d7fec1a55508e24c02bb2754c42baaad1d3c8394 hiram Thu Apr 30 10:12:42 2026 -0700 remove all the cruft from pairLastz.sh copy, not needed here refs #31811 diff --git src/hg/utils/otto/userRequests/kegAlignLastz.sh src/hg/utils/otto/userRequests/kegAlignLastz.sh index 274881974c0..b6a516901b3 100755 --- src/hg/utils/otto/userRequests/kegAlignLastz.sh +++ src/hg/utils/otto/userRequests/kegAlignLastz.sh @@ -641,202 +641,16 @@ printf \"invocation ID: %%s\\n\" \"\${invocationId}\" 1>&2 # record the invocation ID and associated log file for monitoring cron printf \"%%s\\t%%s\\t%%s\\n\" \"\${DS}\" \"\${invocationId}\" \"\${logDir}/runOutput.\${DS}.json\" > pendingInvocationId.txt fi printf \"### workflow submitted, invocation ID in: %%s/pendingInvocationId.txt\\n\" \"\${buildDir}\" 1>&2 " > ${buildDir}/kegAlign.sh chmod +x ${buildDir}/kegAlign.sh ### run the primary alignment, galaxy kegAlign style printf "running: time (${buildDir}/kegAlign.sh) >> ${buildDir}/kegAlign.log 2>&1\n" 1>&2 time (${buildDir}/kegAlign.sh) >> ${buildDir}/keg.log 2>&1 -### run the primary alignment, UCSC lastz style -printf "running: time (${buildDir}/lastzRun.sh) >> ${buildDir}/lastzRun.log 2>&1\n" 1>&2 - -# time (${buildDir}/lastzRun.sh) >> ${buildDir}/lastzRun.log 2>&1 - - -exit $? - -### typical contents of the invocation_download: -### ls result/2026-04-02_16:00:02_1775170802 -### 'Batched LASTZ on dataset 5__70a08f89-a77d-4333-b425-b13959e40d1b.axt' -### 'KegAlign on dataset 3 and 4__a32df3e9-13d0-4c5e-b765-df69c657ae89.tgz' -### allChainSwap__5e11f323-58fc-43f9-afbd-6cff21f0e7af.chain -### allChain__74038a6d-d735-4784-8b17-31a25ddbb036.chain -###'netChainSubset on dataset 8 and 22__72cbd3a9-4136-4e72-86c9-9da0c230c5d0.chain' -###'netChainSubset on dataset 9 and 36__9acc344f-19da-4ef9-a578-7282940badc0.chain' - -# rebuild trackDb if possible here -if [ -x "${tTdb}" ]; then - ${tTdb} -else - printf "# do not find tTdb '%s'\n" "${tTdb}" 1>&2 -fi - -fi ### if [ $primaryDone -eq 0 ]; then - exit $? - -#### print out the makeDoc.txt to this point into buildDir/makeDoc.txt - -printf "############################################################################## -# kegAlign LASTZ ${tOrgName} ${Target} vs. $qOrgName ${Query} -# (DONE - $DS - $userName) - - mkdir $buildDir - cd $buildDir - - printf '${yamlString} -' > DEF - - time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl ${trackHub} -verbose=2 \`pwd\`/DEF -syntenicNet \\ - ${tFullName} ${qFullName} -workhorse=${workHorse} -smallClusterHub=${smallClusterHub} -fileServer=${fileServer} -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 >> ${buildDir}/makeDoc.txt - -printf "\n sed -e 's/^/ # /;' fb.${tAccId}.chain${Query}Link.txt\n" >> ${buildDir}/makeDoc.txt -sed -e 's/^/ # /;' $buildDir/fb.${tAccId}.chain${Query}Link.txt >> ${buildDir}/makeDoc.txt - -printf " sed -e 's/^/ # /;' fb.${tAccId}.chainSyn${Query}Link.txt\n" >> ${buildDir}/makeDoc.txt -sed -e 's/^/ # /;' $buildDir/fb.${tAccId}.chainSyn${Query}Link.txt >> ${buildDir}/makeDoc.txt - -printf "\n time (~/kent/src/hg/utils/automation/doRecipBest.pl ${rBestTrackHub} -load -workhorse=${workHorse} -buildDir=\`pwd\` \\ - ${tRbestArgs} \\ - ${qRbestArgs} \\ - ${tAccId} ${qAccId}) > rbest.log 2>&1 - - grep -w real rbest.log | sed -e 's/^/ # /;'\n" >> ${buildDir}/makeDoc.txt - -(grep -w real $buildDir/rbest.log || true) | sed -e 's/^/ # /;' >> ${buildDir}/makeDoc.txt - -printf "\n sed -e 's/^/ # /;' fb.${tAccId}.chainRBest.${Query}.txt\n" >> ${buildDir}/makeDoc.txt -(sed -e 's/^/ # /;' ${buildDir}/fb.