60273bfc304c4c57c18aa443f6fe6f96705058f9
hiram
  Mon Feb 3 15:13:20 2025 -0800
should be passing along the gff3 file to download directory - get the symLinked file here refs #35027

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 5538def72ec..d24fc1e81e1 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -663,49 +663,55 @@
   fi
 
   $scriptDir/asmHubNcbiRefSeq.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.refSeqComposite.html
 
 haveNcbiRefSeq="yes"
 fi	# ncbiRefSeq composite track
 
 ### assume there is no ncbiGene track
 ### it figures into setting the visibility of the augustus gene track
 export haveNcbiGene="no"
 
 ###################################################################
 ## setup ncbiGene only if ncbiRefSeq is not present
 if [ "${haveNcbiRefSeq}" = "no" ]; then
 
+
 # may or may not have a searchTrix for ncbiGene, assume none
 searchTrix=""
 # check to see if there is a index for ncbiGene
 if [ -s ${buildDir}/trackData/ncbiGene/$asmId.ncbiGene.ix ]; then
   searchTrix="
 searchTrix ixIxx/$asmId.ncbiGene.ix"
 fi
 
 
 if [ -s ${buildDir}/trackData/ncbiGene/$asmId.ncbiGene.bb ]; then
 rm -f $buildDir/bbi/${asmId}.ncbiGene.bb
 rm -f $buildDir/ixIxx/${asmId}.ncbiGene.ix
 rm -f $buildDir/ixIxx/${asmId}.ncbiGene.ixx
+rm -f ${buildDir}/genes/${asmId}.ncbiGene.gtf.gz
 export longLabel="Gene models submitted to NCBI"
 export shortLabel="Gene models"
 if [ "$asmType" = "refseq" ]; then
   longLabel="NCBI gene predictions"
   shortLabel="NCBI Genes"
 fi
+if [ -s ${buildDir}/trackData/ncbiGene/${asmId}.ncbiGene.gtf.gz ]; then
+  mkdir -p $buildDir/genes
+  ln -s ../trackData/ncbiGene/${asmId}.ncbiGene.gtf.gz $buildDir/genes/${asmId}.ncbiGene.gtf.gz
+fi
 ln -s ../trackData/ncbiGene/$asmId.ncbiGene.bb $buildDir/bbi/${asmId}.ncbiGene.bb
 ln -s ../trackData/ncbiGene/$asmId.ncbiGene.ix $buildDir/ixIxx/${asmId}.ncbiGene.ix
 ln -s ../trackData/ncbiGene/$asmId.ncbiGene.ixx $buildDir/ixIxx/${asmId}.ncbiGene.ixx
   printf "track ncbiGene
 longLabel $longLabel
 shortLabel $shortLabel
 visibility pack
 color 0,80,150
 altColor 150,80,0
 colorByStrand 0,80,150 150,80,0
 bigDataUrl bbi/%s.ncbiGene.bb
 type bigGenePred
 html html/%s.ncbiGene
 searchIndex name%s
 url https://www.ncbi.nlm.nih.gov/gene/?term=\$\$