e22f7956c30a5490adb028364bbc2c1e45b2da8b
hiram
  Wed Nov 2 16:17:28 2022 -0700
turn off mouse strain bigMaf tracks since they do not work and now with the new style copy link to paste buffer feature for gateway description pages refs #30199

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 04c0611..2ee490f 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -55,31 +55,31 @@
 if [ -s ${buildDir}/trackData/assemblyGap/${asmId}.assembly.bb ]; then
 rm -f $buildDir/bbi/${asmId}.assembly.bb
 ln -s ../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
+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 ../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
@@ -612,31 +612,31 @@
 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 $shortLabel
 visibility pack
 color 0,80,150
 altColor 150,80,0
 colorByStrand 0,80,150 150,80,0
 bigDataUrl bbi/%s.ncbiGene.bb
 type bigGenePred
 html html/%s.ncbiGene
 searchIndex name%s
 url https://www.ncbi.nlm.nih.gov/gene/?term=\$\$
-urlLabel Entrez gene
+urlLabel Entrez gene:
 labelFields geneName,geneName2
 defaultLabelFields geneName2
 group genes\n\n" "${asmId}" "${asmId}" "${searchTrix}"
 
   $scriptDir/asmHubNcbiGene.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.ncbiGene.html
 
 haveNcbiGene="yes"
 fi	#	if [ -s ${buildDir}/trackData/ncbiGene/$asmId.ncbiGene.bb ]
 fi	#	if [ "${haveNcbiRefSeq}" = "no" ]
 ###################################################################
 
 ###################################################################
 # CpG Islands composite
 export cpgVis="off"
 # if there is no unmasked track, then set cpgVis to pack
@@ -761,30 +761,32 @@
     mkdir -p $buildDir/genes
     ln -s ../trackData/xenoRefGene/${asmId}.xenoRefGene.gtf.gz ${buildDir}/genes/${asmId}.xenoRefGene.gtf.gz
   fi
 ln -s ../trackData/xenoRefGene/${asmId}.xenoRefGene.bb ${buildDir}/bbi/${asmId}.xenoRefGene.bb
 ln -s ../trackData/xenoRefGene/$asmId.xenoRefGene.ix $buildDir/ixIxx/${asmId}.xenoRefGene.ix
 ln -s ../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
+url https://www.ncbi.nlm.nih.gov/nuccore/\$\$
+urlLabel NCBI Nucleotide database:
 labelFields name,geneName,geneName2
 defaultLabelFields geneName
 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
 
 ###################################################################
 # Ensembl genes
 if [ -s ${buildDir}/trackData/ensGene/bbi/${asmId}.ensGene.bb ]; then
 ls -og ${buildDir}/trackData/ensGene/bbi/${asmId}.ensGene.bb 1>&2
 printf "# link: ../trackData/ensGene/bbi/${asmId}.ensGene.bb ${buildDir}/bbi/${asmId}.ensGene.bb\n" 1>&2
 rm -f ${buildDir}/bbi/${asmId}.ensGene.bb
 ln -s ../trackData/ensGene/bbi/${asmId}.ensGene.bb ${buildDir}/bbi/${asmId}.ensGene.bb
@@ -813,33 +815,35 @@
 searchTrix ixIxx/%s.ensGene.ix
 html html/%s.ensGene\n\n" "${ensVersion}" "${asmId}" "${asmId}" "${asmId}"
 
 $scriptDir/asmHubEnsGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.ensGene.html "${ensVersion}"
 
 else
   printf "# no ensGene found\n" 1>&2
 fi
 
 # hubLinks is for mouseStrains specific hub only
 export hubLinks="/hive/data/genomes/asmHubs/hubLinks"
 if [ -s ${hubLinks}/${asmId}/rnaSeqData/$asmId.trackDb.txt ]; then
   printf "include rnaSeqData/%s.trackDb.txt\n\n" "${asmId}"
 fi
 ##  for mouse strain hubs only
-if [ -s "${buildDir}/$asmId.bigMaf.trackDb.txt" ]; then
-  printf "include %s.bigMaf.trackDb.txt\n\n" "${asmId}"
-fi
+## turned off 2022-11-02 until these can be correctly translated
+## to GenArk naming schemes
+### if [ -s "${buildDir}/$asmId.bigMaf.trackDb.txt" ]; then
+###   printf "include %s.bigMaf.trackDb.txt\n\n" "${asmId}"
+### fi
 
 ###################################################################
 # check for lastz/chain/net available
 
 export lz=`ls -d ${buildDir}/trackData/lastz.* 2> /dev/null | wc -l`
 
 if [ "${lz}" -gt 0 ]; then
   if [ "${lz}" -eq 1 ]; then
 printf "single chainNet\n" 1>&2
     export lastzDir=`ls -d ${buildDir}/trackData/lastz.*`
     export oOrganism=`basename "${lastzDir}" | sed -e 's/lastz.//;'`
     # single chainNet here, no need for a composite track, does the symLinks too
     $scriptDir/asmHubChainNetTrackDb.sh $asmId $buildDir
     $scriptDir/asmHubChainNet.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab $oOrganism > $buildDir/html/$asmId.chainNet.html
   else