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
@@ -357,64 +357,64 @@
 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
@@ -462,44 +462,49 @@
 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 .