1940e5051adfdd71d35c9a329cd8e3bc407421a1
max
  Wed Aug 16 05:22:45 2023 -0700
fixing kent-core problem where a lot of tools were missing, refs #30812

diff --git src/hg/utils/makefile src/hg/utils/makefile
index 46e508d..357af4d 100644
--- src/hg/utils/makefile
+++ src/hg/utils/makefile
@@ -13,31 +13,30 @@
 # can not build this on Mac OSX - has functions not supported
 ifeq ($(UNAME_S),Darwin)
   buildRefresh=
 else
   buildRefresh=refreshNamedSessionCustomTracks
 endif
 
 # List of directories to build for userApps
 UTILS_APPLIST = \
 	bedExtendRanges \
 	bedToPsl \
 	bedWeedOverlapping \
 	bedMergeAdjacent \
 	bedPartition \
 	bigChainBreaks \
-	bigChainToChain \
 	bigGenePredToGenePred \
 	bigMafToMaf \
 	bigPslToPsl \
 	binFromRange \
 	chromGraphFromBin \
 	chromGraphToBin \
 	crTreeIndexBed \
 	crTreeSearchBed \
 	faToVcf \
 	gapToLift \
 	genePredFilter \
 	genePredToBigGenePred \
 	genePredToProt \
 	gencodeVersionForGenes \
 	gff3ToGenePred \
@@ -107,51 +106,52 @@
 	gff3ToPsl \
 	gtfToGenePred \
 	hgvsToVcf \
 	hubCheck \
 	overlapSelect \
 	pslToBigPsl \
 	refSeqGet \
 	transMapPslToGenePred \
 	vcfToHgvs
 
 APPS = $(DIRS) $(UTILS_APPLIST)
 
 all:: utils
 
 utils: $(APPS:%=%.utils) $(APP_SCRIPTS:%=%.appScript)
+# tolerate missing directories, as some were removed in kent-core
 %.utils:
-	cd $* && echo $* && $(MAKE)
+	if test -d $* ; then cd $* && echo $* && $(MAKE) ; fi
 %.appScript:
 	chmod +x $*
 	rm -f ${DESTDIR}${SCRIPTS}/$*
 	cp -p $* ${DESTDIR}${SCRIPTS}/$*
 
 userApps: $(UTILS_APPLIST:%=%.userApp) $(USER_APP_SCRIPTS:%=%.userAppScript)
 %.userApp:
-	cd $* && echo $* && $(MAKE)
+	if test -d $* ; then cd $* && echo $* && $(MAKE) ; fi
 %.userAppScript:
 	chmod +x $*
 	rm -f ${DESTDIR}${BINDIR}/$*
 	cp -p $* ${DESTDIR}${BINDIR}/$*
 
 scripts: $(SCRIPT_FILES:%=%.scripts)
 %.scripts:
 	chmod +x $*
 	rm -f ${SCRIPTS}/$*
 	cp -p $* ${SCRIPTS}/$*
 
 alpha: scripts all
 
 test::	${TEST_DIRS:%=%.test}
 %.test:
 	(cd $* && ${MAKE} test)
 
 clean:: $(APPS:%=%.clean)
 	- find . -name '*.o' -exec rm {} \;
 %.clean:
-	(cd $* && ${MAKE} clean)
+	(if test -d $* ; then cd $* && echo $* && $(MAKE) ; fi)
 
 compile:: $(APPS:%=%.compile)
 	- find . -name '*.o' -exec rm {} \;
 %.compile:
 	(cd $* && ${MAKE} compile)