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/doCpgIslands.pl src/hg/utils/automation/doCpgIslands.pl
index 78819b2..d621312 100755
--- src/hg/utils/automation/doCpgIslands.pl
+++ src/hg/utils/automation/doCpgIslands.pl
@@ -165,40 +165,32 @@
 export result=\$2
 twoBitToFa \$part2bit stdout | /hive/data/staging/data/cpgIslandExt/cpglh /dev/stdin > \$result
 _EOF_
     ;
     close($fh);
 
     my $fh = &HgAutomate::mustOpen(">$runDir/oneSplit.bash");
     print $fh <<_EOF_
 #!/bin/bash
 set -beEu -o pipefail
 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
 
 export tmpFile=`mktemp -p \$TMPDIR doCpg.\$\$.XXXXX`
 export chromSizes=$chromSizes
 export fileSpec="\${1}"
 export file=`echo \$fileSpec | cut -d':' -f1`
 export seq=`echo \$fileSpec | cut -d':' -f2`
 export range=`echo \$fileSpec | cut -d':' -f3`
 export start=`echo \$range | cut -d'-' -f1`
 export end=`echo \$range | cut -d'-' -f2`
 export seqSize=`grep -w "\${seq}" \$chromSizes | awk '{print \$2}'`
 
 twoBitToFa \$fileSpec stdout | maskOutFa stdin hard stdout | /hive/data/staging/data/cpgIslandExt/cpglh \\
    /dev/stdin | sed -e "s/\\t /\\t/g;" > "\${tmpFile}"
 printf "%d\\t%s:%d-%d\\t%d\\t%s\\t%d\\n" "\${start}" "\${seq}"  "\${start}" "\${end}" "\${seqSize}" "\${seq}" "\${seqSize}" \\
   | liftUp -type=.bed results/\${seq}:\${start}-\${end}.cpg stdin error "\${tmpFile}"