3c1b9cee5a4152b70e2fc10b432082ea89fecae6
hiram
  Tue Sep 29 15:06:19 2026 -0700
add trackDb construction for miniMap2 chain tracks refs #34360

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 9d189c6de3b..7c3654111c1 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -1096,30 +1096,51 @@
   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
     $scriptDir/asmHubChainNetTrackDb.pl $buildDir
     $scriptDir/asmHubChainNetComposite.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab > $buildDir/html/$asmId.chainNet.html
   fi
 fi
 
+###################################################################
+# check for miniMap2/chain/net available
+
+export mm2=`ls -d ${buildDir}/trackData/miniMap2.* 2> /dev/null | wc -l`
+
+if [ "${mm2}" -gt 0 ]; then
+  if [ "${mm2}" -eq 1 ]; then
+printf "single miniMap2 chainNet\n" 1>&2
+    export miniMap2Dir=`ls -d ${buildDir}/trackData/miniMap2.*`
+    export oOrganism=`basename "${miniMap2Dir}" | sed -e 's/miniMap2.//;'`
+    # single chainNet here, no need for a composite track, does the symLinks too
+    $scriptDir/asmHubMiniMap2ChainNetTrackDb.sh $asmId $buildDir
+    $scriptDir/asmHubMiniMap2ChainNet.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab $oOrganism > $buildDir/html/$asmId.miniMap2ChainNet.html
+  else
+printf "composite miniMap2 chainNet\n" 1>&2
+    # multiple chainNets here, create composite track, does the symLinks too
+    $scriptDir/asmHubMiniMap2ChainNetTrackDb.pl $buildDir
+    $scriptDir/asmHubMiniMap2ChainNetComposite.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab > $buildDir/html/$asmId.miniMap2ChainNet.html
+  fi
+fi
+
 ###################################################################
 # crisprAll track
 
 if [ -s ${buildDir}/trackData/crisprAll/crispr.bb ]; then
 
 rm -f $buildDir/bbi/${asmId}.crisprAll.bb
 rm -f $buildDir/bbi/${asmId}.crisprAllDetails.tab
 ln -s ../trackData/crisprAll/crispr.bb ${buildDir}/bbi/${asmId}.crisprAll.bb
 ln -s ../trackData/crisprAll/crisprDetails.tab $buildDir/bbi/${asmId}.crisprAllDetails.tab
 
 printf "track crisprAllTargets
 visibility hide
 shortLabel CRISPR Targets
 longLabel CRISPR/Cas9 -NGG Targets, whole genome
 group genes