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',