2121928a798a7119f00eb7e198bd06cf4ea36d2f
hiram
  Wed Oct 5 10:14:36 2022 -0700
correctly recognize the presence of the chain net files no redmine

diff --git src/hg/utils/automation/asmHubChainNetTrackDb.sh src/hg/utils/automation/asmHubChainNetTrackDb.sh
index 4845b31..8cdf0da 100755
--- src/hg/utils/automation/asmHubChainNetTrackDb.sh
+++ src/hg/utils/automation/asmHubChainNetTrackDb.sh
@@ -50,51 +50,51 @@
   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${OtherDb}.bb ]; then
+  if [ -s "$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${OtherDb}Link.bb
   fi
-  if [ -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.net.bb ]; then
+  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${OtherDb}Link.bb
   fi
-  if [ -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.synNet.bb ]; then
+  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}.$otherDb.synNet.summary.bb
   fi
   if [ -s "$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
+  if [ -s "$buildDir/trackData/$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