67731d2ba246fec0ba68843228e1fe7d18afd64c
hiram
  Tue Sep 1 13:35:40 2026 -0700
enable the gcOnFly track for the GenArk hubs refs #35958

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index ebec1439ab9..16ffeccf3bd 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -101,52 +101,89 @@
 # html html/%s.cytoBand\n\n" "${asmId}" "${asmId}"
 
 # only the ideoGram is needed, not the track
 
 printf "track cytoBandIdeo
 shortLabel Chromosome Band (Ideogram)
 longLabel Ideogram for Orientation
 group map
 visibility dense
 type bigBed 4 +
 bigDataUrl bbi/%s.cytoBand.bb\n\n" "${asmId}"
 
 # $scriptDir/asmHubCytoBand.pl $asmId $buildDir/html/$asmId.names.tab $buildDir > $buildDir/html/$asmId.cytoBand.html
 fi
 
+# GCA_964261385.2_aLisVul1.2_alternate_haplotype.gcOnFly.bw
+
+if [ -s ${buildDir}/trackData/gc5Base/${asmId}.gcOnFly.bw ]; then
+  rm -f $buildDir/bbi/${asmId}.gcOnFly.bw
+  rm -f $buildDir/bbi/${asmId}.gc5Base.bw
+  rm -f $buildDir/html/$asmId.gcOnFly.html
+  rm -f $buildDir/html/$asmId.gc5Base.html
+  ln -s ../trackData/gc5Base/${asmId}.gcOnFly.bw $buildDir/bbi/${asmId}.gcOnFly.bw
+  printf "# gcOnFly is a synthetic track, computed at run time
+# this trackDb entry will allow it to operate properly with
+# correct visibility when a saved session is restored
+track gcOnFly
+shortLabel GC Percent
+longLabel GC Percent in 5-Base Windows
+group map
+visibility dense
+type bigWig 0 100
+bigDataUrl bbi/%s/gcOnFly.bw
+gcOnFlyMaxDensity 50000
+syntheticTrack on
+calcWinSize 5
+autoScale Off
+viewLimits 30:70
+maxHeightPixels 128:36:16
+graphTypeDefault Bar
+gridDefault OFF
+windowingFunction Mean
+color 0,0,0
+altColor 128,128,128
+html html/%s.gcOnFly\n\n" "${asmId}" "${asmId}"
+  $scriptDir/asmHubGc5Percent.pl $asmId $buildDir/html/$asmId.names.tab $buildDir > $buildDir/html/$asmId.gcOnFly.html
+
+else
   if [ -s ${buildDir}/trackData/gc5Base/${asmId}.gc5Base.bw ]; then
   rm -f $buildDir/bbi/${asmId}.gc5Base.bw
+  rm -f $buildDir/bbi/${asmId}.gcOnFly.bw
+  rm -f $buildDir/html/$asmId.gcOnFly.html
+  rm -f $buildDir/html/$asmId.gc5Base.html
   ln -s ../trackData/gc5Base/${asmId}.gc5Base.bw $buildDir/bbi/${asmId}.gc5Base.bw
   printf "track gc5Base
 shortLabel GC Percent
 longLabel GC Percent in 5-Base Windows
 group map
 visibility dense
 autoScale Off
 maxHeightPixels 128:36:16
 graphTypeDefault Bar
 gridDefault OFF
 windowingFunction Mean
 color 0,0,0
 altColor 128,128,128
 viewLimits 30:70
 type bigWig 0 100
 bigDataUrl bbi/%s.gc5Base.bw
 html html/%s.gc5Base\n\n" "${asmId}" "${asmId}"
 
   $scriptDir/asmHubGc5Percent.pl $asmId $buildDir/html/$asmId.names.tab $buildDir > $buildDir/html/$asmId.gc5Base.html
   fi
+fi
 
 # see if there are gapOverlap or tandemDup bb files
 export gapOverlapCount=0
 export tanDupCount=0
 if [ -s $buildDir/trackData/gapOverlap/${asmId}.gapOverlap.bb ]; then
   gapOverlapCount=`zcat $buildDir/trackData/gapOverlap/${asmId}.gapOverlap.bed.gz | wc -l`
   rm -f $buildDir/bbi/${asmId}.gapOverlap.bb
   ln -s ../trackData/gapOverlap/${asmId}.gapOverlap.bb $buildDir/bbi/${asmId}.gapOverlap.bb
 fi
 if [ -s $buildDir/trackData/tandemDups/${asmId}.tandemDups.bb ]; then
   tanDupCount=`zcat $buildDir/trackData/tandemDups/${asmId}.tandemDups.bed.gz | wc -l`
   rm -f $buildDir/bbi/${asmId}.tandemDups.bb
   ln -s ../trackData/tandemDups/${asmId}.tandemDups.bb $buildDir/bbi/${asmId}.tandemDups.bb
 fi