1857a999455044505e7c0395b5b6b68b59c15906
hiram
  Thu Oct 15 09:25:58 2020 -0700
allow optional user data tracks in a trackDb (VGP work) refs #23891

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 16af62c..3c63121 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -1,29 +1,30 @@
 #!/bin/bash
 
 set -beEux -o pipefail
 
 if [ $# -ne 2 ]; then
   printf "usage: trackDb.sh <asmId> <pathTo/assembly hub build directory> > trackDb.txt\n" 1>&2
   printf "expecting to find *.ucsc.2bit and bbi/ files at given path\n" 1>&2
   printf "the ncbi|ucsc selects the naming scheme\n" 1>&2
   exit 255
 fi
 
 export asmId=$1
 export buildDir=$2
 export hubLinks="/hive/data/genomes/asmHubs/hubLinks"
+export accessionId=`echo "$asmId" | awk -F"_" '{printf "%s_%s", $1, $2}'`
 
 export scriptDir="$HOME/kent/src/hg/utils/automation"
 
 mkdir -p $buildDir/bbi
 mkdir -p $buildDir/ixIxx
 
 # may or may not have a searchTrix for assembly, assume none
 export searchTrix=""
 # check to see if there is a searchTrix assembly index
 if [ -s ${buildDir}/trackData/assemblyGap/${asmId}.assembly.ix ]; then
   rm -f $buildDir/ixIxx/${asmId}.assembly.ix*
   ln -s ../trackData/assemblyGap/${asmId}.assembly.ix $buildDir/ixIxx
   ln -s ../trackData/assemblyGap/${asmId}.assembly.ixx $buildDir/ixIxx
   searchTrix="
 searchTrix ixIxx/${asmId}.assembly.ix"
@@ -707,15 +708,19 @@
 type bigBed 12 .
 bigDataUrl bbi/%s.ensGene.bb
 searchIndex name
 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
 
 if [ -s ${hubLinks}/${asmId}/rnaSeqData/$asmId.trackDb.txt ]; then
   printf "include rnaSeqData/%s.trackDb.txt\n\n" "${asmId}"
 fi
+
+if [ -s "${buildDir}/$asmId.userTrackDb.txt" ]; then
+  printf "include %s.userTrackDb.txt\n\n" "${accessionId}"
+fi