a939f7e2ddc1a11f641e065b0d49a57f4ee8ae14
max
  Mon Mar 23 06:21:52 2026 -0700
moving genePredCompare tool to non-apps build, email from Hiram

diff --git src/utils/makefile src/utils/makefile
index 4d1a2131c02..8c40897ee63 100644
--- src/utils/makefile
+++ src/utils/makefile
@@ -1,26 +1,29 @@
 # Build all directories in utils
 
 kentSrc = ..
 
 include ${kentSrc}/inc/localEnvironment.mk
 include ${kentSrc}/inc/common.mk
 
 # note: lists such as the following need to be defined *before*
 # they are used in the wildcard target rules.  An oddity of gnu make
 
 # define the list of user applications to build
+# These will be distributed as part of the user apps build and we provide them 
+# as binaries and collect usage messages
+# These are C programs, so make clean will be run
 
 UTILS_APPLIST = \
 	addCols \
 	ave \
 	aveCols \
 	bamToPsl \
 	bedClip \
 	bedGraphToBigWig \
 	bedJoinTabOffset \
 	bedToBigBed \
 	bigBedInfo \
 	bigBedNamedItems \
 	bigBedSummary \
 	bigBedToBed \
 	bedCommonRegions \
@@ -107,30 +110,32 @@
 	tailLines \
 	textHistogram \
 	tickToDate \
 	timing \
 	toLower \
 	toUpper \
         trackDbIndexBb \
 	twoBitDup \
 	twoBitInfo \
 	twoBitToFa \
 	wigCorrelate \
 	wigToBigWig \
 	wordLine \
 
 # list of utilities to build of interest only at UCSC
+# These are C tools and will run a make clean on each
+# These are not part of the user apps build.
 
 UCSC_APPS = \
 	addCols \
 	aNotB \
 	aveCols \
 	ccCp \
 	convolve \
 	detab \
 	dnsInfo \
 	faFlyBaseToUcsc \
 	faGapLocs \
 	faGapSizes \
 	faNcbiToUcsc \
 	faRenameRecords \
 	faSimplify \
@@ -148,72 +153,75 @@
 	nt4Frag \
 	pslToXa \
 	scrambleFa \
 	subs \
 	tabToMmHash \
 	tableSum \
 	textHist2 \
 	udcCleanup \
 	undupFa \
 	upper \
 	vcfFilter \
 	venn \
 	verticalSplitSqlTable \
 	weedLines
 
-# list of scripts to install
+# These are parts of the user apps build, so they will land on hgdownload
+# These are not C programs, so no clean up
 
 USER_APP_SCRIPTS = \
 	bedJoinTabOffset.py \
 	expMatrixToBarchartBed \
 	barChartMaxLimit \
 	ucscApiClient \
 	tdbRename \
 	tdbSort \
 	webSync \
-	genePredCompare \
 	chromToUcsc \
 	bigHeat \
 	bigGuessDb
 
+# Scripts that are not distributed outside of UCSC
+# They are not part of the user-apps build
 SCRIPT_FILES = \
 	agpToLift \
 	apacheLogParse \
 	bedCollapse.pl \
 	bedFixBlockOverlaps \
 	bedOverlapMerge \
 	bedSingleCover.pl \
 	bedBetween \
 	doLocusName \
 	extToolsChromeParse \
 	iSync \
 	lodToBedScore \
 	matrixMerge \
 	mkMafFrames.pl \
 	patSeqFilterBulkAndAnnotate \
 	patSeqSummarizeDocs \
 	pslProtCnv \
 	pslSameGene \
 	tabRepl \
 	uniprotToTab \
 	ggTables \
 	ggGeneClasses \
 	ggGpmlToTab \
 	ggKgmlToTab \
 	ggMsrToTab \
 	ggPidToTab \
 	ggPpiToTab \
+	genePredCompare \
 	ggSpfToTab \
 	bedNamePickFirst \
 	bedBestTranscript \
 	genePredToBed \
 	cgiSmokeTest \
 	phegenToBed \
 	bigMaxPercDiff \
 	cancerMafToBigBed \
 	pq \
 	bedAppendPaperInfo \
 	googleSheetToBigBed \
 	doClinvarLift \
 	codeReviewAi.py \
 	redmineCli \
 	browserRace \