a1790e2b1d8c1d197bb1348554322a783a9b2adf
hiram
  Thu Dec 12 13:49:09 2024 -0800
this process really wants to be on /dev/shm/ before /scratch/tmp/ refs #34370

diff --git src/hg/utils/automation/doRepeatModeler.pl src/hg/utils/automation/doRepeatModeler.pl
index d28e111..f1ee03c 100755
--- src/hg/utils/automation/doRepeatModeler.pl
+++ src/hg/utils/automation/doRepeatModeler.pl
@@ -182,34 +182,34 @@
   }
 
   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
 
 unset TMPDIR
 if [ -d "/data/tmp" ]; then
   export TMPDIR="/data/tmp"
-elif [ -d "/scratch/tmp" ]; then
-  export TMPDIR="/scratch/tmp"
 elif [ -d "/dev/shm" ]; then
   export TMPDIR="/dev/shm"
+elif [ -d "/scratch/tmp" ]; then
+  export TMPDIR="/scratch/tmp"
 else
   export TMPDIR="/tmp"
 fi
 
 export tmpDir=`mktemp -d -p \$TMPDIR rModeler.XXXXXX`
 
 # working directory
 cd "\${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