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/doBlastzChainNet.pl src/hg/utils/automation/doBlastzChainNet.pl
index 96efc7c..5630072 100755
--- src/hg/utils/automation/doBlastzChainNet.pl
+++ src/hg/utils/automation/doBlastzChainNet.pl
@@ -1662,40 +1662,32 @@
 mkdir -p $gbdbLiftOverDir
 rm -f $gbdbLiftOverDir/$over
 ln -s $liftOverDir/$over $gbdbLiftOverDir/$over
 hgAddLiftOverChain -minMatch=0.1 -multiple -path=$gbdbLiftOverDir/$over \\
   $tDb $qDb
 _EOF_
       );
     }
 
     $bossScript->add(<<_EOF_
 if [ -d "/data/tmp" ]; then
   export TMPDIR="/data/tmp"
 elif [ -d "/scratch/tmp" ]; then
   export TMPDIR="/scratch/tmp"
 else
-  tmpSz=`df --output=avail -k /tmp | tail -1`
-  shmSz=`df --output=avail -k /dev/shm | tail -1`
-  if [ "\${shmSz}" -gt "\${tmpSz}" ]; then
-     mkdir -p /dev/shm/tmp
-     chmod 777 /dev/shm/tmp
-     export TMPDIR="/dev/shm/tmp"
-  else
   export TMPDIR="/tmp"
 fi
-fi
 # Update (or create) liftOver/md5sum.txt with the new .over.chain.gz.
 if (-e $gpLiftOverDir/md5sum.txt) then
   set tmpFile = `mktemp -t tmpMd5.XXXXXX`
   csh -c "grep -v $over $gpLiftOverDir/md5sum.txt || true" > \$tmpFile
   md5sum $gpLiftOverDir/$over \\
   | sed -e 's\@$gpLiftOverDir/\@\@' >> \$tmpFile
   sort \$tmpFile > $gpLiftOverDir/md5sum.txt
   rm \$tmpFile
 else
   md5sum $gpLiftOverDir/$over | sed -e 's\@$gpLiftOverDir/\@\@' \\
 	> $gpLiftOverDir/md5sum.txt
 endif
 _EOF_
       );
   }