9ef9b760d157a71c1ab0564b5b5f28597b015931
hiram
  Mon Oct 4 14:23:58 2021 -0700
no need to show error when looking for rmsk and it does not exist no redmine

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 19df450..e26aaee 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -155,59 +155,56 @@
   fi
 
   if [ "${tanDupCount}" -gt 0 ]; then
     printf "    track tandemDups
     parent tanDups on
     shortLabel Tandem Dups
     longLabel Paired exactly identical sequence survey over entire genome assembly
     bigDataUrl bbi/%s.tandemDups.bb
     type bigBed 12\n\n" "${asmId}"
   fi
 
   $scriptDir/asmHubTanDups.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.tanDups.html
 
 fi
 
-export rmskCount=`(ls $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.*.bb | wc -l) || true`
-
-
 # see if there are repeatMasker bb files
-export rmskCount=`(ls $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.*.bb | wc -l) || true`
+export rmskCount=`(ls $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.*.bb 2> /dev/null | wc -l) || true`
 
 if [ "${rmskCount}" -gt 0 ]; then
 
 if [ ! -s "$buildDir/trackData/repeatMasker/$asmId.sorted.fa.out.gz" ]; then
   printf "ERROR: can not find trackData/repeatMasker/$asmId.sorted.fa.out.gz\n" 1>&2
   exit 255
 fi
 
 rm -f $buildDir/$asmId.repeatMasker.out.gz
 ln -s trackData/repeatMasker/$asmId.sorted.fa.out.gz $buildDir/$asmId.repeatMasker.out.gz
 
 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
-fi
+fi      #       if [ "${rmskCount}" -gt 0 ]; then
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.SINE.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.SINE.bb
 ln -s ../trackData/repeatMasker/bbi/${asmId}.rmsk.SINE.bb $buildDir/bbi/${asmId}.rmsk.SINE.bb
 printf "    track repeatMaskerSINE
     parent repeatMasker
     shortLabel SINE
     longLabel SINE Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 1
     bigDataUrl bbi/%s.rmsk.SINE.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.LINE.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.LINE.bb