7a5cff1bced06596181624623f86a803c4be59f6
hiram
  Mon Aug 12 14:00:53 2019 -0700
correct searching enabled on xenoRefGene track refs #23734

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index bd3aa91..67f8cfc 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -1,539 +1,544 @@
 #!/bin/bash
 
 set -beEux -o pipefail
 
 if [ $# -ne 3 ]; then
   printf "usage: trackDb.sh <genbank|refseq> <asmId> <pathTo/assembly hub build directory> > trackDb.txt\n" 1>&2
   printf "expecting to find *.ucsc.2bit and bbi/ files at given path\n" 1>&2
   printf "the ncbi|ucsc selects the naming scheme\n" 1>&2
   exit 255
 fi
 
 export genbankRefseq=$1
 export asmId=$2
 export buildDir=$3
 export hubLinks="/hive/data/genomes/asmHubs/hubLinks"
 
 export scriptDir="$HOME/kent/src/hg/utils/automation"
 
 mkdir -p $buildDir/bbi
 mkdir -p $buildDir/ixIxx
 
 # may or may not have a searchTrix for assembly, assume none
 export searchTrix=""
 # check to see if there is a searchTrix assembly index
 if [ -s ${buildDir}/trackData/assemblyGap/${asmId}.assembly.ix ]; then
   rm -f $buildDir/ixIxx/${asmId}.assembly.ix*
   ln -s ${buildDir}/trackData/assemblyGap/${asmId}.assembly.ix $buildDir/ixIxx
   ln -s ${buildDir}/trackData/assemblyGap/${asmId}.assembly.ixx $buildDir/ixIxx
   searchTrix="
 searchTrix ixIxx/${asmId}.assembly.ix"
 fi
 
 if [ -s ${buildDir}/trackData/assemblyGap/${asmId}.assembly.bb ]; then
 rm -f $buildDir/bbi/${asmId}.assembly.bb
 ln -s $buildDir/trackData/assemblyGap/${asmId}.assembly.bb $buildDir/bbi/${asmId}.assembly.bb
 printf "track assembly
 longLabel Assembly
 shortLabel Assembly
 visibility pack
 colorByStrand 150,100,30 230,170,40
 color 150,100,30
 altColor 230,170,40
 bigDataUrl bbi/%s.assembly.bb
 type bigBed 6
 html html/%s.assembly
 searchIndex name%s
 url https://www.ncbi.nlm.nih.gov/nuccore/\$\$
 urlLabel NCBI Nucleotide database
 group map\n\n" "${asmId}" "${asmId}" "${searchTrix}"
 $scriptDir/asmHubAssembly.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/$asmId.agp.gz https://hgdownload.soe.ucsc.edu/hubs/VGP/genomes/$asmId > $buildDir/html/$asmId.assembly.html
 fi
 
 if [ -s ${buildDir}/trackData/assemblyGap/${asmId}.gap.bb ]; then
 rm -f $buildDir/bbi/${asmId}.gap.bb
 ln -s $buildDir/trackData/assemblyGap/${asmId}.gap.bb $buildDir/bbi/${asmId}.gap.bb
 printf "track gap
 longLabel AGP gap
 shortLabel Gap (AGP defined)
 visibility dense
 color 0,0,0
 bigDataUrl bbi/%s.gap.bb
 type bigBed 4
 group map
 html html/%s.gap\n\n" "${asmId}" "${asmId}"
 $scriptDir/asmHubGap.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/$asmId.agp.gz https://hgdownload.soe.ucsc.edu/hubs/VGP/genomes/$asmId > $buildDir/html/$asmId.gap.html
 fi
 
 if [ -s ${buildDir}/trackData/cytoBand/${asmId}.cytoBand.bb ]; then
 rm -f $buildDir/bbi/${asmId}.cytoBand.bb
 ln -s $buildDir/trackData/cytoBand/${asmId}.cytoBand.bb $buildDir/bbi/${asmId}.cytoBand.bb
 
 # printf "track cytoBand
 # shortLabel Chromosome Band
 # longLabel Ideogram
 # group map
 # visibility dense
 # type bigBed 4 +
 # bigDataUrl bbi/%s.cytoBandIdeo.bb
 # 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
 
 if [ -s ${buildDir}/trackData/gc5Base/${asmId}.gc5Base.bw ]; then
 rm -f $buildDir/bbi/${asmId}.gc5Base.bw
 ln -s $buildDir/trackData/gc5Base/${asmId}.gc5Base.bw $buildDir/bbi/${asmId}.gc5Base.bw
 printf "track gc5Base
 shortLabel GC Percent
 longLabel GC Percent in 5-Base Windows
 group map
 visibility full
 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
 
