78377989820616cc99f1e3aca34aca1cd27bafa2
hiram
  Fri May 8 10:00:45 2026 -0700
fortify against cron job usage full path to kent commands refs #31811

diff --git src/hg/makeDb/trackDb/maybeBuildHub src/hg/makeDb/trackDb/maybeBuildHub
index e28657383d1..21771743849 100755
--- src/hg/makeDb/trackDb/maybeBuildHub
+++ src/hg/makeDb/trackDb/maybeBuildHub
@@ -1,105 +1,105 @@
 #!/bin/bash
 
 # exit on any error
 set -beEu -o pipefail
 user=$1
 trackDb=$2
 db=$3
 
 hubParent=/gbdb/$db/hubs
 hubDir=$hubParent/$user
 
 ##############################################################################
 # check if there is an entry in dbDb for name==$db
 function hasDbDb() {
   local db="$1"
-  local dbDb=$(hgsql hgcentraltest -Ne 'select count(*) from dbDb where name ="'$db'"')
+  local dbDb=$(/cluster/bin/x86_64/hgsql hgcentraltest -Ne 'select count(*) from dbDb where name ="'$db'"')
   if [ "${dbDb}" -eq 1 ]; then
     return 0	# true: does exist
   else
     return 1	# false: does not exist
   fi
 }
 
 ##############################################################################
 # try to get the GCx accession name out of dbDb sourceName
 function acc() {
   local db="$1"
-  local src=$(hgsql hgcentraltest -Ne 'select sourceName from dbDb where name ="'$db'"')
+  local src=$(/cluster/bin/x86_64/hgsql hgcentraltest -Ne 'select sourceName from dbDb where name ="'$db'"')
   if [[ "$src" == *GC* ]]; then
     ret=`echo "${src}" | sed -e 's#.*GC#GC#;' | sed -e 's#[^ACGF0-9_.]\+##;'`
     if [ "x${ret}y" = "xy" ]; then
        printf "ERROR: can not find GCx_... accession in dbDb name=$db\n" 1>&2
        exit 255
     else
        echo $ret
     fi
   else
     printf "ERROR: can not find GCx_... accession in dbDb name=$db\n" 1>&2
     exit 255
   fi
 }
 
 ##############################################################################
 # check if a database exists, print note and return non-zero if it doesn't
 function dbExists() {
     local db="$1"
-    local dbChk=$(hgsql -Ne 'show databases like "'$db'"')
+    local dbChk=$(/cluster/bin/x86_64/hgsql -Ne 'show databases like "'$db'"')
     if [ -z "$dbChk" ] ; then
         printf "Note: database $db does not exist, skipping\n" 1>&2
         return 1
     else
         return 0
     fi
 }
 
 ##############################################################################
 ### begin main process here
 ##############################################################################
 # if the directory /gbdb/<db>/hubs does not exist, we have no business here
 if test ! -d $hubParent ; then
   exit 0
 fi
 
 # process 'hs1' and 'mpxvRivers' just like they have always been processed
 if [[ "${db}" = "hs1" || "${db}" = "mpxvRivers" ]]; then
   if dbExists $db ; then
-     trackDbToTxt $db $trackDb $hubDir
+     /cluster/bin/x86_64/trackDbToTxt $db $trackDb $hubDir
      # creates $hubDir/hubAndGenome.txt
-     dbDbToHubTxt $db genome-www@soe.ucsc.edu ../groups.txt $hubDir/hubAndGenome.txt
+     /cluster/bin/x86_64/dbDbToHubTxt $db genome-www@soe.ucsc.edu ../groups.txt $hubDir/hubAndGenome.txt
      cat $hubDir/hubAndGenome.txt $hubDir/trackDb.txt > $hubDir/hub.txt
   fi
   exit 0
 fi
 
 # maybe this is a GenArk hub becoming a curated hub
 if hasDbDb $db ; then
   gcX=`acc $db`
   oneOnly=`ls -d */${db} | wc -l`
   if [ "${oneOnly}" -eq 1 ]; then
     genArkTdb=`ls -d */${db}/genArk.trackDb.ra`
     tmpDbTxt="test.$$.trackDb.txt"
     ./hubTxtFromGenArk.pl $db $gcX "${tmpDbTxt}" > $db.hAndG.txt
     if cmp -s "${genArkTdb}" "${tmpDbTxt}" ; then
       :
     else
        printf "ERROR: need to update the $genArkTdb file\n" 1>&2
        printf "note new contents in: $tmpDbTxt\n" 1>&2
        exit 255
     fi
     rm -f "${tmpDbTxt}"
     mkdir -p $hubDir
     rm -f $hubDir/hubAndGenome.txt
     mv $db.hAndG.txt $hubDir/hubAndGenome.txt
-    trackDbToTxt $db $trackDb $hubDir
+    /cluster/bin/x86_64/trackDbToTxt $db $trackDb $hubDir
     cat $hubDir/hubAndGenome.txt $hubDir/trackDb.txt > $hubDir/hub.txt
   else
      printf "ERROR: finding multiple directories */$db ?\n" 1>&2
      ls -d */${db} 1>&2
      exit 255
   fi
 else
   exit 0
 fi
 
 exit $?