f0f02218613a6cce438e7ce73694f7539587118d
hiram
  Mon Jan 2 09:33:12 2023 -0800
preserve the do.log during the rsync no redmine

diff --git src/hg/utils/automation/doRepeatModeler.pl src/hg/utils/automation/doRepeatModeler.pl
index 948b453..e956cac 100755
--- src/hg/utils/automation/doRepeatModeler.pl
+++ src/hg/utils/automation/doRepeatModeler.pl
@@ -183,38 +183,38 @@
 
   my $whatItDoes =
 "runs single cluster job to perform the RepeatModeler process.";
 
   my $bossScript = newBash HgRemoteScript("$runDir/doCluster.bash", $paraHub,
 				      $runDir, $whatItDoes);
   $bossScript->add(<<_EOF_
 printf '#!/bin/bash
 
 set -beEu -o pipefail
 
 export tmpDir=`mktemp -d -p /dev/shm rModeler.XXXXXX`
 
 # working directory
 cd "\${tmpDir}"
-rsync -a -P "${runDir}/" "\${tmpDir}/"
+rsync --exclude "do.log" -a -P "${runDir}/" "\${tmpDir}/"
 
 export asmId="\${1}"
 export threadCount="${threadCount}"
 export rModeler="${RepeatModeler}"
 
 time (\$rModeler -engine ncbi \$threadCount -database "\${asmId}") > modeler.log 2>&1
-rsync -a -P ./ "${runDir}/"
+rsync --exclude "do.log" -a -P ./ "${runDir}/"
 cd "${runDir}"
 rm -fr "\${tmpDir}/"
 chmod 775 "${runDir}"
 ' > oneJob
 chmod +x oneJob
 printf "oneJob ${db} {check out line+ ${db}-rmod.log}\n" > jobList
 para make $parasolOpts jobList
 para check
 para time > run.time
 cat run.time
 
 _EOF_
   );
   $bossScript->execute() if (! $opt_debug);
 } # doCluster