083fc14e534ca67e2355bab5b3e8f399bb0dc1f4
hiram
  Wed May 21 12:22:52 2025 -0700
beware some viral genomes will not have ix ixx files for ncbiGene track refs #34337

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 934426fc80a..41a94402f53 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -689,32 +689,34 @@
 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
+if [ -s  $buildDir/ixIxx/${asmId}.ncbiGene.ix ]; then
   ln -s ../trackData/ncbiGene/$asmId.ncbiGene.ix $buildDir/ixIxx/${asmId}.ncbiGene.ix
   ln -s ../trackData/ncbiGene/$asmId.ncbiGene.ixx $buildDir/ixIxx/${asmId}.ncbiGene.ixx
+fi
   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=\$\$
 urlLabel Entrez gene:
 labelFields geneName,geneName2
 defaultLabelFields geneName2