c6c34d96e660ffad5ca588f14a461c1da30b0e46
hiram
  Fri Jan 20 10:25:10 2023 -0800
correctly link in lift over chain files to download liftOver directory refs #30517

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index a46fb84..a019e3f 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -827,30 +827,45 @@
 fi
 
 # hubLinks is for mouseStrains specific hub only
 export hubLinks="/hive/data/genomes/asmHubs/hubLinks"
 if [ -s ${hubLinks}/${asmId}/rnaSeqData/$asmId.trackDb.txt ]; then
   printf "include rnaSeqData/%s.trackDb.txt\n\n" "${asmId}"
 fi
 ##  for mouse strain hubs only
 ## turned off 2022-11-02 until these can be correctly translated
 ## to GenArk naming schemes
 ### if [ -s "${buildDir}/$asmId.bigMaf.trackDb.txt" ]; then
 ###   printf "include %s.bigMaf.trackDb.txt\n\n" "${asmId}"
 ### fi
 
 ###################################################################
+# check for blat sameSpecies liftOver, then link to lift over chain file
+export lo=`ls -d ${buildDir}/trackData/blat.* 2> /dev/null | wc -l`
+
+if [ "${lo}" -gt 0 ]; then
+  mkdir -p ${buildDir}/liftOver
+  for loS in `ls -d ${buildDir}/trackData/blat.* 2> /dev/null`
+  do
+     blatDir=`basename "${loS}"`
+     overChain=`ls ${loS}/*.over.chain.gz | awk -F'/' "{print \\$NF}"`
+     rm -f ${buildDir}/liftOver/${overChain}
+     ln -s ../trackData/${blatDir}/${overChain} ${buildDir}/liftOver
+  done
+fi
+
+###################################################################
 # check for lastz/chain/net available
 
 export lz=`ls -d ${buildDir}/trackData/lastz.* 2> /dev/null | wc -l`
 
 if [ "${lz}" -gt 0 ]; then
   if [ "${lz}" -eq 1 ]; then
 printf "single chainNet\n" 1>&2
     export lastzDir=`ls -d ${buildDir}/trackData/lastz.*`
     export oOrganism=`basename "${lastzDir}" | sed -e 's/lastz.//;'`
     # single chainNet here, no need for a composite track, does the symLinks too
     $scriptDir/asmHubChainNetTrackDb.sh $asmId $buildDir
     $scriptDir/asmHubChainNet.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab $oOrganism > $buildDir/html/$asmId.chainNet.html
   else
 printf "composite chainNet\n" 1>&2
     # multiple chainNets here, create composite track, does the symLinks too