 # 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 $buildDir/trackData/gapOverlap/${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 $buildDir/trackData/tandemDups/${asmId}.tandemDups.bb $buildDir/bbi/${asmId}.tandemDups.bb
 fi
 
 if [ "${gapOverlapCount}" -gt 0 -o "${tanDupCount}" -gt 0 ]; then
 
   printf "track tanDups
 shortLabel Tandem Dups
 longLabel Paired identical sequences
 compositeTrack on
 visibility hide
 type bigBed 12
 group map
 html html/%s.tanDups\n\n" "${asmId}"
 
   if [ "${gapOverlapCount}" -gt 0 ]; then
     printf "    track gapOverlap
     parent tanDups on
     shortLabel Gap Overlaps
     longLabel Paired exactly identical sequence on each side of a gap
     bigDataUrl bbi/%s.gapOverlap.bb
     type bigBed 12\n\n" "${asmId}"
   fi
 
   if [ "${tanDupCount}" -gt 0 ]; then
     printf "    track tandemDups
     parent tanDups on
     shortLabel Tandem Dups
     longLabel Paired exactly identical sequence survey over entire genome assembly
     bigDataUrl bbi/%s.tandemDups.bb
     type bigBed 12\n\n" "${asmId}"
   fi
 
   $scriptDir/asmHubTanDups.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.tanDups.html
 
 fi
 
 export rmskCount=`(ls $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.*.bb | wc -l) || true`
 
 
 # see if there are repeatMasker bb files
 export rmskCount=`(ls $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.*.bb | wc -l) || true`
 
