81edac3824e0dd89d6cd13e1d668011cd3695ea0
hiram
  Wed Feb 26 14:44:12 2020 -0800
begining to function OK for assembly hubs refs #24963

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index b42fa75..b43b0fb 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -679,42 +679,44 @@
 
 # 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
+export assemblyId=`echo ${asmId} | cut -d_ -f1-2`
+
 ###################################################################
 # 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
+if [ -s ${buildDir}/trackData/ensGene/bbi/${assemblyId}.ensGene.bb ]; then
+ls -og ${buildDir}/trackData/ensGene/bbi/${assemblyId}.ensGene.bb 1>&2
+printf "# link: ${buildDir}/trackData/ensGene/process/bbi/${assemblyId}.ensGene.bb ${buildDir}/bbi/${asmId}.ensGene.bb\n" 1>&2
 rm -f ${buildDir}/bbi/${asmId}.ensGene.bb
-ln -s ../trackData/ensGene/process/bbi/${asmId}.ensGene.bb ${buildDir}/bbi/${asmId}.ensGene.bb
+ln -s ../trackData/ensGene/bbi/${assemblyId}.ensGene.bb ${buildDir}/bbi/${asmId}.ensGene.bb
 rm -f ${buildDir}/ixIxx/${asmId}.ensGene.ix
 rm -f ${buildDir}/ixIxx/${asmId}.ensGene.ixx
 
-ln -s ../trackData/ensGene/process/${asmId}.ensGene.ix $buildDir/ixIxx
-ln -s ../trackData/ensGene/process/${asmId}.ensGene.ixx $buildDir/ixIxx
+ln -s ../trackData/ensGene/process/${assemblyId}.ensGene.ix $buildDir/ixIxx/${asmId}.ensGene.ix
+ln -s ../trackData/ensGene/process/${assemblyId}.ensGene.ixx $buildDir/ixIxx/${asmId}.ensGene.ixx
 
 export ensVersion="v86"
 
 if [ -s ${buildDir}/trackData/ensGene/version.txt ]; then
   ensVersion=`cat "${buildDir}/trackData/ensGene/version.txt"`
 fi
 
 printf "track ensGene
 shortLabel Ensembl genes
 longLabel Ensembl genes %s
 group genes
 priority 40
 visibility pack
 color 150,0,0
 type bigBed 12 .