ee7b6397b91a4225028990e70517db4d89ce2058
hiram
  Thu May 23 15:46:43 2013 -0700
expanding the list of userApps in hg refs #9104
diff --git src/hg/makefile src/hg/makefile
index de327d6..38e4838 100644
--- src/hg/makefile
+++ src/hg/makefile
@@ -19,166 +19,169 @@
 
 ifneq ($(findstring $(shell hostname),hgwdev hgwbeta),)
     ENCODE_FILES =
 endif
 
 
 TEST_DIRS = lib autoDtd autoSql blastToPsl checkTableCoords embossToPsl \
             genePredSingleCover genePredHisto genePredToBed genePredToGtf \
 	    genePredToMafFrames gbGetEntries hgGetAnn liftAcross \
             mrnaToGene pslCDnaFilter pslDiff pslHisto \
             pslPartition pslSelect pslStats pslSwap pslToBed spideyToPsl \
 	    sqlToXml xmlToSql utils
 
 BROKEN_TEST_DIRS = liftOver scaffoldFaToAgp
 
-# List of directories to build
-USE_DIRS = $(UTIL_DIRS)
-
 BAD_DIRS = \
 	altGraph \
 	cgiExample \
 	geneOverlap \
 	hgBatch \
 	makeSeqs \
 	oneShot \
 	synMap \
 	encode \
 	wikiPlot 
 
+# List of directories to build for userApps
+UTILS_APPLIST = \
+	bedSort \
+	liftUp \
+	liftOver \
+	bedIntersect \
+	bedItemOverlapCount \
+	bedToGenePred \
+	blastToPsl \
+	checkCoverageGaps \
+	checkHgFindSpec \
+	checkTableCoords \
+	dbTrash \
+	encode3/validateFiles \
+	encode3/validateManifest \
+	estOrient \
+	featureBits \
+	genePredHisto \
+	genePredSingleCover \
+	genePredToBed \
+	genePredToFakePsl \
+	genePredToMafFrames \
+	gigAssembler/checkAgpAndFa \
+	hgsql \
+	ratStuff/mafsInRegion \
+	ratStuff/mafSpeciesSubset \
+	pslCDnaFilter \
+	genePredCheck \
+	genePredToGtf \
+	pslPretty \
+	pslReps \
+	pslSort
+
+# List of directories to build at UCSC
 UTIL_DIRS = \
 	affyTransciptome \
 	agpCloneCheck \
 	agpCloneList \
 	agpAllToFaFile \
 	agpToFa \
 	agpToGl \
 	altSplice \
 	autoDtd \
 	autoSql \
 	autoXml \
 	bedOrBlocks \
-	bedIntersect \
-	bedItemOverlapCount \
-	bedSort \
-	bedToGenePred \
 	bedSplitOnChrom \
-	blastToPsl \
 	borfBig \
-	checkCoverageGaps \
-	checkHgFindSpec \
-	checkTableCoords \
 	ctgFaToFa \
 	ctgToChromFa \
-	dbTrash \
-	estOrient \
 	embossToPsl \
-	encode3/validateFiles \
-	encode3/validateManifest \
 	fakeFinContigs \
 	fakeOut \
-	featureBits \
 	ffaToFa \
 	fishClones \
 	fqToQa \
 	fqToQac \
 	fragPart \
 	gbGetEntries \
 	gbOneAcc \
 	gbToFaRa \
 	geneBounds \
-	genePredCheck \
-	genePredHisto \
-	genePredSingleCover \
-	genePredToBed \
-	genePredToGtf \
-	genePredToFakePsl \
-	genePredToMafFrames \
 	getFeatDna \
 	getRna \
 	getRnaPred \
-	gigAssembler/checkAgpAndFa \
 	gpStats \
 	gpToGtf \
 	gpcrParser \
 	gsBig \
 	hgTablesTest \
 	hgChroms \
 	hgGetAnn \
 	hgKnownGeneList \
 	hgSelect \
 	hgSpeciesRna \
-	hgsql \
 	hgsqlLocal \
 	hgsqladmin \
 	hgsqldump \
 	hgsqldumpLocal \
 	hgsqlimport \
         hgsqlSwapTables \
         hgsqlTableDate \
 	intronEnds \
 	lib \
 	liftAcross \
 	liftAgp \
 	liftFrags \
-	liftOver \
-	liftUp \
 	lfsOverlap \
 	makeDb \
 	maskOutFa \
 	mdToNcbiLift \
 	mouseStuff \
 	mrnaToGene \
 	near/hgCeOrfToGene \
 	near/hgClusterGenes \
 	near/hgEmblProtLinks \
 	near/hgExpDistance \
 	near/hgGoAssociation \
 	near/hgKnownToSuper \
 	near/hgMapToGene \
 	near/hgMapViaSwissProt \
 	near/hgProtIdToGenePred \
 	near/hgWormLinks \
 	near/pepPredToFa \
 	near/hgNearTest \
 	near/hgNetDist \
 	near/knownToHprd \
 	nci60 \
 	orthoMap \
 	patCount \
 	perf \
-	pslCDnaFilter \
 	pslCat \
 	pslCheck \
 	pslCoverage \
 	pslDiff \
 	pslDropOverlap \
 	pslFilter \
 	pslFilterPrimers \
 	pslGlue \
 	pslHisto \
 	pslHitPercent \
 	pslIntronsOnly \
 	pslPartition \
 	pslPairs \
-	pslPretty \
 	pslQuickFilter \
 	pslRecalcMatch \
-	pslReps \
 	pslSelect \
 	pslSimp \
-	pslSort \
 	pslSortAcc \
 	pslSplitOnTarget \
 	pslStats \
 	pslSwap \
 	pslToBed \
 	pslUnpile \
 	pslxToFa \
 	qa \
 	qaToQac \
 	qacAgpLift \
 	qacToQa \
 	qacToWig \
 	ratStuff \
 	relPairs \
 	recycleDb \
@@ -194,38 +197,44 @@
 	splitFa \
 	splitFaIntoContigs \
 	sqlToXml \
 	test \
 	trfBig \
 	txCds \
 	txGene \
 	txGraph \
 	utils \
 	uniqSize \
 	updateStsInfo \
 	visiGene/knownToVisiGene \
 	xmlCat \
 	xmlToSql
 
+APPS = $(UTIL_DIRS) $(UTILS_APPLIST)
+USE_DIRS = $(UTIL_DIRS)
 
 all::    cgi utils
 
 hgLib:
 	@./sqlEnvTest.sh
 	cd lib && ${MAKE}
 
-utils: $(USE_DIRS:%=%.utils)
+userApps: $(UTILS_APPLIST:%=%.userApp)
+%.userApp: hgLib
+	( cd $* && echo $* && $(MAKE) )
+
+utils: $(APPS:%=%.utils)
 %.utils: hgLib
 	( cd $* && echo $* && $(MAKE) )
 
 # Compile only, the cgi's for those builds without write access
 #	to apache cgi-bin directories  (this compiles and links executables)
 
 compile: ${BROWSER_BINS:%=%.compile} ${BROWSER_LOADERS:%=%.compile}
 %.compile: hgLib
 	( cd $* && echo $* && $(MAKE) compile)
 
 # Build cgi's
 #   cgi: Destination for the binaries is /usr/local/apache/cgi-bin-${USER}
 
 cgi: ${BROWSER_BINS:%=%.bins} ${BROWSER_LOADERS:%=%.cgi} ${BROWSER_LOADERS:%=%.cgi} ${ENCODE_FILES:%=%.cgi}
 %.bins: hgLib