4165c71e12cef21e41d7042b9f8f1ba71d9cd910
hiram
  Fri Oct 18 13:29:11 2024 -0700
eliminate direct use of /scratch/tmp and instead use appropriate tmpDir function no redmine

diff --git src/hg/utils/automation/doSimpleRepeat.pl src/hg/utils/automation/doSimpleRepeat.pl
index 1fc05f4..e80e975 100755
--- src/hg/utils/automation/doSimpleRepeat.pl
+++ src/hg/utils/automation/doSimpleRepeat.pl
@@ -150,57 +150,58 @@
   my $clusterSeq = "$clusterSeqDir/$db.doSimp.2bit";
   if ($inHive) {
     $clusterSeq = "$clusterSeqDir/$db.unmasked.2bit";
   }
   $clusterSeq = "$unmaskedSeq" if ($opt_unmaskedSeq);
   my $partDir .= "$okOut[0]/$db/TrfPart";
   $partDir = "$buildDir/TrfPart" if ($opt_unmaskedSeq);
 
   my $trf409Option = "";
   my $trfCmd = "trf";
   if ($trf409 ne 0) {
      $trf409Option = "-l=$trf409";
      $trfCmd = "trf.4.09";
   }
   # Cluster job script:
+  my $tmpDir = &HgAutomate::tmpDir();
   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
 
 $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 /scratch/tmp doSimpleRepeat.cluster.XXXXXX`
+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 \\
   | sed -e "s/^>.*/>\$base/" \\
   | $clusterBin/trfBig $trf409Option -trf=$clusterBin/$trfCmd \\
-      stdin /dev/null -bedAt=\$base.bed -tempDir=/scratch/tmp
+      stdin /dev/null -bedAt=\$base.bed -tempDir=$tmpDir
 end
 
 # Due to the large chunk size, .lft files can have thousands of lines.
 # Even though the liftUp code does &lineFileClose, somehow we still
 # run out of filehandles.  So limit the size of liftSpecs:
 split -a 3 -d -l 500 \$inLft SplitLft.
 
 # Lift up:
 foreach splitLft (SplitLft.*)
   set bedFiles = `awk '{print \$2 ".bed"};' \$splitLft`
   endsInLf -zeroOk \$bedFiles
   set lineCount=`cat \$bedFiles | wc -l`
   if (\$lineCount > 0) then
     cat \$bedFiles \\
       | liftUp -type=.bed tmpOut.\$splitLft \$splitLft error stdin
@@ -284,35 +285,36 @@
 sub doSingle {
   my $runDir = "$buildDir";
   &HgAutomate::mustMkdir($runDir);
 
   my $workhorse = &HgAutomate::chooseWorkhorse();
   my $whatItDoes = "It runs trfBig on the entire (small) genome in one pass.";
   my $bossScript = new HgRemoteScript("$runDir/doTrf.csh", $workhorse,
 				      $runDir, $whatItDoes);
 
   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
 twoBitToFa $unmaskedSeq stdout \\
 | $clusterBin/trfBig $trf409Option -trf=$clusterBin/$trfCmd \\
-      stdin /dev/null -bedAt=simpleRepeat.bed -tempDir=/scratch/tmp
+      stdin /dev/null -bedAt=simpleRepeat.bed -tempDir=$tmpDir
 _EOF_
   );
   $bossScript->execute();
 } # doSingle
 
 sub doTrf {
   if ($useCluster) {
     &doCluster();
   } else {
     &doSingle();
   }
 } # doTrf
 
 
 #########################################################################