2c720ad5f45b1111583f17a95b58cc9750f4c5c5
hiram
  Tue Aug 6 09:44:15 2019 -0700
fixup links to hgdownload for AGP and JPG image refs #23734

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 4f38728..89b5ccf 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -35,46 +35,46 @@
 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 ../hubs/ncbiAssemblies/$genbankRefseq/$asmId > $buildDir/html/$asmId.assembly.html
+$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 ../hubs/ncbiAssemblies/$genbankRefseq/$asmId > $buildDir/html/$asmId.gap.html
+$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}"
 
@@ -325,54 +325,57 @@
 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
 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
 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
@@ -424,48 +427,53 @@
 
 ###################################################################
 # 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 ../hubs/ncbiAssemblies/$genbankRefseq/$asmId $buildDir/bbi/$asmId > $buildDir/html/$asmId.allGaps.html
+$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 [ "${haveNcbiGene}" = "no" ]; then
+   augustusVis="pack"
+fi
 printf "track augustus
 shortLabel Augustus
 longLabel Augustus Gene Predictions
 group genes
-visibility dense
+visibility %s
 color 180,0,0
 type bigGenePred
 bigDataUrl bbi/%s.augustus.bb
-html html/%s.augustus\n\n" "${asmId}" "${asmId}"
+html html/%s.augustus\n\n" "${augustusVis}" "${asmId}" "${asmId}"
 $scriptDir/asmHubAugustusGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.augustus.html
 fi
 
 ###################################################################
 # 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 .