4165c71e12cef21e41d7042b9f8f1ba71d9cd910 hiram Fri Oct 18 13:29:11 2024 -0700 eliminate direct use of /scratch/tmp and instead use appropriate tmpDir function no redmine diff --git src/hg/utils/automation/doRepeatMasker.pl src/hg/utils/automation/doRepeatMasker.pl index 77d21ea..19586ad 100755 --- src/hg/utils/automation/doRepeatMasker.pl +++ src/hg/utils/automation/doRepeatMasker.pl @@ -223,47 +223,48 @@ # Script to do a dummy run of RepeatMasker, to test our invocation and # unpack library files before kicking off a large cluster run. # And now that RM is being run from local /scratch/data/RepeatMasker/ # this is also done in the cluster run script so each node will have # its library initialized my $fh = &HgAutomate::mustOpen(">$runDir/dummyRun.csh"); print $fh <<_EOF_ #!/bin/csh -ef set path = (/cluster/software/bin \$path) $RepeatMasker $RepeatMaskerEngine $repeatLib /dev/null _EOF_ ; close($fh); + my $tmpDir = &HgAutomate::tmpDir(); # Cluster job script: $fh = &HgAutomate::mustOpen(">$runDir/RMRun.csh"); print $fh <<_EOF_ #!/bin/csh -ef set path = (/cluster/software/bin \$path) set finalOut = \$1 set inLst = \$finalOut:r set inLft = \$inLst:r.lft set alignOut = \$finalOut:r.align set catOut = \$finalOut:r.cat # Use local disk for output, and move the final result to \$outPsl # when done, to minimize I/O. -set tmpDir = `mktemp -d -p /scratch/tmp doRepeatMasker.cluster.XXXXXX` +set tmpDir = `mktemp -d -p $tmpDir doRepeatMasker.cluster.XXXXXX` pushd \$tmpDir # Initialize local library $RepeatMasker $RepeatMaskerEngine $repeatLib /dev/null foreach spec (`cat \$inLst`) # Remove path and .2bit filename to get just the seq:start-end spec: set base = `echo \$spec | sed -r -e 's/^[^:]+://'` # RM has a limitation of the length of a sequence name # in the case of name too long, create a shorter name, then lift set nameLength = `echo \$base | wc -c` set shortName = `echo \$base | sed -e 's/>//;' | md5sum | cut -d' ' -f1` # If \$spec is the whole sequence, twoBitToFa removes the :start-end part, # which causes liftUp to barf later. So tweak the header back to # seq:start-end for liftUp's sake: