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/ottoRequestAlign.sh src/hg/utils/otto/userRequests/ottoRequestAlign.sh
index 7501624ad8d..89085a7f0e4 100755
--- src/hg/utils/otto/userRequests/ottoRequestAlign.sh
+++ src/hg/utils/otto/userRequests/ottoRequestAlign.sh
@@ -1,70 +1,72 @@
 #!/bin/bash
 
 # ottoRequestAlign.sh - look up an ottoRequest row by id and construct
 #   the kegAlignLastz.sh command line from genark metadata
 #
 # usage: ottoRequestAlign.sh <id>
 #
-# Queries hgcentraltest.ottoRequest for fromDb/toDb, then looks up
-# each accession in hgcentraltest.genark for asmName and clade.
+# Queries ${centDb}.ottoRequest for fromDb/toDb, then looks up
+# each accession in ${centDb}.genark for asmName and clade.
 # Prints and executes the resulting kegAlignLastz.sh command.
 
 set -eEu -o pipefail
+export centDb="hgcentral"
+export hgSql="hgsql -hgenome-centdb"
 
 ############################################################################
 ### verify arguments
 ############################################################################
 if [ $# != 1 ]; then
   printf "usage: ottoRequestAlign.sh <id>\n" 1>&2
-  printf "  where <id> is a row id from hgcentraltest.ottoRequest\n" 1>&2
+  printf "  where <id> is a row id from ${centDb}.ottoRequest\n" 1>&2
   exit 255
 fi
 
 export requestId="$1"
 export scriptDir=$(cd "$(dirname "$0")" && pwd)
 
 # validate id is a positive integer
 case "${requestId}" in
   ''|*[!0-9]*)
     printf "ERROR: id must be a positive integer, got: '%s'\n" "${requestId}" 1>&2
     exit 255
     ;;
 esac
 
 ############################################################################
 ### function definitions
 ############################################################################
 ### errors - set error status in the table
 function setErrorStatus() {
   id="${1}"
-  /cluster/bin/x86_64/hgsql -N -e \
-      "UPDATE ottoRequest SET status=7 WHERE id=${id};" hgcentraltest
+  /cluster/bin/x86_64/${hgSql} -N -e \
+      "UPDATE ottoRequest SET status=7 WHERE id=${id};" "${centDb}"
 }
 
 ############################################################################
 # genarkLookup - query genark table for accession, asmName, clade
 #   arg: gcAccession (e.g. GCF_000002285.3)
 #   sets: _acc, _asmName, _clade
 ############################################################################
 function genarkLookup() {
   local acc=$1
-  local result=$(/cluster/bin/x86_64/hgsql -N -e \
+  local result=$(/cluster/bin/x86_64/${hgSql} -N -e \
     "SELECT gcAccession,asmName,clade from genark WHERE gcAccession='${acc}';" \
-    hgcentraltest)
+    ${centDb})
   if [ -z "${result}" ]; then
-    printf "ERROR: accession '%s' not found in hgcentraltest.genark\n" "${acc}" 1>&2
+    printf "ERROR: accession '%s' not found in ${centDb}.genark\n" "${acc}" 1>&2
     setErrorStatus ${requestId}
     return 1
   fi
   _acc=$(printf "%s" "${result}" | cut -f1)
   _asmName=$(printf "%s" "${result}" | cut -f2)
   _clade=$(printf "%s" "${result}" | cut -f3)
 }
 
 ############################################################################
 # dbDbCladeLookup - look up clade for a UCSC database name
 #   from dbDb.name.clade.tsv (in same directory as this script)
 #   arg: dbName (e.g. hg38, rn7)
 #   sets: _clade
 ############################################################################
 function dbDbCladeLookup() {
@@ -123,36 +125,36 @@
   /cluster/bin/x86_64/twoBitInfo "${twoBit}" stdout \
     | /cluster/bin/scripts/n50.pl stdin 2>&1 \
     | grep -A1 "^[0-9].*one half size" \
     | tail -1 \
     | awk '{print $NF}'
 }
 ############################################################################
 
 ############################################################################
 ### main() scripting begins here
 ############################################################################
 
 ############################################################################
 # step 1: look up fromDb and toDb from ottoRequest
 ############################################################################
-export ottoResult=$(/cluster/bin/x86_64/hgsql -N -e \
-  "SELECT fromDb,toDb from ottoRequest WHERE id=${requestId} AND status = 1 AND requestType = 'liftOver';" hgcentraltest)
+export ottoResult=$(/cluster/bin/x86_64/${hgSql} -N -e \
+  "SELECT fromDb,toDb from ottoRequest WHERE id=${requestId} AND status = 1 AND requestType = 'liftOver';" ${centDb})
 
 if [ -z "${ottoResult}" ]; then
   printf "ERROR: no ottoRequest row found for id=%s AND status = 1\n" "${requestId}" 1>&2
-  /cluster/bin/x86_64/hgsql -e "SELECT fromDb,toDb,status from ottoRequest WHERE id=${requestId};" hgcentraltest 1>&2
+  /cluster/bin/x86_64/${hgSql} -e "SELECT fromDb,toDb,status from ottoRequest WHERE id=${requestId};" "${centDb}" 1>&2
   exit 255
 fi
 
 export fromDb=$(printf "%s" "${ottoResult}" | cut -f1)
 export toDb=$(printf "%s" "${ottoResult}" | cut -f2)
 
 if [ -z "${fromDb}" -o -z "${toDb}" ]; then
   printf "ERROR: empty fromDb or toDb for ottoRequest id=%s\n" "${requestId}" 1>&2
   printf "  got: fromDb='%s' toDb='%s'\n" "${fromDb}" "${toDb}" 1>&2
   setErrorStatus ${requestId}
   exit 255
 fi
 
 # printf "# ottoRequest id=%s: fromDb='%s' toDb='%s'\n" \
 #   "${requestId}" "${fromDb}" "${toDb}" 1>&2
@@ -251,31 +253,31 @@
     ;;
 esac
 
 # reuse existing build directory if one is already in progress
 working=$(ls -d ${targetExists}/lastz${Query}.* 2> /dev/null | wc -l || true)
 if [ "${working}" -gt 0 ]; then
   buildDir=$(ls -d ${targetExists}/lastz${Query}.* | tail -1)
 # printf "# existing buildDir: %s\n" "${buildDir}" 1>&2
 fi
 
 mkdir -p  "${buildDir}"
 
 # printf "# buildDir: %s\n" "${buildDir}" 1>&2
 
 # store buildDir in ottoRequest table for workflowMonitor.sh
-/cluster/bin/x86_64/hgsql -N -e \
+/cluster/bin/x86_64/${hgSql} -N -e \
   "UPDATE ottoRequest SET buildDir='${buildDir}', status=2 WHERE id=${requestId};" \
-  hgcentraltest
+  "${centDb}"
 
 ############################################################################
 # step 5: map clades and build the kegAlignLastz.sh command
 ############################################################################
 export fromCladeArg=$(cladeMap "${fromClade}")
 export toCladeArg=$(cladeMap "${toClade}")
 
 export cmd="${scriptDir}/kegAlignLastz.sh ${fromId} ${toId} ${fromCladeArg} ${toCladeArg}"
 
 # printf "# launching: %s\n" "${cmd}" 1>&2
 nohup ${cmd} > "${buildDir}/kegAlign.log" 2>&1 < /dev/null &
 # printf "# launched pid %s, log=%s/kegAlign.log\n" "$!" "${buildDir}" 1>&2
 exit 0