be74d8809a2098b04088f8bebbe2f90ddf017bee
hiram
  Fri May 24 13:33:12 2013 -0700
updating userApps buildlist refs #9149
diff --git src/hg/mouseStuff/makefile src/hg/mouseStuff/makefile
index f403cc3..677292f 100644
--- src/hg/mouseStuff/makefile
+++ src/hg/mouseStuff/makefile
@@ -1,82 +1,90 @@
 # Build all directories in makeDb 
 
 include ../../inc/common.mk
 
-# List of directories to build
-USE_DIRS = ${DIRS}
-
 BADDIRS = \
         correctEst
 
+# List of directories to build for userApps
+UTILS_APPLIST = \
+	axtChain \
+	axtSort \
+	axtToMaf \
+	axtToPsl \
+	chainAntiRepeat \
+	chainMergeSort \
+	chainPreNet \
+	chainSort \
+	chainSplit \
+	chainStitchId \
+	chainSwap \
+	chainToAxt \
+	chainToPsl \
+	lavToAxt \
+	lavToPsl \
+	mafCoverage \
+	mafFetch \
+	mafRanges \
+	mafToAxt \
+	mafToPsl
+
+# List of directories to build at UCSC
 DIRS = \
 	axtAndBed \
 	axtBest \
 	axtCalcMatrix \
-	axtChain \
 	axtDropOverlap \
 	axtDropSelf \
 	axtFilter \
 	axtIndex \
 	axtPretty \
 	axtQueryCount \
 	axtRecipBest \
 	axtRescore \
-	axtSort \
 	axtSplitByTarget \
 	axtSwap \
 	axtToBed \
 	axtToChain \
-	axtToMaf \
-	axtToPsl \
 	bedCoverage \
 	calcGap \
-	chainAntiRepeat \
 	chainDbToFile \
 	chainFilter \
-	chainMergeSort \
 	chainNet \
-	chainPreNet \
-	chainSort \
-	chainSplit \
 	chainStats \
-	chainStitchId \
-	chainSwap \
-	chainToAxt \
-	chainToPsl \
 	gcForBed \
 	knownVsBlat \
-	lavToAxt \
-	lavToPsl \
 	libScan \
-	mafCoverage \
-	mafFetch \
-	mafRanges \
-	mafToAxt \
-	mafToPsl \
 	mousePoster \
 	netChainSubset \
 	netClass \
 	netFilter \
 	netSplit \
 	netStats \
 	netSyntenic \
 	netToAxt \
 	netToBed \
 	netToBedWithId \
 	orthologBySynteny \
 	phToPsl \
 	pslMrnaCover \
 	regionPicker \
 	rikenBestInCluster \
 	simpleChain \
 	splitSim \
 	subsetAxt \
 	subsetTraces \
 	whyConserved 
 
+# List of directories to build
+USE_DIRS = $(DIRS) $(UTILS_APPLIST)
+
 all: ${USE_DIRS:%=%.all}
 %.all:
-	( cd $* && echo $* && ${MAKE} )
+	cd $* && echo $* && ${MAKE}
+
+userApps: $(UTILS_APPLIST:%=%.userApp)
+%.userApp:
+	cd $* && echo $* && $(MAKE)
 
 clean::
 	cd simpleChain && ${MAKE} clean