6ed25cfed02721ee6b38518c73096800f0340b40
hiram
  Fri Oct 18 13:37:51 2024 -0700
eliminate direct use of /scratch/tmp and instead use appropriate tmpDir function no redmine

diff --git src/hg/utils/automation/doSameSpeciesLiftOver.pl src/hg/utils/automation/doSameSpeciesLiftOver.pl
index aa596b1..ed36cff 100755
--- src/hg/utils/automation/doSameSpeciesLiftOver.pl
+++ src/hg/utils/automation/doSameSpeciesLiftOver.pl
@@ -104,31 +104,31 @@
 1. /scratch/data/\$db/\$db.2bit contains RepeatMasked sequence for
    database/assembly \$db.
 2. $HgAutomate::clusterData/\$db/chrom.sizes contains all sequence names and sizes from
    \$db.2bit.
 3. The \$db.2bit files have already been distributed to cluster-scratch
    (/scratch/data/<db>/).
 " if ($detailed);
   print "\n";
   exit $status;
 }
 
 
 # Globals:
 # Command line args: tDb=fromDb, qDb=toDb
 my ($tDb, $qDb);
-my $localTmp = "/scratch/tmp";	# UCSC default cluster temporary I/O
+my $localTmp = &HgAutomate::tmpDir();	# do the right thing in UCSC environment
 
 # Other:
 my ($buildDir);
 my ($tSeq, $tSizes, $qSeq, $qSizes, $QDb, $fileServer);
 my ($liftOverChainDir, $liftOverChainFile, $liftOverChainPath, $dbExists);
 
 sub checkOptions {
   # Make sure command line options are valid/supported.
   my $ok = GetOptions(@HgStepManager::optionSpec,
 		      'buildDir=s',
 		      'ooc=s',
 		      'target2Bit=s',
 		      'targetSizes=s',
 		      'query2Bit=s',
 		      'querySizes=s',