 if [ "${rmskCount}" -gt 0 ]; then
 printf "track repeatMasker
 compositeTrack on
 shortLabel RepeatMasker
 longLabel Repeating Elements by RepeatMasker
 group varRep
 visibility dense
 type bed 3 .
 noInherit on
 html html/%s.repeatMasker\n\n" "${asmId}"
 $scriptDir/asmHubRmsk.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData/repeatMasker/$asmId.rmsk.class.profile.txt > $buildDir/html/$asmId.repeatMasker.html
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.SINE.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.SINE.bb
 ln -s $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.SINE.bb $buildDir/bbi/${asmId}.rmsk.SINE.bb
 printf "    track repeatMaskerSINE
     parent repeatMasker
     shortLabel SINE
     longLabel SINE Repeating Elements by RepeatMasker
     priority 1
     spectrum on
     maxWindowToDraw 10000000
     colorByStrand 50,50,150 150,50,50
     type bigBed 6 +
     bigDataUrl bbi/%s.rmsk.SINE.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.LINE.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.LINE.bb
 ln -s $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.LINE.bb $buildDir/bbi/${asmId}.rmsk.LINE.bb
 printf "    track repeatMaskerLINE
     parent repeatMasker
     shortLabel LINE
     longLabel LINE Repeating Elements by RepeatMasker
     priority 2
     spectrum on
     maxWindowToDraw 10000000
     colorByStrand 50,50,150 150,50,50
     type bigBed 6 +
     bigDataUrl bbi/%s.rmsk.LINE.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.LTR.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.LTR.bb
 ln -s $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.LTR.bb $buildDir/bbi/${asmId}.rmsk.LTR.bb
 printf "    track repeatMaskerLTR
     parent repeatMasker
     shortLabel LTR
     longLabel LTR Repeating Elements by RepeatMasker
     priority 3
     spectrum on
     maxWindowToDraw 10000000
     colorByStrand 50,50,150 150,50,50
     type bigBed 6 +
     bigDataUrl bbi/%s.rmsk.LTR.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.DNA.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.DNA.bb
 ln -s $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.DNA.bb $buildDir/bbi/${asmId}.rmsk.DNA.bb
 printf "    track repeatMaskerDNA
     parent repeatMasker
     shortLabel DNA
     longLabel DNA Repeating Elements by RepeatMasker
     priority 4
     spectrum on
     maxWindowToDraw 10000000
     colorByStrand 50,50,150 150,50,50
     type bigBed 6 +
     bigDataUrl bbi/%s.rmsk.DNA.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.Simple.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.Simple.bb
 ln -s $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.Simple.bb $buildDir/bbi/${asmId}.rmsk.Simple.bb
 printf "    track repeatMaskerSimple
     parent repeatMasker
     shortLabel Simple
     longLabel Simple Repeating Elements by RepeatMasker
     priority 5
     spectrum on
     maxWindowToDraw 10000000
     colorByStrand 50,50,150 150,50,50
     type bigBed 6 +
     bigDataUrl bbi/%s.rmsk.Simple.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.Low_complexity.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.Low_complexity.bb
 ln -s $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.Low_complexity.bb $buildDir/bbi/${asmId}.rmsk.Low_complexity.bb
 printf "    track repeatMaskerLowComplexity
     parent repeatMasker
     shortLabel Low Complexity
     longLabel Low Complexity Repeating Elements by RepeatMasker
     priority 6
     spectrum on
     maxWindowToDraw 10000000
     colorByStrand 50,50,150 150,50,50
     type bigBed 6 +
     bigDataUrl bbi/%s.rmsk.Low_complexity.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.Satellite.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.Satellite.bb
 ln -s $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.Satellite.bb $buildDir/bbi/${asmId}.rmsk.Satellite.bb
 printf "    track repeatMaskerSatellite
     parent repeatMasker
     shortLabel Satellite
     longLabel Satellite Repeating Elements by RepeatMasker
     priority 7
     spectrum on
     maxWindowToDraw 10000000
     colorByStrand 50,50,150 150,50,50
     type bigBed 6 +
     bigDataUrl bbi/%s.rmsk.Satellite.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.RNA.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.RNA.bb
 ln -s $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.RNA.bb $buildDir/bbi/${asmId}.rmsk.RNA.bb
 printf "    track repeatMaskerRNA
     parent repeatMasker
     shortLabel RNA
     longLabel RNA Repeating Elements by RepeatMasker
     priority 8
     spectrum on
     maxWindowToDraw 10000000
     colorByStrand 50,50,150 150,50,50
     type bigBed 6 +
     bigDataUrl bbi/%s.rmsk.RNA.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/repeatMasker/bbi/${asmId}.rmsk.Other.bb ]; then
 rm -f $buildDir/bbi/${asmId}.rmsk.Other.bb
 ln -s $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.Other.bb $buildDir/bbi/${asmId}.rmsk.Other.bb
 printf "    track repeatMaskerOther
     parent repeatMasker
     shortLabel Other
     longLabel Other Repeating Elements by RepeatMasker
     priority 9
     spectrum on
     maxWindowToDraw 10000000
     colorByStrand 50,50,150 150,50,50
     type bigBed 6 +
     bigDataUrl bbi/%s.rmsk.Other.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/simpleRepeat/simpleRepeat.bb ]; then
 rm -f $buildDir/bbi/${asmId}.simpleRepeat.bb
 ln -s $buildDir/trackData/simpleRepeat/simpleRepeat.bb $buildDir/bbi/${asmId}.simpleRepeat.bb
 printf "track simpleRepeat
 shortLabel Simple Repeats
 longLabel Simple Tandem Repeats by TRF
 group varRep
 visibility dense
 type bigBed 4 +
 bigDataUrl bbi/%s.simpleRepeat.bb
 html html/%s.simpleRepeat\n\n" "${asmId}" "${asmId}"
 $scriptDir/asmHubSimpleRepeat.pl $asmId $buildDir/html/$asmId.names.tab $buildDir > $buildDir/html/$asmId.simpleRepeat.html
 fi
 
 # 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
 
 export haveNcbiGene="no"
 
 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
 ln -s $buildDir/trackData/ncbiGene/$asmId.ncbiGene.bb $buildDir/bbi/${asmId}.ncbiGene.bb
 ln -s $buildDir/trackData/ncbiGene/$asmId.ncbiGene.ix $buildDir/ixIxx/${asmId}.ncbiGene.ix
 ln -s $buildDir/trackData/ncbiGene/$asmId.ncbiGene.ixx $buildDir/ixIxx/${asmId}.ncbiGene.ixx
   printf "track ncbiGene
 longLabel NCBI gene predictions
 shortLabel NCBI Genes
 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
 group genes\n\n" "${asmId}" "${asmId}" "${searchTrix}"
 
