060c692dfeda837e9fd0385123f75abbf378ceb7
hiram
  Thu Sep 30 12:07:23 2021 -0700
add download file for repeatMasker.out.gz results no redmine

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 38df94c..19df450 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -162,30 +162,39 @@
     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`
 
 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
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.SINE.bb ]; then