9df5ecf8842547ecb2a7c6fd2338a3f3a6fb5e26
hiram
  Tue Dec 20 10:39:21 2022 -0800
setup the custom RepeatModeler lib for download reference no redmine

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index ffa5458..a46fb84 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -198,38 +198,43 @@
   printf "ERROR: can not find trackData/repeatMasker/$asmId.sorted.fa.out.gz\n" 1>&2
   exit 255
 fi
 
 # see if there are actually rmsk items in the track, this has to be > 3
 export rmskItemCount=`zcat $buildDir/trackData/repeatMasker/$asmId.sorted.fa.out.gz | head | wc -l`
 
 # clean up garbage from previous errors here
 if [ "${rmskItemCount}" -lt 4 ]; then
   rm -f $buildDir/$asmId.repeatMasker.out.gz
   rm -f "$buildDir/${asmId}.repeatMasker.version.txt"
   rm -f $buildDir/bbi/${asmId}.rmsk.align.bb
   rm -f $buildDir/bbi/${asmId}.rmsk.bb
   rm -f $buildDir/${asmId}.fa.align.tsv.gz
   rm -f $buildDir/${asmId}.fa.join.tsv.gz
+  rm -f $buildDir/${asmId}.rmsk.customLib.fa.gz
 else
 
 rm -f $buildDir/$asmId.repeatMasker.out.gz
 ln -s trackData/repeatMasker/$asmId.sorted.fa.out.gz $buildDir/$asmId.repeatMasker.out.gz
 if [ -s "$buildDir/trackData/repeatMasker/versionInfo.txt" ]; then
    rm -f "$buildDir/${asmId}.repeatMasker.version.txt"
    ln -s trackData/repeatMasker/versionInfo.txt "$buildDir/${asmId}.repeatMasker.version.txt"
 fi
+if [ -s "$buildDir/trackData/repeatModeler/${asmId}-families.fa" ]; then
+   cp -p "$buildDir/trackData/repeatModeler/${asmId}-families.fa" "$buildDir/${asmId}.rmsk.customLib.fa"
+   gzip "$buildDir/${asmId}.rmsk.customLib.fa"
+fi
 
 if [ "${newRmsk}" -gt 0 ]; then
   rm -f $buildDir/bbi/${asmId}.rmsk.align.bb
   rm -f $buildDir/bbi/${asmId}.rmsk.bb
   rm -f $buildDir/${asmId}.fa.align.tsv.gz
   rm -f $buildDir/${asmId}.fa.join.tsv.gz
   if [ -s "$buildDir/bbi/${asmId}.rmsk.align.bb" ]; then
     ln -s ../trackData/repeatMasker/${asmId}.rmsk.align.bb $buildDir/bbi/${asmId}.rmsk.align.bb
     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