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/doSameSpeciesLiftOver.pl src/hg/utils/automation/doSameSpeciesLiftOver.pl
index ed36cff..c76c413 100755
--- src/hg/utils/automation/doSameSpeciesLiftOver.pl
+++ src/hg/utils/automation/doSameSpeciesLiftOver.pl
@@ -66,31 +66,31 @@
 ";
   print STDERR $stepper->getOptionHelp();
   print STDERR <<_EOF_
     -buildDir dir         Use dir instead of default
                           $HgAutomate::clusterData/\$fromDb/$HgAutomate::trackBuild/blat.\$toDb.\$date
                           (necessary when continuing at a later date).
     -ooc /path/11.ooc     Use this instead of the default
                           /hive/data/genomes/fromDb/11.ooc
                           Can be "none".
     -target2Bit /path/target.2bit  Full path to target sequence (fromDb)
     -query2Bit /path/query.2bit    Full path to query sequence (toDb)
     -targetSizes /path/target.chrom.sizes  Full path to target chrom.sizes (fromDb)
     -querySizes  /path/query.chrom.sizes   Full path to query chrom.sizes (toDb)
     -chainRam  Ng  Cluster ram size for chain step, default: -chainRam=$chainRam
     -chainCpu  N   Cluster CPUs number for chain step, default: -chainCpu=$chainCpu
-    -localTmp  /dev/shm  Full path to temporary storage for heavy I/O usage
+    -localTmp  /tmp  Full path to temporary storage for heavy I/O usage
 _EOF_
   ;
   print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost,
 						'workhorse' => '',
 						'fileServer' => '',
 						'ram' => $ramG,
 						'cpu' => $cpu,
 						'bigClusterHub' => '');
   print STDERR "
 Automates UCSC's same-species liftOver (blat/chain/net) pipeline, based on
 Kate's suite of makeLo-* scripts:
     align: Aligns the assemblies using blat -fastMap on a big cluster.
     chain: Chains the alignments on a big cluster.
     net:   Nets the alignments, uses netChainSubset to extract liftOver chains.
     load:  Installs liftOver chain files, calls hgAddLiftOverChain on $dbHost.
@@ -521,31 +521,31 @@
   &HgAutomate::checkExistsUnlessDebug('net', 'load',
 				      "$buildDir/$liftOverChainFile");
 
   my $whatItDoes =
 "It makes links from $HgAutomate::gbdb/ and goldenPath/ (download area) to the liftOver
 chains file, and calls hgAddLiftOverChain to register the $HgAutomate::gbdb location.";
   my $bossScript = new HgRemoteScript("$runDir/doLoad.csh", $dbHost,
 				      $runDir, $whatItDoes);
 
   if ($dbExists) {
     $bossScript->add(<<_EOF_
 # Link to standardized location of liftOver files:
 mkdir -p $liftOverChainDir
 rm -f $liftOverChainPath
 ln -s $buildDir/$liftOverChainFile $liftOverChainPath
-set tmpFile = `mktemp -t -p /dev/shm tmpMd5.XXXXXX`
+set tmpFile = `mktemp -t -p /tmp tmpMd5.XXXXXX`
 csh -c "grep -v $liftOverChainFile $liftOverChainDir/md5sum.txt || true" > \$tmpFile
 md5sum $buildDir/$liftOverChainFile | sed -e "s#$buildDir/##;" >> \$tmpFile
 sort \$tmpFile > $liftOverChainDir/md5sum.txt
 rm -f \$tmpFile
 
 # Link from download area:
 mkdir -p $HgAutomate::goldenPath/$tDb/liftOver
 rm -f $HgAutomate::goldenPath/$tDb/liftOver/$liftOverChainFile
 ln -s $liftOverChainPath $HgAutomate::goldenPath/$tDb/liftOver/
 
 # Link from genome browser fileserver:
 mkdir -p $HgAutomate::gbdb/$tDb/liftOver
 rm -f $HgAutomate::gbdb/$tDb/liftOver/$liftOverChainFile
 ln -s $liftOverChainPath $HgAutomate::gbdb/$tDb/liftOver/