7b95c46185395e1500ab3a56bd185a11be4b9517
hiram
  Wed Oct 30 21:17:55 2024 -0700
not a good idea to use /tmp/ for the simple repeat - that filesystem is way too small for the long running hippos refs #34685

diff --git src/hg/utils/automation/doSimpleRepeat.pl src/hg/utils/automation/doSimpleRepeat.pl
index 8e82288..6677cc0 100755
--- src/hg/utils/automation/doSimpleRepeat.pl
+++ src/hg/utils/automation/doSimpleRepeat.pl
@@ -169,32 +169,40 @@
   my $fh = &HgAutomate::mustOpen(">$runDir/TrfRun.csh");
   print $fh <<_EOF_
 #!/bin/csh -ef
 
 set finalOut = \$1
 
 set inLst = \$finalOut:r
 set inLft = \$inLst:r.lft
 
 unsetenv TMPDIR
 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
 $HgAutomate::setMachtype
 
 # Use local disk for output, and move the final result to \$finalOut
 # when done, to minimize I/O.
 set tmpDir = `mktemp -d -p \$TMPDIR doSimpleRepeat.cluster.XXXXXX`
 pushd \$tmpDir
 
 foreach spec (`cat \$inLst`)
   # Remove path and .2bit filename to get just the seq:start-end spec:
   set base = `echo \$spec | sed -r -e 's/^[^:]+://'`
 
   # If \$spec is the whole sequence, twoBitToFa removes the :start-end part,
   # which causes liftUp to barf later.  So tweak the header back to
   # seq:start-end for liftUp's sake:
   twoBitToFa \$spec stdout \\
@@ -305,32 +313,40 @@
   my $trf409Option = "";
   my $trfCmd = "trf";
   if ($trf409 ne 0) {
      $trf409Option = "-l=$trf409";
      $trfCmd = "trf.4.09";
   }
   my $tmpDir = &HgAutomate::tmpDir();
   $bossScript->add(<<_EOF_
 $HgAutomate::setMachtype
 unsetenv TMPDIR
 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
 twoBitToFa $unmaskedSeq stdout \\
 | $clusterBin/trfBig $trf409Option -trf=$clusterBin/$trfCmd \\
       stdin /dev/null -bedAt=simpleRepeat.bed -tempDir=\$TMPDIR
 _EOF_
   );
   $bossScript->execute();
 } # doSingle
 
 sub doTrf {
   if ($useCluster) {
     &doCluster();
   } else {
     &doSingle();
   }
 } # doTrf