3a85cb72b4b01663b80635ce8c7196100627d188
hiram
  Thu Apr 30 23:49:28 2026 -0700
cron jobs expose PATH issues refs #31811

diff --git src/hg/utils/otto/userRequests/kegAlignLastz.sh src/hg/utils/otto/userRequests/kegAlignLastz.sh
index 5002da20730..d71cbf51d5a 100755
--- src/hg/utils/otto/userRequests/kegAlignLastz.sh
+++ src/hg/utils/otto/userRequests/kegAlignLastz.sh
@@ -118,31 +118,31 @@
   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:" ${asmRpt} | tr -d '\r' | sed -e 's/.*(//; s/).*//'`
        ;;
      *)
-       oName=`hgsql -N -e "select organism from dbDb where name=\"${asmName}\";" hgcentraltest`
+       oName=`/cluster/bin/x86_64/hgsql -N -e "select organism from dbDb where name=\"${asmName}\";" hgcentraltest`
        ;;
   esac
   printf "%s" "${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}"
        ;;
      *)
@@ -161,31 +161,31 @@
        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
 #   returns 0 if found, 1 if not found
 function verifyGenark() {
   local asmAccession=$1
   local fullName=$2
-  local count=$(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='${asmAccession}';" hgcentraltest)
   if [ "$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="$3"
@@ -596,36 +596,36 @@
 export queryDb=\"${qAccId}\"
 export QueryDb=\"${Query}\"
 export Target=\"${Target}\"
 export tSizes=\"${targetSizes}\"
 export qSizes=\"${querySizes}\"
 
 ############################################################################
 # chainBigBedFb - convert chain to bigBed and compute featureBits
 # args: db chainName chainGz sizesFile fbFile
 function chainBigBedFb() {
   local db=\$1
   local chainName=\$2
   local chainGz=\$3
   local sizesFile=\$4
   local fbFile=\$5
-  chainToBigChain \"\${chainGz}\" \${chainName}.tab \${chainName}Link.tab
-  bedToBigBed -type=bed6+6 -as=\$HOME/kent/src/hg/lib/bigChain.as -tab \${chainName}.tab \${sizesFile} \${chainName}.bb
-  bedToBigBed -type=bed4+1 -as=\$HOME/kent/src/hg/lib/bigLink.as -tab \${chainName}Link.tab \${sizesFile} \${chainName}Link.bb
+  /cluster/bin/x86_64/chainToBigChain \"\${chainGz}\" \${chainName}.tab \${chainName}Link.tab
+  /cluster/bin/x86_64/bedToBigBed -type=bed6+6 -as=\$HOME/kent/src/hg/lib/bigChain.as -tab \${chainName}.tab \${sizesFile} \${chainName}.bb
+  /cluster/bin/x86_64/bedToBigBed -type=bed4+1 -as=\$HOME/kent/src/hg/lib/bigLink.as -tab \${chainName}Link.tab \${sizesFile} \${chainName}Link.bb
   rm -f \${chainName}.tab \${chainName}Link.tab chain.tab link.tab
-  local totalBases=\`ave -col=2 \${sizesFile} | grep \"^total\" | awk '{printf \"%%d\", \$2}'\`
-  local basesCovered=\`bigBedInfo \${chainName}Link.bb | grep \"basesCovered\" | cut -d' ' -f2 | tr -d ','\`
+  local totalBases=\`/cluster/bin/x86_64/ave -col=2 \${sizesFile} | grep \"^total\" | awk '{printf \"%%d\", \$2}'\`
+  local basesCovered=\`/cluster/bin/x86_64/bigBedInfo \${chainName}Link.bb | grep \"basesCovered\" | cut -d' ' -f2 | tr -d ','\`
   local percentCovered=\`echo \${basesCovered} \${totalBases} | awk '{printf \"%%.3f\", 100.0*\$1/\$2}'\`
   printf \"%%d bases of %%d (%%s%%) in intersection\\\n\" \"\${basesCovered}\" \"\${totalBases}\" \"\${percentCovered}\" > \${fbFile}
 }
 ############################################################################
 
 cd \${buildDir}
 mkdir -p log
 export DS=\`date \"+%%F_%%T_%%s\"\`
 if [ -s pendingInvocationId.txt ]; then
   DS=\`cut -f1 pendingInvocationId.txt\`
 fi
 export logDir=\"\${buildDir}/log\"
 export logFile=\"\${logDir}/\${DS}.log\"
 ### only try to submit if the workflow has not already been submitted
 if [ ! -s \"pendingInvocationId.txt\" ]; then