5e8e9e71229d664fe260e7d6943357586a47dbe2
hiram
  Fri Feb 13 08:58:36 2026 -0800
fix bug in ix links for ncbiGene tracks refs #37109

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index ba12649ff75..ca8de5279fa 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -689,50 +689,51 @@
 ###################################################################
 ## 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
+printf "working on ncbiGene\n" 1>&2
 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 GenBank, ENA, DDBJ"
 export shortLabel="NCBI GenBank"
 # Note: 2025-12-02 - this isn't valid, since we are in this section due
 #                    to there being no NCBI RefSeq track.  Even though this
 #                    is a RefSeq assembly, these are other gene models, not
 #                    from RefSeq
 # if [ "$asmType" = "refseq" ]; then
 #   longLabel="RefSeq gene predictions from NCBI"
 #   shortLabel="NCBI RefSeq"
 # 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
+if [ -s  $buildDir/trackData/ncbiGene/${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
 urls name2=\"https://www.ncbi.nlm.nih.gov/gene/?term=\$\$\" geneName=\"https://www.ncbi.nlm.nih.gov/gene/\$\$\" geneName2=\"https://www.ncbi.nlm.nih.gov/nuccore/\$\$\"
 html html/%s.ncbiGene
 searchIndex name%s