2ce16411b0f909e7e1dfd27a01af34316c260f2f
hiram
  Mon Jul 5 11:58:27 2021 -0700
catching up the edge cases for pair wise alignment to assembly hub genome no redmine

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index a770611..80da841 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -1,28 +1,29 @@
 #!/bin/bash
 
 set -beEu -o pipefail
 
 if [ $# -ne 2 ]; then
   printf "usage: trackDb.sh <asmId> <pathTo/assembly hub build directory> > trackDb.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=$2
+# hubLinks is for mouseStrains specific hub only
 export hubLinks="/hive/data/genomes/asmHubs/hubLinks"
 export accessionId=`echo "$asmId" | awk -F"_" '{printf "%s_%s", $1, $2}'`
 export gcX=`echo $asmId | cut -c1-3`
 export d0=`echo $asmId | cut -c5-7`
 export d1=`echo $asmId | cut -c8-10`
 export d2=`echo $asmId | cut -c11-13`
 export hubPath="$gcX/$d0/$d1/$d2/$asmId"
 
 export scriptDir="$HOME/kent/src/hg/utils/automation"
 
 mkdir -p $buildDir/bbi
 mkdir -p $buildDir/ixIxx
 
 # may or may not have a searchTrix for assembly, assume none
 export searchTrix=""
@@ -695,30 +696,34 @@
 type bigBed 12 .
 bigDataUrl bbi/%s.ensGene.bb
 searchIndex name
 searchTrix ixIxx/%s.ensGene.ix
 html html/%s.ensGene\n\n" "${ensVersion}" "${asmId}" "${asmId}" "${asmId}"
 
 $scriptDir/asmHubEnsGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.ensGene.html "${ensVersion}"
 
 else
   printf "# no ensGene found\n" 1>&2
 fi
 
 if [ -s ${hubLinks}/${asmId}/rnaSeqData/$asmId.trackDb.txt ]; then
   printf "include rnaSeqData/%s.trackDb.txt\n\n" "${asmId}"
 fi
+##  for mouse strain hubs only
+if [ -s "${buildDir}/$asmId.bigMaf.trackDb.txt" ]; then
+  printf "include %s.bigMaf.trackDb.txt\n\n" "${asmId}"
+fi
 
 if [ -s "${buildDir}/$asmId.userTrackDb.txt" ]; then
   printf "include %s.userTrackDb.txt\n\n" "${accessionId}"
 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
     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