d0f0487213a1ad3654555e8ffd12d6c9478798aa
hiram
  Tue May 28 11:21:30 2013 -0700
adding to the userUtils build refs #9149
diff --git src/hg/makefile src/hg/makefile
index fef5f4b..7cdf61a 100644
--- src/hg/makefile
+++ src/hg/makefile
@@ -80,31 +80,30 @@
 	pslCat \
 	pslCheck \
 	pslDropOverlap \
 	pslFilter \
 	pslHisto \
 	pslPairs \
 	pslPartition \
 	pslPretty \
 	pslRecalcMatch \
 	pslReps \
 	pslSelect \
 	pslSort \
 	pslStats \
 	pslSwap \
 	pslToBed \
-	pslToChain \
 	pslxToFa \
 	qaToQac \
 	qacAgpLift \
 	qacToQa \
 	qacToWig \
 	sqlToXml \
 	trfBig \
 	xmlCat \
 	xmlToSql
 
 # List of directories to build at UCSC
 UTIL_DIRS = \
 	affyTransciptome \
 	agpCloneCheck \
 	agpCloneList \
@@ -173,30 +172,31 @@
 	near/knownToHprd \
 	nci60 \
 	orthoMap \
 	patCount \
 	perf \
 	pslCoverage \
 	pslDiff \
 	pslFilterPrimers \
 	pslGlue \
 	pslHitPercent \
 	pslIntronsOnly \
 	pslQuickFilter \
 	pslSimp \
 	pslSortAcc \
 	pslSplitOnTarget \
+	pslToChain \
 	pslUnpile \
 	qa \
 	ratStuff \
 	relPairs \
 	recycleDb \
 	reviewSanity \
 	rnaStructure \
 	sage \
 	scanRa \
 	semiNorm \
 	sim4big \
 	snpException \
 	snp \
 	spideyToPsl \
 	splitFa \
@@ -207,30 +207,32 @@
 	txGraph \
 	utils \
 	uniqSize \
 	updateStsInfo \
 	visiGene/knownToVisiGene
 
 APPS = $(UTIL_DIRS) $(UTILS_APPLIST)
 
 all::    cgi utils
 
 hgLib:
 	@./sqlEnvTest.sh
 	cd lib && ${MAKE}
 
 userApps: $(UTILS_APPLIST:%=%.userApp)
+	cd altSplice/lib && $(MAKE)
+	cd altSplice/altSplice && $(MAKE) bedToExons
 	cd mouseStuff && $(MAKE) userApps
 	cd ratStuff && $(MAKE) userApps
 
 %.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