be74d8809a2098b04088f8bebbe2f90ddf017bee
hiram
  Fri May 24 13:33:12 2013 -0700
updating userApps buildlist refs #9149
diff --git src/hg/makefile src/hg/makefile
index 6e81019..9e47b83 100644
--- src/hg/makefile
+++ src/hg/makefile
@@ -56,30 +56,31 @@
 	checkTableCoords \
 	dbTrash \
 	encode3/validateFiles \
 	encode3/validateManifest \
 	estOrient \
 	featureBits \
 	genePredHisto \
 	genePredSingleCover \
 	genePredToBed \
 	genePredToFakePsl \
 	genePredToMafFrames \
 	gigAssembler/checkAgpAndFa \
 	hgsql \
 	hgsqldump \
 	maskOutFa \
+	mrnaToGene \
 	ratStuff/mafsInRegion \
 	ratStuff/mafSpeciesSubset \
 	pslCDnaFilter \
 	genePredCheck \
 	genePredToGtf \
 	pslCat \
 	pslCheck \
 	pslDropOverlap \
 	pslFilter \
 	pslHisto \
 	pslPairs \
 	pslPartition \
 	pslPretty \
 	pslRecalcMatch \
 	pslReps \
@@ -143,31 +144,30 @@
 	hgsqlLocal \
 	hgsqladmin \
 	hgsqldumpLocal \
 	hgsqlimport \
         hgsqlSwapTables \
         hgsqlTableDate \
 	intronEnds \
 	lib \
 	liftAcross \
 	liftAgp \
 	liftFrags \
 	lfsOverlap \
 	makeDb \
 	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 \
@@ -207,69 +207,69 @@
 	utils \
 	uniqSize \
 	updateStsInfo \
 	visiGene/knownToVisiGene
 
 APPS = $(UTIL_DIRS) $(UTILS_APPLIST)
 
 all::    cgi utils
 
 hgLib:
 	@./sqlEnvTest.sh
 	cd lib && ${MAKE}
 
 userApps: $(UTILS_APPLIST:%=%.userApp)
 %.userApp: hgLib
-	( cd $* && echo $* && $(MAKE) )
+	cd $* && echo $* && $(MAKE)
 
 utils: $(APPS:%=%.utils)
 %.utils: hgLib
-	( cd $* && echo $* && $(MAKE) )
+	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)
+	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
-	( cd $* && echo $* && $(MAKE) )
+	cd $* && echo $* && $(MAKE)
 %.cgi: hgLib
-	( cd $* && echo $* && $(MAKE) cgi)
+	cd $* && echo $* && $(MAKE) cgi
 
 #   alpha: Destination for the binaries is /usr/local/apache/cgi-bin/
 
 alpha:	 ${BROWSER_BINS:%=%.alpha} ${BROWSER_LOADERS:%=%.alpha} ${ENCODE_FILES:%=%.alpha}
 %.alpha: hgLib
-	( cd $* && echo $* && $(MAKE) alpha)
+	cd $* && echo $* && $(MAKE) alpha
 
 #   beta: Destination for the binaries is /usr/local/apache/cgi-bin-beta/
 
 beta: ${BROWSER_BINS:%=%.beta} ${BROWSER_LOADERS:%=%.beta}
 %.beta: hgLib
-	( cd $* && echo $* && $(MAKE) beta)
+	cd $* && echo $* && $(MAKE) beta
 
 # install: Destination for the binaries is ${DESTDIR}/usr/local/apache/cgi-bin
 
 install: ${BROWSER_BINS:%=%.install} ${BROWSER_LOADERS:%=%.install}
 %.install: hgLib
-	( cd $* && echo $* && $(MAKE) install)
+	cd $* && echo $* && $(MAKE) install
 
 clean::
 	cd lib && ${MAKE} clean
 	@for D in ${BROWSER_BINS} ${BROWSER_LOADERS}; do \
 		(cd $${D} && ${MAKE} clean;) \
 	done
 	touch non-empty-rm.o
 	- find . -name \*.o -print | xargs rm
 
 clean_utils::
 	@for D in ${UTIL_DIRS}; do \
 		(cd $${D} && ${MAKE} clean;) \
 	done
 
 test::	${TEST_DIRS:%=%.test}