e69db257480ddc4aae24ca6ae0130c9450abc362
hiram
  Mon Oct 28 14:07:47 2024 -0700
do not use /dev/shm as a temporary directory refs #34685

diff --git src/hg/utils/automation/doRepeatMasker.pl src/hg/utils/automation/doRepeatMasker.pl
index 3c1afdd..c09eafb 100755
--- src/hg/utils/automation/doRepeatMasker.pl
+++ src/hg/utils/automation/doRepeatMasker.pl
@@ -234,40 +234,32 @@
 _EOF_
   ;
   close($fh);
 
   my $tmpDir = &HgAutomate::tmpDir();
   # Cluster job script:
   $fh = &HgAutomate::mustOpen(">$runDir/RMRun.csh");
   print $fh <<_EOF_
 #!/bin/csh -ef
 
 if ( -d "/data/tmp" ) then
   setenv TMPDIR "/data/tmp"
 else if ( -d "/scratch/tmp" ) then
   setenv TMPDIR "/scratch/tmp"
 else
-  set tmpSz = `df --output=avail -k /tmp | tail -1`
-  set shmSz = `df --output=avail -k /dev/shm | tail -1`
-  if ( "\${shmSz}" > "\${tmpSz}" ) then
-     mkdir -p /dev/shm/tmp
-     chmod 777 /dev/shm/tmp
-     setenv TMPDIR "/dev/shm/tmp"
-  else
   setenv TMPDIR "/tmp"
 endif
-endif
 set path = (/cluster/software/bin \$path)
 
 set finalOut = \$1
 
 set inLst = \$finalOut:r
 set inLft = \$inLst:r.lft
 set alignOut = \$finalOut:r.align
 set catOut = \$finalOut:r.cat
 
 # Use local disk for output, and move the final result to \$outPsl
 # when done, to minimize I/O.
 set tmpDir = `mktemp -d -p \$TMPDIR doRepeatMasker.cluster.XXXXXX`
 pushd \$tmpDir
 
 # Initialize local library