2df91f181b1639297e87adfaee146fedcebd2f4a
hiram
  Mon Oct 21 13:53:37 2024 -0700
now using hgwdev cluster for lastz runs and lastz only needs 3gb memory to run refs #34688

diff --git src/hg/utils/automation/pairLastz.sh src/hg/utils/automation/pairLastz.sh
index 0c05ca4..c7bd906 100755
--- src/hg/utils/automation/pairLastz.sh
+++ src/hg/utils/automation/pairLastz.sh
@@ -1,21 +1,23 @@
 #!/bin/bash
 
 set -beEu -o pipefail
 
 export userName="`whoami`"
 
+export bigHub="hgwdev"
+
 if [ $# != 4 ]; then
   printf "ERROR: arg count: %d != 4\n" "$#" 1>&2
 
   printf "usage: pairLastz.sh <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
 
 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
@@ -423,31 +425,31 @@
 ### setup the DEF file
 printf "%s" "${defString}" > ${buildDir}/DEF
 
 ### setup the buildDir/run.sh script
 printf "#!/bin/bash
 
 set -beEu -o pipefail
 
 export targetDb=\"${tAsmId}\"
 export queryDb=\"${qAsmId}\"
 export QueryDb=\"${Query}\"
 
 cd ${buildDir}
 time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl ${trackHub} -verbose=2 \`pwd\`/DEF -syntenicNet \\
   $tFullName $qFullName -workhorse=hgwdev -smallClusterHub=hgwdev \\
-    -bigClusterHub=ku \\
+    -bigClusterHub=$bigHub \\
     -chainMinScore=${minScore} -chainLinearGap=${linearGap}) > do.log 2>&1
 
 grep -w real do.log | sed -e 's/^/    # /;'
 
 sed -e 's/^/    # /;' fb.\${targetDb}.chain\${QueryDb}Link.txt
 sed -e 's/^/    # /;' fb.\${targetDb}.chainSyn\${QueryDb}Link.txt
 
 time (~/kent/src/hg/utils/automation/doRecipBest.pl ${rBestTrackHub} -load -workhorse=hgwdev -buildDir=\`pwd\` \\
    ${tRbestArgs} \\
    ${qRbestArgs} \\
    \${targetDb} \${queryDb}) > rbest.log 2>&1
 
 grep -w real rbest.log | sed -e 's/^/    # /;'
 
 sed -e 's/^/    #/;' fb.\${targetDb}.chainRBest.\${QueryDb}.txt
@@ -469,31 +471,31 @@
 fi      ###     if [ $primaryDone -eq 0 ]; then
 
 #### print out the makeDoc.txt to this point into buildDir/makeDoc.txt
 
 printf "##############################################################################
 # LASTZ ${tOrgName} ${Target} vs. $qOrgName ${Query}
 #    (DONE - $DS - $userName)
 
     mkdir $buildDir
     cd $buildDir
 
     printf '${defString}
 ' > DEF
 
     time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl ${trackHub} -verbose=2 \`pwd\`/DEF -syntenicNet \\
-      ${tFullName} ${qFullName} -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \\
+      ${tFullName} ${qFullName} -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=$bigHub \\
         -chainMinScore=${minScore} -chainLinearGap=${linearGap}) > do.log 2>&1
     grep -w real do.log | sed -e 's/^/    # /;'
 " > ${buildDir}/makeDoc.txt
 
 (grep -w real $buildDir/do.log || true) | sed -e 's/^/    # /;' | head -1 >> ${buildDir}/makeDoc.txt
 
 printf "\n    sed -e 's/^/    # /;' fb.${tAsmId}.chain${Query}Link.txt\n" >> ${buildDir}/makeDoc.txt
 sed -e 's/^/    # /;' $buildDir/fb.${tAsmId}.chain${Query}Link.txt >> ${buildDir}/makeDoc.txt
 
