1b17e173bde7713fe7080825f27efb8e952419f4
hiram
  Thu Aug 1 14:51:39 2019 -0700
updating text after QA comments refs #23734

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 587dce0..4f38728 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -132,39 +132,41 @@
 
   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 [ "${gapOverlapCount}" -gt 0 ]; then
     printf "    track gapOverlap
     parent tanDups on
     shortLabel Gap Overlaps
     longLabel Paired exactly identical sequence on each side of a gap
-    bigDataUrl bbi/%s.gapOverlap.bb\n\n" "${asmId}"
+    bigDataUrl bbi/%s.gapOverlap.bb
+    type bigBed 12\n\n" "${asmId}"
   fi
 
   if [ "${tanDupCount}" -gt 0 ]; then
     printf "    track tandemDups
     parent tanDups on
     shortLabel Tandem Dups
     longLabel Paired exactly identical sequence survey over entire genome assembly
-    bigDataUrl bbi/%s.tandemDups.bb\n\n" "${asmId}"
+    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
@@ -318,58 +320,60 @@
 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/geneTrack/ucsc.NZO_HlLtJ.ix ]; then
+if [ -s ${buildDir}/trackData/ncbiGene/$asmId.ncbiGene.ix ]; then
   searchTrix="
-searchTrix ixIxx/$asmId.geneTrack.ix"
-fi
-
-if [ -s ${buildDir}/trackData/geneTrack/ucsc.NZO_HlLtJ.bb ]; then
-rm -f $buildDir/bbi/${asmId}.geneTrack.bb
-rm -f $buildDir/ixIxx/${asmId}.geneTrack.ix
-rm -f $buildDir/ixIxx/${asmId}.geneTrack.ixx
-ln -s $buildDir/trackData/geneTrack/ucsc.NZO_HlLtJ.bb $buildDir/bbi/${asmId}.geneTrack.bb
-ln -s $buildDir/trackData/geneTrack/ucsc.NZO_HlLtJ.ix $buildDir/ixIxx/${asmId}.geneTrack.ix
-ln -s $buildDir/trackData/geneTrack/ucsc.NZO_HlLtJ.ixx $buildDir/ixIxx/${asmId}.geneTrack.ixx
-  printf "track geneTrack
-longLabel geneTrack - gene predictions
-shortLabel geneTrack
+searchTrix ixIxx/$asmId.ncbiGene.ix"
+fi
+
+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.geneTrack.bb
+bigDataUrl bbi/%s.ncbiGene.bb
 type bigGenePred
-html html/%s.geneTrack
+html html/%s.ncbiGene
 searchIndex name%s
+url https://www.ncbi.nlm.nih.gov/gene/?term=\$\$
+urlLabel Entrez gene
 group genes\n\n" "${asmId}" "${asmId}" "${searchTrix}"
-fi
 
-# url https://www.ncbi.nlm.nih.gov/nuccore/\$\$
-# urlLabel NCBI Nucleotide database
+  $scriptDir/asmHubNcbiGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/trackData > $buildDir/html/$asmId.ncbiGene.html
+
+fi
 
 ###################################################################
 # CpG Islands composite
 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}"
@@ -443,46 +447,46 @@
 
 printf "track augustus
 shortLabel Augustus
 longLabel Augustus Gene Predictions
 group genes
 visibility dense
 color 180,0,0
 type bigGenePred
 bigDataUrl bbi/%s.augustus.bb
 html html/%s.augustus\n\n" "${asmId}" "${asmId}"
 $scriptDir/asmHubAugustusGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.augustus.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
+# 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}"
+# 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
+# $scriptDir/asmHubGapOverlap.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.gapOverlap.html
 
-fi
+# 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