92509db0231e9b1ae83aa0c85182883dd8eabc9b
hiram
  Wed Sep 14 13:59:35 2022 -0700
fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811

diff --git src/hg/utils/automation/asmHubChainNetTrackDb.sh src/hg/utils/automation/asmHubChainNetTrackDb.sh
index a5dce42..4845b31 100755
--- src/hg/utils/automation/asmHubChainNetTrackDb.sh
+++ src/hg/utils/automation/asmHubChainNetTrackDb.sh
@@ -1,82 +1,100 @@
 #!/bin/bash
 
 set -beEu -o pipefail
 
 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=$2
 export hubLinks="/hive/data/genomes/asmHubs/hubLinks"
-export accessionId=`echo "$asmId" | awk -F"_" '{printf "%s_%s", $1, $2}'`
+
+export accessionId="${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
 
 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 $buildDir/download/*assembly_report.txt 2> /dev/null`
+printf "asmReport: %s\n" "${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}.$otherDb.liftOverNet.summary.bb
+  if [ -s ../trackData/$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${OtherDb}Link.bb
+  fi
+  if [ -s ../trackData/$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${OtherDb}Link.bb
+  fi
+  if [ -s ../trackData/$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}.$otherDb.synNet.summary.bb
   fi
   if [ -s "$buildDir/trackData/$lastzDir/axtChain/chainRBest${OtherDb}.bb" ]; then
     ln -s ../trackData/$lastzDir/axtChain/chainRBest${OtherDb}.bb $buildDir/bbi/${asmId}.chainRBest$OtherDb.bb
     ln -s ../trackData/$lastzDir/axtChain/chainRBest${OtherDb}Link.bb $buildDir/bbi/${asmId}.chainRBest${OtherDb}Link.bb
+  fi
+  if [ -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.rbestNet.bb ]; then
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.rbestNet.bb $buildDir/bbi/${asmId}.$otherDb.rbestNet.bb
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.rbestNet.summary.bb $buildDir/bbi/${asmId}.$otherDb.rbestNet.summary.bb
   fi
   if [ -s "$buildDir/trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}.bb" ]; then
 printf "# making chainLiftOver${OtherDb}.bb\n" 1>&2
     ln -s ../trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}.bb $buildDir/bbi/${asmId}.chainLiftOver$OtherDb.bb
     ln -s ../trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}Link.bb $buildDir/bbi/${asmId}.chainLiftOver${OtherDb}Link.bb
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.liftOverNet.bb $buildDir/bbi/${asmId}.$otherDb.liftOverNet.bb
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.liftOverNet.summary.bb $buildDir/bbi/${asmId}.$otherDb.liftOverNet.summary.bb
   else
 printf "# there is NO chainLiftOver${OtherDb}.bb\n" 1>&2
   fi
 
   otherPrefix=`echo $otherDb | cut -c1-2`
   if [ "${otherPrefix}" = "GC" ]; then