2b42d05e58a971f49afdd6d52c2ad415e165add0
hiram
  Tue Jul 6 12:37:28 2021 -0700
create a GTF file for the xenoRefGene result refs #27512

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 80da841..38df94c 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -635,31 +635,36 @@
 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
+rm -f $buildDir/bbi/${asmId}.xenoRefGene.bb
+rm -f $buildDir/genes/${asmId}.xenoRefGene.gtf.gz
+  if [ -s ${buildDir}/trackData/xenoRefGene/${asmId}.xenoRefGene.gtf.gz ]; then
+    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
 labelFields name,geneName,geneName2
 searchIndex name
 searchTrix ixIxx/%s.xenoRefGene.ix