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/doWindowMasker.pl src/hg/utils/automation/doWindowMasker.pl
index c980898..b946726 100755
--- src/hg/utils/automation/doWindowMasker.pl
+++ src/hg/utils/automation/doWindowMasker.pl
@@ -111,40 +111,32 @@
   &HgAutomate::checkCleanSlate('count', 'mask', "$runDir/windowmasker.counts");
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "It does WindowMasker counts step.";
   my $workhorse = &HgAutomate::chooseWorkhorse();
   my $bossScript = new HgRemoteScript("$runDir/doCount.csh", $workhorse,
 				      $runDir, $whatItDoes);
 
   my $tmpDir = &HgAutomate::tmpDir();
   $bossScript->add(<<_EOF_
 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 windowMaskerDir = /cluster/bin/\$MACHTYPE
 set windowMasker = \$windowMaskerDir/windowmasker
 set fa = $db.fa
 set tmpDir = `mktemp -d -p \$TMPDIR doWindowMasker.XXXXXX`
 chmod 775 \$tmpDir
 set inputTwoBit = $unmaskedSeq
 pushd \$tmpDir
 twoBitToFa \$inputTwoBit \$fa
 \$windowMasker -mk_counts true -input \$fa -output windowmasker.counts
 popd
 cp \$tmpDir/windowmasker.counts .
 rm -rf \$tmpDir
 _EOF_
   );
   $bossScript->execute();
@@ -162,40 +154,32 @@
 # * step: sdust [workhorse]
 sub doSdust {
   my $runDir = "$buildDir";
   &HgAutomate::checkExistsUnlessDebug('mask', 'sdust', "$runDir/windowmasker.counts");
   my $whatItDoes = "It does WindowMasker masking step with -sdust true.";
   my $workhorse = &HgAutomate::chooseWorkhorse();
   my $bossScript = new HgRemoteScript("$runDir/doSdust.csh", $workhorse,
 				      $runDir, $whatItDoes);
   my $tmpDir = &HgAutomate::tmpDir();
   $bossScript->add(<<_EOF_
 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 windowMaskerDir = /cluster/bin/\$MACHTYPE
 set windowMasker = \$windowMaskerDir/windowmasker
 set fa = $db.fa
 set tmpDir = `mktemp -d -p \$TMPDIR doWindowMasker.XXXXXX`
 chmod 775 \$tmpDir
 set inputTwoBit = $unmaskedSeq
 cp windowmasker.counts \$tmpDir
 pushd \$tmpDir
 twoBitToFa \$inputTwoBit \$fa
 \$windowMasker -ustat windowmasker.counts -sdust true -input \$fa -output windowmasker.intervals
 perl -wpe \'if \(s\/^\>lcl\\\|\(\.\*\)\\n\$\/\/\) { \$chr = \$1\; } \\
    if \(\/^\(\\d+\) \- \(\\d+\)\/\) { \\
    \$s=\$1\; \$e=\$2+1\; s\/\(\\d+\) \- \(\\d+\)\/\$chr\\t\$s\\t\$e\/\; \\
    }\' windowmasker.intervals > windowmasker.sdust.bed
 popd