   $scriptDir/asmHubNcbiGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.ncbiGene.html
 
 haveNcbiGene="yes"
 fi
 
 ###################################################################
 # CpG Islands composite
-export cpgVis="hide"
+export cpgVis="off"
 # if there is no unmasked track, then set cpgVis to pack
 if [ ! -s ${buildDir}/trackData/cpgIslands/unmasked/${asmId}.cpgIslandExtUnmasked.bb ]; then
-  cpgVis="pack"
+  cpgVis="on"
 fi
 if [ -s ${buildDir}/trackData/cpgIslands/unmasked/${asmId}.cpgIslandExtUnmasked.bb -o -s ${buildDir}/trackData/cpgIslands/masked/${asmId}.cpgIslandExt.bb ]; then
 rm -f ${buildDir}/bbi/${asmId}.cpgIslandExtUnmasked.bb ${buildDir}/bbi/${asmId}.cpgIslandExt.bb
 
 printf "track cpgIslands
 compositeTrack on
 shortLabel CpG Islands
 longLabel CpG Islands (Islands < 300 Bases are Light Green)
 group regulation
 visibility pack
 type bed 3 .
 noInherit on
 html html/%s.cpgIslands\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/cpgIslands/masked/${asmId}.cpgIslandExt.bb ]; then
 ln -s ${buildDir}/trackData/cpgIslands/masked/${asmId}.cpgIslandExt.bb ${buildDir}/bbi/${asmId}.cpgIslandExt.bb
 printf "    track cpgIslandExt
     parent cpgIslands %s
     shortLabel CpG Islands
     longLabel CpG Islands (Islands < 300 Bases are Light Green)
     priority 1
     type bigBed 4 +
     bigDataUrl bbi/%s.cpgIslandExt.bb\n\n" "${cpgVis}" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/cpgIslands/unmasked/${asmId}.cpgIslandExtUnmasked.bb ]; then
 ln -s ${buildDir}/trackData/cpgIslands/unmasked/${asmId}.cpgIslandExtUnmasked.bb ${buildDir}/bbi/${asmId}.cpgIslandExtUnmasked.bb
 printf "    track cpgIslandExtUnmasked
-    parent cpgIslands pack
+    parent cpgIslands on
     shortLabel Unmasked CpG
     longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
     priority 2
     type bigBed 4 +
     bigDataUrl bbi/%s.cpgIslandExtUnmasked.bb\n\n" "${asmId}"
 fi
 
 if [ -s ${buildDir}/trackData/cpgIslands/unmasked/${asmId}.cpgIslandExtUnmasked.bb -o -s ${buildDir}/trackData/cpgIslands/masked/${asmId}.cpgIslandExt.bb ]; then
   $scriptDir/asmHubCpG.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.cpgIslands.html
 fi
 
 ###################################################################
 # windowMasker
 if [ -s ${buildDir}/trackData/windowMasker/${asmId}.windowMasker.bb ]; then
 rm -f ${buildDir}/bbi/${asmId}.windowMasker.bb
 ln -s ${buildDir}/trackData/windowMasker/${asmId}.windowMasker.bb ${buildDir}/bbi/${asmId}.windowMasker.bb
 
 printf "track windowMasker
 shortLabel WM + SDust
 longLabel Genomic Intervals Masked by WindowMasker + SDust
 group varRep
 visibility dense
 type bigBed 3
 bigDataUrl bbi/%s.windowMasker.bb
 html html/%s.windowMasker\n\n" "${asmId}" "${asmId}"
 $scriptDir/asmHubWindowMasker.pl $asmId $buildDir/html/$asmId.names.tab $buildDir > $buildDir/html/$asmId.windowMasker.html
 fi
 
 ###################################################################
 # allGaps
 if [ -s ${buildDir}/trackData/allGaps/${asmId}.allGaps.bb ]; then
 rm -f ${buildDir}/bbi/${asmId}.allGaps.bb
 ln -s ${buildDir}/trackData/allGaps/${asmId}.allGaps.bb ${buildDir}/bbi/${asmId}.allGaps.bb
 
 printf "track allGaps
 shortLabel All Gaps
 longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
 group map
 visibility dense
 type bigBed 3
 bigDataUrl bbi/%s.allGaps.bb
 html html/%s.allGaps\n\n" "${asmId}" "${asmId}"
 $scriptDir/asmHubAllGaps.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/$asmId.agp.gz https://hgdownload.soe.ucsc.edu/hubs/VGP/genomes/$asmId $buildDir/bbi/$asmId > $buildDir/html/$asmId.allGaps.html
 fi
 
 ###################################################################
 # augustus genes
 if [ -s ${buildDir}/trackData/augustus/${asmId}.augustus.bb ]; then
 rm -f ${buildDir}/bbi/${asmId}.augustus.bb
 ln -s ${buildDir}/trackData/augustus/${asmId}.augustus.bb ${buildDir}/bbi/${asmId}.augustus.bb
 
 export augustusVis="dense"
 
 if [ "${haveNcbiGene}" = "no" ]; then
    augustusVis="pack"
 fi
 printf "track augustus
 shortLabel Augustus
 longLabel Augustus Gene Predictions
 group genes
 visibility %s
 color 180,0,0
 type bigGenePred
 bigDataUrl bbi/%s.augustus.bb
 html html/%s.augustus\n\n" "${augustusVis}" "${asmId}" "${asmId}"
 $scriptDir/asmHubAugustusGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.augustus.html
 fi
 
