8f99feed6b400b329aa5eb37bdb020425782631c
hiram
  Mon May 20 13:36:49 2013 -0700
begin to segregate the utilities into categories all, userApps, cellar refs #9104
diff --git src/makefile src/makefile
index 89a9da7..3388377 100644
--- src/makefile
+++ src/makefile
@@ -43,56 +43,47 @@
 	cd webBlat && ${MAKE}
 	cd hg/pslPretty && ${MAKE}
 	cd hg/pslReps && ${MAKE}
 	cd hg/pslSort && ${MAKE}
 	cd utils/nibFrag && ${MAKE}
 	cd utils/faToNib && ${MAKE}
 	cd utils/faToTwoBit && ${MAKE}
 	cd utils/twoBitToFa && ${MAKE}
 	cd utils/twoBitInfo && ${MAKE}
 	cd isPcr && ${MAKE}
 	cd blatz && ${MAKE}
 
 # all of these application makefiles have been updated to include use
 #	of DESTDIR and BINDIR
 
-UTILS_APPLIST = bedClip bedGraphToBigWig bedToBigBed \
-        bigBedInfo bigBedSummary bigBedToBed bigWigAverageOverBed  \
-	bigWigInfo bigWigSummary bigWigToBedGraph bigWigToWig\
-	faCount faFrag faOneRecord faPolyASizes faRandomize faSize \
-	faSomeRecords faToNib \
-	faToTwoBit htmlCheck nibFrag paraFetch paraSync sizeof stringify \
-	textHistogram twoBitDup twoBitInfo twoBitToFa userApps wigCorrelate wigToBigWig
-
 HG_APPLIST = bedSort liftUp liftOver bedItemOverlapCount encode/validateFiles \
 	 featureBits ratStuff/mafsInRegion ratStuff/mafSpeciesSubset \
 	 pslCDnaFilter genePredToGtf pslPretty pslReps pslSort 
 
 
 HG_UTILS_APPLIST = bedExtendRanges gff3ToGenePred gtfToGenePred \
 	hubCheck overlapSelect makeTableList pslMap
 
 HG_HGWIGGLE_APP = hgWiggle
 
 HG_LOAD_APPLIST = hgGcPercent
 
 BLAT_APPLIST = blat gfClient gfServer
 
 userApps: topLibs hgLib
-	@for P in ${UTILS_APPLIST}; do \
-	    ( cd utils/$${P} && echo utils/$${P} && ${MAKE} ) ; \
-	done
+	cd utils && echo utils && ${MAKE} userApps
+	cd utils/userApps && echo utils/userApps && ${MAKE}
 	@for P in ${HG_APPLIST}; do \
 	    ( cd hg/$${P} && echo hg/$${P} && ${MAKE} ) ; \
 	done
 	@for P in ${HG_UTILS_APPLIST}; do \
 	    ( cd hg/utils/$${P} && echo hg/utils/$${P} && ${MAKE} ) ; \
 	done
 	@for P in ${HG_HGWIGGLE_APP}; do \
 	    ( cd hg/makeDb/hgLoadWiggle && echo hg/makeDb/hgLoadWiggle && ${MAKE} $${P} ) ; \
 	done
 	@for P in ${HG_LOAD_APPLIST}; do \
 	    ( cd hg/makeDb/$${P} && echo hg/makeDb/$${P} && ${MAKE} $${P} ) ; \
 	done
 	@for P in ${BLAT_APPLIST}; do \
 	    ( cd $${P} && echo $${P} && ${MAKE} ) ; \
 	done