3c8ffb11a3e0a8830f64c3e19ca7f7ff8b167f33
hiram
  Wed Jul 20 17:19:51 2022 -0700
handle cases where there is no result from RepeatMasker or TRF simple repeats for virus browser building refs #29484

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 8aaa97a..ecec619 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -212,33 +212,36 @@
     ln -s trackData/repeatMasker/${asmId}.fa.align.tsv.gz $buildDir/${asmId}.fa.align.tsv.gz
   fi
   ln -s ../trackData/repeatMasker/${asmId}.rmsk.bb $buildDir/bbi/${asmId}.rmsk.bb
   ln -s trackData/repeatMasker/${asmId}.sorted.fa.join.tsv.gz $buildDir/${asmId}.fa.join.tsv.gz
 
 printf "track repeatMasker
 shortLabel RepeatMasker
 longLabel RepeatMasker Repetitive Elements
 type bigRmsk 9 +
 visibility pack
 group varRep
 bigDataUrl bbi/%s.rmsk.bb\n" "${asmId}"
 if [ -s "$buildDir/bbi/${asmId}.rmsk.align.bb" ]; then
 printf "xrefDataUrl bbi/%s.rmsk.align.bb\n" "${asmId}"
 fi
+export rmskClassProfile="$buildDir/trackData/repeatMasker/$asmId.rmsk.class.profile.txt"
+if [ -s "${rmskClassProfile}" ]; then
   printf "html html/%s.repeatMasker\n\n" "${asmId}"
   $scriptDir/asmHubRmskJoinAlign.pl $asmId $buildDir > $buildDir/html/$asmId.repeatMasker.html
 
+fi
 else	#	if [ "${newRmsk}" -eq 2 ]; then
 
 printf "track repeatMasker
 compositeTrack on
 shortLabel RepeatMasker
 longLabel Repeating Elements by RepeatMasker
 group varRep
 visibility dense
 type bigBed 6 +
 colorByStrand 50,50,150 150,50,50
 maxWindowToDraw 10000000
 spectrum on
 html html/%s.repeatMasker\n\n" "${asmId}"
 $scriptDir/asmHubRmsk.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData/repeatMasker/$asmId.rmsk.class.profile.txt > $buildDir/html/$asmId.repeatMasker.html