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/asmHubChainNetTrackDb.sh src/hg/utils/automation/asmHubChainNetTrackDb.sh
index 8cdf0da..9dcc899 100755
--- src/hg/utils/automation/asmHubChainNetTrackDb.sh
+++ src/hg/utils/automation/asmHubChainNetTrackDb.sh
@@ -1,79 +1,86 @@
 #!/bin/bash
 
 set -beEu -o pipefail
+set -x
 
 if [ $# -ne 2 ]; then
   printf "usage: asmHubChainNetTrackDb.pl <asmId> <pathTo/assembly hub build directory> > chainNettrackDb.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="${asmId}"
 case ${asmId} in
    GC*)
      accessionId=`echo "$asmId" | awk -F"_" '{printf "%s_%s", $1, $2}'`
      ;;
 esac
 
 
 export scriptDir="$HOME/kent/src/hg/utils/automation"
 
 mkdir -p $buildDir/bbi
-mkdir -p $buildDir/ixIxx
+mkdir -p $buildDir/liftOver
 
 export chainNetPriority=1
 
 printf "# asmHubChainNetTrackDb.pl $asmId $buildDir\n" 1>&2
 
 for D in ${buildDir}/trackData/lastz.*
 do
   targetDb=$accessionId
   lastzDir=`basename "${D}"`
   otherDb=`echo $lastzDir | sed -e 's/lastz.//;'`
   OtherDb="${otherDb^}"
   asmReport=`ls -d $buildDir/download/*assembly_report.txt 2> /dev/null`
+  overChain="${targetDb}.${otherDb}.over.chain.gz"
+  overToChain="${targetDb}To${OtherDb}.over.chain.gz"
 printf "asmReport: %s\n" "${asmReport}" 1>&2
   if [ ! -s "${asmReport}" ]; then
  printf "# ERROR: can not find assembly_report.txt in $buildDir/download\n" 1>&2
     exit 255
   fi
   if [ ! -s ${buildDir}/trackData/$lastzDir/axtChain/chain${OtherDb}.bb ]; then
  printf "# ERROR: can not find chain${OtherDb}.bb in $buildDir/trackData/$lastzDir/axtChain/\n" 1>&2
     exit 255
   fi
   rm -f $buildDir/bbi/${asmId}.chain$OtherDb.bb
   rm -f $buildDir/bbi/${asmId}.chain${OtherDb}Link.bb
   rm -f $buildDir/bbi/${asmId}.chainSyn$OtherDb.bb
   rm -f $buildDir/bbi/${asmId}.chainSyn${OtherDb}Link.bb
   rm -f $buildDir/bbi/${asmId}.chainRBest$OtherDb.bb
   rm -f $buildDir/bbi/${asmId}.chainRBest${OtherDb}Link.bb
   rm -f $buildDir/bbi/${asmId}.chainLiftOver$OtherDb.bb
   rm -f $buildDir/bbi/${asmId}.chainLiftOver${OtherDb}Link.bb
   rm -f $buildDir/bbi/${asmId}.$otherDb.net.bb
   rm -f $buildDir/bbi/${asmId}.$otherDb.net.summary.bb
   rm -f $buildDir/bbi/${asmId}.$otherDb.synNet.bb
   rm -f $buildDir/bbi/${asmId}.$otherDb.synNet.summary.bb
   rm -f $buildDir/bbi/${asmId}.$otherDb.rbestNet.bb
   rm -f $buildDir/bbi/${asmId}.$otherDb.rbestNet.summary.bb
   rm -f $buildDir/bbi/${asmId}.$otherDb.liftOverNet.bb
   rm -f $buildDir/bbi/${asmId}.$otherDb.liftOverNet.summary.bb
+  rm -f $buildDir/liftOver/${overToChain}
+  if [ -s "$buildDir/trackData/$lastzDir/axtChain/${overChain}" ]; then
+     ln -s ../trackDb/$lastzDir/axtChain/${overChain} $buildDir/liftOver/${overToChain}
+  fi
   if [ -s "$buildDir/trackData/$lastzDir/axtChain/chain${OtherDb}.bb" ]; then
     ln -s ../trackData/$lastzDir/axtChain/chain${OtherDb}.bb $buildDir/bbi/${asmId}.chain$OtherDb.bb
     ln -s ../trackData/$lastzDir/axtChain/chain${OtherDb}Link.bb $buildDir/bbi/${asmId}.chain${OtherDb}Link.bb
   fi
   if [ -s "$buildDir/trackData/$lastzDir/bigMaf/$accessionId.$otherDb.net.bb" ]; then
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.net.bb $buildDir/bbi/${asmId}.$otherDb.net.bb
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.net.summary.bb $buildDir/bbi/${asmId}.$otherDb.net.summary.bb
   fi
   if [ -s "$buildDir/trackData/$lastzDir/axtChain/chainSyn${OtherDb}.bb" ]; then
     ln -s ../trackData/$lastzDir/axtChain/chainSyn${OtherDb}.bb $buildDir/bbi/${asmId}.chainSyn$OtherDb.bb
     ln -s ../trackData/$lastzDir/axtChain/chainSyn${OtherDb}Link.bb $buildDir/bbi/${asmId}.chainSyn${OtherDb}Link.bb
   fi
   if [ -s "$buildDir/trackData/$lastzDir/bigMaf/$accessionId.$otherDb.synNet.bb" ]; then
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.synNet.bb $buildDir/bbi/${asmId}.$otherDb.synNet.bb
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.synNet.summary.bb $buildDir/bbi/${asmId}.$otherDb.synNet.summary.bb