 ###################################################################
 # xenoRefGene genes
 if [ -s ${buildDir}/trackData/xenoRefGene/${asmId}.xenoRefGene.bb ]; then
+rm -f $buildDir/ixIxx/${asmId}.xenoRefGene.ix
+rm -f $buildDir/ixIxx/${asmId}.xenoRefGene.ixx
 rm -f ${buildDir}/bbi/${asmId}.xenoRefGene.bb
 ln -s ${buildDir}/trackData/xenoRefGene/${asmId}.xenoRefGene.bb ${buildDir}/bbi/${asmId}.xenoRefGene.bb
+ln -s $buildDir/trackData/xenoRefGene/$asmId.xenoRefGene.ix $buildDir/ixIxx/${asmId}.xenoRefGene.ix
+ln -s $buildDir/trackData/xenoRefGene/$asmId.xenoRefGene.ixx $buildDir/ixIxx/${asmId}.xenoRefGene.ixx
 
 printf "track xenoRefGene
 shortLabel RefSeq mRNAs
 longLabel RefSeq mRNAs mapped to this assembly
 group rna
 visibility pack
 color 180,0,0
 type bigGenePred
 bigDataUrl bbi/%s.xenoRefGene.bb
-labelFields geneName,geneName2
-searchIndex name,geneName
-html html/%s.xenoRefGene\n\n" "${asmId}" "${asmId}"
+labelFields name,geneName,geneName2
+searchIndex name
+searchTrix ixIxx/%s.xenoRefGene.ix
+html html/%s.xenoRefGene\n\n" "${asmId}" "${asmId}" "${asmId}"
 $scriptDir/asmHubXenoRefGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.xenoRefGene.html
 fi
 
 ###################################################################
 # gapOverlap
 # if [ -s ${buildDir}/trackData/gapOverlap/${asmId}.gapOverlap.bb ]; then
 # rm -f ${buildDir}/bbi/${asmId}.gapOverlap.bb
 # ln -s ${buildDir}/trackData/gapOverlap/${asmId}.gapOverlap.bb ${buildDir}/bbi/${asmId}.gapOverlap.bb
 
 # printf "track gapOverlap
 # shortLabel Gap Overlaps
 # longLabel Exactly identical sequence on each side of a gap
 # group map
 # visibility hide
 # type bigBed 12 .
 # bigDataUrl bbi/%s.gapOverlap.bb
 # html html/%s.gapOverlap\n\n" "${asmId}" "${asmId}"
 
 # $scriptDir/asmHubGapOverlap.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.gapOverlap.html
 
 # fi
 ###################################################################
 
 printf "# Plink: ${buildDir}/trackData/ensGene/process/bbi/${asmId}.ensGene.bb ${buildDir}/bbi/${asmId}.ensGene.bb\n" 1>&2
 ###################################################################
 # Ensembl genes
 if [ -s ${buildDir}/trackData/ensGene/process/bbi/${asmId}.ensGene.bb ]; then
 printf "# link: ${buildDir}/trackData/ensGene/process/bbi/${asmId}.ensGene.bb ${buildDir}/bbi/${asmId}.ensGene.bb\n" 1>&2
 rm -f ${buildDir}/bbi/${asmId}.ensGene.bb
 ln -s ${buildDir}/trackData/ensGene/process/bbi/${asmId}.ensGene.bb ${buildDir}/bbi/${asmId}.ensGene.bb
 
 printf "track ensGene
 shortLabel Ensembl genes
 longLabel Ensembl genes v86
 group genes
 priority 40
 visibility pack
 color 150,0,0
 type bigBed 12 .
 bigDataUrl bbi/%s.ensGene.bb
 searchIndex name
 searchTrix ixIxx/%s.ensGene.name.ix
 html html/%s.ensGene\n\n" "${asmId}" "${asmId}" "${asmId}"
 $scriptDir/asmHubEnsGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.ensGene.html
 fi
 
 if [ -s ${hubLinks}/${asmId}/rnaSeqData/$asmId.trackDb.txt ]; then
   printf "include rnaSeqData/%s.trackDb.txt\n\n" "${asmId}"
 fi