65a21f5c7cdda8de27c2054ddffdd391284c3aa1
hiram
  Mon Jun 1 09:03:06 2026 -0700
switching entirely to genome-centdb hgcentral refs #31811

diff --git src/hg/utils/otto/userRequests/kegAlignLastz.sh src/hg/utils/otto/userRequests/kegAlignLastz.sh
index d71cbf51d5a..af71984abd6 100755
--- src/hg/utils/otto/userRequests/kegAlignLastz.sh
+++ src/hg/utils/otto/userRequests/kegAlignLastz.sh
@@ -1,46 +1,48 @@
 #!/bin/bash
 
 set -eEu -o pipefail
 
 export userName="`whoami`"
 
 export bigHub="hgwdev"
 export workHorse="hgwdev"
 export smallClusterHub="hgwdev"
 export fileServer="hgwdev"
 #  a python virtual environment to run this
 export planemoCmd="/hive/users/hiram/galaxy/venv3.12/bin/planemo"
+export centDb="hgcentral"
+export hgSql="hgsql -hgenome-centdb"
 
 # parse optional -force flag to skip genark table verification
 export forceRun=0
 if [ $# -gt 0 ] && [ "$1" = "-force" ]; then
   forceRun=1
   shift
 fi
 
 if [ $# != 4 ]; then
   printf "ERROR: arg count: %d != 4\n" "$#" 1>&2
 
   printf "usage: kegAlignLastz.sh [-force] <target> <query> <tClade> <qClade>
 
 Where target/query is either a UCSC db name, or is an
    assembly hub identifier, e.g.: GCA_002844635.1_USMARCv1.0.1
 
 And [tq]Clade is one of: primate|mammal|other
 
-The -force option skips the hgcentraltest.genark table verification
+The -force option skips the ${centDb}.genark table verification
    for GenArk assembly identifiers.
 
 Will create directory to work in, for example if, UCSC db:
   /hive/data/target/bed/lastzQuery.yyyy-mm-dd/
 
 Or, in the assembly hub build directory:
 /hive/data/genomes/asmHubs/allBuild/GCA/002/844/635/GCA_002844635.1_USMARCv1.0/trackData/lastzQuery.yyyy-mm-dd
 
 Will set up a DEF file there, and a kegAlign.sh script to run all steps
   and output makeDoc text to document what happened.
   Also sets up a lastzRun.sh script that could be used to run the UCSC
   lastz procedure.
 
 AND MORE, it will run the swap operation into the corresponding
   blastz.target.swap directory in the query genome work space.
@@ -118,31 +120,31 @@
   esac
   printf "%s" "${count}"
 }
 
 # obtain the organism name out of the assembly_report.txt file
 function orgName() {
   export asmName=$1
   case $asmName in
      GC[AF]_*)
        gcxPath=$(gcPath $asmName)
        asmDir="/hive/data/outside/ncbi/genomes/${gcxPath}/${asmName}"
        asmRpt="${asmDir}/${asmName}_assembly_report.txt"
        oName=`egrep -m 1 -i "^# organism name:" ${asmRpt} | tr -d '\r' | sed -e 's/.*(//; s/).*//'`
        ;;
      *)
-       oName=`/cluster/bin/x86_64/hgsql -N -e "select organism from dbDb where name=\"${asmName}\";" hgcentraltest`
+       oName=`/cluster/bin/x86_64/${hgSql} -N -e "select organism from dbDb where name=\"${asmName}\";" "${centDb}"`
        ;;
   esac
   printf "%s" "${oName}"
 }
  
 # generate URL to the fa.gz files to pass off to galaxy
 function faGzUrl() {
   export asmName=$1
   case $asmName in
      GC[AF]_*)
        gcxPath=$(gcPath $asmName)
        id=$(accId $asmName)
        printf "https://hgdownload.soe.ucsc.edu/hubs/%s/%s/%s.fa.gz" "${gcxPath}" "${id}" "${id}"
        ;;
      *)
@@ -156,59 +158,59 @@
   export asmName=$1
   case $asmName in
      GC[AF]_*)
        gcxPath=$(gcPath $asmName)
        asmDir="/hive/data/outside/ncbi/genomes/${gcxPath}/${asmName}"
        asmRpt="${asmDir}/${asmName}_assembly_report.txt"
        oDate=`egrep -m 1 -i "^#[[:space:]]*Date:" ${asmRpt} | tr -d '\r' | sed -e 's/.*ate: \+//;'`
        ;;
      *)
        oDate=""
        ;;
   esac
   printf "%s" "${oDate}"
 }
 
-# verifyGenark - verify a GenArk accession exists in hgcentraltest.genark
+# verifyGenark - verify a GenArk accession exists in ${centDb}.genark
 #   returns 0 if found, 1 if not found
 function verifyGenark() {
   local asmAccession=$1
   local fullName=$2
-  local count=$(/cluster/bin/x86_64/hgsql -N -e "SELECT COUNT(*) FROM genark WHERE gcAccession='${asmAccession}';" hgcentraltest)
+  local count=$(/cluster/bin/x86_64/${hgSql} -N -e "SELECT COUNT(*) FROM genark WHERE gcAccession='${asmAccession}';" "${centDb}")
   if [ "$count" -eq 0 ]; then
     printf "ERROR: assembly '%s' not found in GenArk\n" "$fullName" 1>&2
     return 1
   fi
   return 0
 }
 
 ##############################################################################
 ##############################################################################
 ### start seconds
 export startT=`date "+%s"`
 
 export target="$1"
 export query="$2"
 export tClade="$3"
 export qClade="$4"
 
 export tGcPath=$(gcPath $target)
 export qGcPath=$(gcPath $query)
 export tAccId=$(accId $target)
 export qAccId=$(accId $query)
 
-# verify GenArk assemblies exist in hgcentraltest.genark unless -force
+# verify GenArk assemblies exist in ${centDb}.genark unless -force
 if [ "$forceRun" -eq 0 ]; then
   export genarkErrors=0
   case $target in
     GC[AF]_*) verifyGenark "$tAccId" "$target" || genarkErrors=$((genarkErrors+1)) ;;
   esac
   case $query in
     GC[AF]_*) verifyGenark "$qAccId" "$query" || genarkErrors=$((genarkErrors+1)) ;;
   esac
   if [ "$genarkErrors" -gt 0 ]; then
     printf "Use -force to skip this check\n" 1>&2
     exit 255
   fi
 fi
 
 printf "# tq: '${target}' '${query}' '${tClade}' '${qClade}'\n" 1>&2