest \
 	htmlCheck \
+	newProg \
 	nibFrag \
 	nibSize \
 	paraFetch \
 	paraSync \
+	pslLiftSubrangeBlat \
+	pslToPslx \
+	randomLines \
+	raSqlQuery \
+	raToTab \
+	raToLines \
+	rmFaDups \
+	rowsToCols \
 	sizeof \
+	splitFile \
+	splitFileByColumn \
 	stringify \
+	subChar \
+	subColumn \
+	tailLines \
 	textHistogram \
+	tickToDate \
+	timing \
 	twoBitDup \
         twoBitInfo \
 	twoBitToFa \
 	wigCorrelate \
 	wigToBigWig
 
-APPS = \
+# list of utilities to build of interest only at UCSC
+
+UCSC_APPS = \
 	addCols \
-	ave \
+	aNotB \
 	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 \
+	faToNib \
 	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
 
-# list of utilities to build of interest only at UCSC
-
-UCSC_APPS = \
-	aNotB
-
 # list of scripts to install
 
 SCRIPT_FILES = \
         agpToLift \
         bedCollapse.pl \
         iSync \
         lodToBedScore \
 	mkMafFrames.pl
 
 # List of all directories to build
 
-ALL_APPS = $(APPS) $(UTILS_APPLIST) $(UCSC_APPS)
+ALL_APPS = $(UTILS_APPLIST) $(UCSC_APPS)
 
 # all: builds all utilities here
 
 all: $(ALL_APPS:%=%.all)
 
 %.all:
 	cd $* && echo $* && $(MAKE)
 
 # userAppsB: builds the user application specific programs
 # it would have been nice to be able to use the target name 'userApps'
 # here, but there is a directory by that name, and thus it always exists
 # and so the target does nothing.
 
 userAppsB: $(UTILS_APPLIST:%=%.userApps)