${tAccId}.chainRBest.${Query}.txt || true) >> ${buildDir}/makeDoc.txt - -printf "\n ### and for the swap\n" >> ${buildDir}/makeDoc.txt - -cat ${buildDir}/makeDoc.txt - -printf "# swap into: ${swapDir}\n" 1>&2 - -if [ "$swapDone" -eq 0 ]; then -mkdir ${swapDir} - -ln -s ${buildDir}/DEF ${swapDir}/DEF - -printf "#!/bin/bash - -set -beEu -o pipefail - -cd $swapDir - -export targetDb=\"${tAccId}\" -export Target=\"${Target}\" -export queryDb=\"${qAccId}\" - -time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl ${trackHub} -swap -verbose=2 \\ - ${tFullName} ${qFullName} ${buildDir}/DEF -swapDir=\`pwd\` \\ - -syntenicNet -workhorse=${workHorse} -smallClusterHub=${smallClusterHub} -fileServer=${fileServer} -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 ${rBestTrackHub} -load -workhorse=${workHorse} -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 - -chmod +x ${swapDir}/runSwap.sh - -printf "# running ${swapDir}/runSwap.sh\n" 1>&2 - -time (${swapDir}/runSwap.sh) >> ${swapDir}/doSwap.log 2>&1 - -# rebuild trackDb if possible here -if [ -x "${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} ${buildDir}/DEF -swapDir=\`pwd\` \\ - -syntenicNet -workhorse=${workHorse} -smallClusterHub=${smallClusterHub} -fileServer=${fileServer} -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/^/ # /;' >> ${buildDir}/makeDoc.txt - -printf "\n sed -e 's/^/ # /;' fb.${qAccId}.chain${Target}Link.txt\n" >> ${buildDir}/makeDoc.txt -sed -e 's/^/ # /;' ${swapDir}/fb.${qAccId}.chain${Target}Link.txt >> ${buildDir}/makeDoc.txt - -printf " sed -e 's/^/ # /;' fb.${qAccId}.chainSyn${Target}Link.txt\n" >> ${buildDir}/makeDoc.txt -sed -e 's/^/ # /;' ${swapDir}/fb.${qAccId}.chainSyn${Target}Link.txt >> ${buildDir}/makeDoc.txt - -printf "\ time (~/kent/src/hg/utils/automation/doRecipBest.pl ${rBestTrackHub} -load -workhorse=${workHorse} -buildDir=\`pwd\` \\ - ${tSwapRbestArgs} \\ - ${qSwapRbestArgs} \\ - ${qAccId} ${tAccId}) > rbest.log 2>&1 - - grep -w real rbest.log | sed -e 's/^/ # /;'\n" >> ${buildDir}/makeDoc.txt -(grep -w real ${swapDir}/rbest.log || true) | sed -e 's/^/ # /;' >> ${buildDir}/makeDoc.txt -printf "\n sed -e 's/^/ # /;' fb.${qAccId}.chainRBest.${Target}.txt\n" >> ${buildDir}/makeDoc.txt -(sed -e 's/^/ # /;' ${swapDir}/fb.${qAccId}.chainRBest.${Target}.txt || true) >> ${buildDir}/makeDoc.txt - -printf "\n##############################################################################\n" >> ${buildDir}/makeDoc.txt - -### show completed makeDoc.txt #### -cat ${buildDir}/makeDoc.txt - -### end seconds -export endT=`date "+%s"` - -export toAddress="$userName" -export fromAddress="$userName" -export subject="kegAlign lastz DONE $target $query" -printf "To: $toAddress -From: $fromAddress -Subject: $subject - -################################################################## -" > /tmp/send.txt.$$ -date >> /tmp/send.txt.$$ -printf "##################################################################\n" >> /tmp/send.txt.$$ -cat ${buildDir}/makeDoc.txt >> /tmp/send.txt.$$ - -### show elapsed time -printf "%s\t%s\n" "${endT}" "${startT}" | awk -F$'\t' '{ -seconds=$1-$2 -hours=int(seconds/3600) -minutes=int((seconds-(hours*3600))/60) -s=seconds % 60 -printf "### elapsed time: %02dh %02dm %02ds\n\n", hours, minutes, s -}' >> /tmp/send.txt.$$ - -date >> /tmp/send.txt.$$ -printf "##################################################################\n" >> /tmp/send.txt.$$ - -cat /tmp/send.txt.$$ | /usr/sbin/sendmail -t -oi - -rm -f /tmp/send.txt.$$