 printf "    sed -e 's/^/    # /;' fb.${tAsmId}.chainSyn${Query}Link.txt\n" >> ${buildDir}/makeDoc.txt
 sed -e 's/^/    # /;' $buildDir/fb.${tAsmId}.chainSyn${Query}Link.txt >> ${buildDir}/makeDoc.txt
 
 printf "\n    time (~/kent/src/hg/utils/automation/doRecipBest.pl ${rBestTrackHub} -load -workhorse=hgwdev -buildDir=\`pwd\` \\
       ${tRbestArgs} \\
       ${qRbestArgs} \\
@@ -518,31 +520,31 @@
 ln -s ${buildDir}/DEF ${swapDir}/DEF
 
 printf "#!/bin/bash
 
 set -beEu -o pipefail
 
 cd $swapDir
 
 export targetDb=\"${tAsmId}\"
 export Target=\"${Target}\"
 export Qarget=\"${Query}\"
 export queryDb=\"${qAsmId}\"
 
 time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl ${trackHub}  -swap -verbose=2 \\
   ${tFullName} ${qFullName} ${buildDir}/DEF -swapDir=\`pwd\` \\
-  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \\
+  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=$bigHub \\
     -chainMinScore=${minScore} -chainLinearGap=${linearGap}) > swap.log 2>&1
 
 grep -w real swap.log | sed -e 's/^/    # /;'
 
 sed -e 's/^/    # /;' fb.\${queryDb}.chain\${Target}Link.txt
 sed -e 's/^/    # /;' fb.\${queryDb}.chainSyn\${Target}Link.txt
 time (~/kent/src/hg/utils/automation/doRecipBest.pl ${rBestTrackHub} -load -workhorse=hgwdev -buildDir=\`pwd\` \\
    ${tSwapRbestArgs} \\
    ${qSwapRbestArgs} \\
    \${queryDb} \${targetDb}) > rbest.log 2>&1
 
 grep -w real rbest.log | sed -e 's/^/    # /;'
 
 sed -e 's/^/    # /;' fb.\${queryDb}.chainRBest.\${Target}.txt
 " > ${swapDir}/runSwap.sh
@@ -556,31 +558,31 @@
 # rebuild trackDb if possible here
 if [ -x "${qTdb}" ]; then
    ${qTdb}
 else
    printf "# do not find qTdb '%s'\n" "${qTdb}" 1>&2
 fi
 
 fi      ### if [ "$swapDone" -eq 0 ]; then
 
 ### continue the make doc
 
 printf "\n    cd ${swapDir}\n" >> ${buildDir}/makeDoc.txt
 
 printf "\n   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl ${trackHub} -swap -verbose=2 \\
   ${tFullName} ${qFullName} ${buildDir}/DEF -swapDir=\`pwd\` \\
-  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \\
+  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=$bigHub \\
     -chainMinScore=${minScore} -chainLinearGap=${linearGap}) > swap.log 2>&1
 
     grep -w real swap.log | sed -e 's/^/    # /;'
 " >> ${buildDir}/makeDoc.txt
 
 (grep -w real ${swapDir}/swap.log || true) | sed -e 's/^/    # /;' >> ${buildDir}/makeDoc.txt
 
 printf "\n    sed -e 's/^/    # /;' fb.${qAsmId}.chain${Target}Link.txt\n" >> ${buildDir}/makeDoc.txt
 sed -e 's/^/    # /;' ${swapDir}/fb.${qAsmId}.chain${Target}Link.txt >> ${buildDir}/makeDoc.txt
 
 printf "    sed -e 's/^/    # /;' fb.${qAsmId}.chainSyn${Target}Link.txt\n" >> ${buildDir}/makeDoc.txt
 sed -e 's/^/    # /;' ${swapDir}/fb.${qAsmId}.chainSyn${Target}Link.txt >> ${buildDir}/makeDoc.txt
 
 printf "\    time (~/kent/src/hg/utils/automation/doRecipBest.pl ${rBestTrackHub} -load -workhorse=hgwdev -buildDir=\`pwd\` \\
    ${tSwapRbestArgs} \\