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/doWindowMasker.pl src/hg/utils/automation/doWindowMasker.pl index 56669e3..1b8d577 100755 --- src/hg/utils/automation/doWindowMasker.pl +++ src/hg/utils/automation/doWindowMasker.pl @@ -104,70 +104,72 @@ } ######################################################################### # * step: count [workhorse] sub doCount { my $runDir = "$buildDir"; &HgAutomate::checkCleanSlate('count', 'mask', "$runDir/windowmasker.counts"); &HgAutomate::mustMkdir($runDir); my $whatItDoes = "It does WindowMasker counts step."; my $workhorse = &HgAutomate::chooseWorkhorse(); my $bossScript = new HgRemoteScript("$runDir/doCount.csh", $workhorse, $runDir, $whatItDoes); + my $tmpDir = &HgAutomate::tmpDir(); $bossScript->add(<<_EOF_ set windowMaskerDir = /cluster/bin/\$MACHTYPE set windowMasker = \$windowMaskerDir/windowmasker set fa = $db.fa -set tmpDir = `mktemp -d -p /scratch/tmp doWindowMasker.XXXXXX` +set tmpDir = `mktemp -d -p $tmpDir doWindowMasker.XXXXXX` chmod 775 \$tmpDir set inputTwoBit = $unmaskedSeq pushd \$tmpDir twoBitToFa \$inputTwoBit \$fa \$windowMasker -mk_counts true -input \$fa -output windowmasker.counts popd cp \$tmpDir/windowmasker.counts . rm -rf \$tmpDir _EOF_ ); $bossScript->execute(); } # doCount ######################################################################### # * step: mask [workhorse] sub doMask { printf STDERR "# doMask: obsolete step, no longer needed\n"; return 0; } # doMask ######################################################################### # * step: sdust [workhorse] sub doSdust { my $runDir = "$buildDir"; &HgAutomate::checkExistsUnlessDebug('mask', 'sdust', "$runDir/windowmasker.counts"); my $whatItDoes = "It does WindowMasker masking step with -sdust true."; my $workhorse = &HgAutomate::chooseWorkhorse(); my $bossScript = new HgRemoteScript("$runDir/doSdust.csh", $workhorse, $runDir, $whatItDoes); + my $tmpDir = &HgAutomate::tmpDir(); $bossScript->add(<<_EOF_ set windowMaskerDir = /cluster/bin/\$MACHTYPE set windowMasker = \$windowMaskerDir/windowmasker set fa = $db.fa -set tmpDir = `mktemp -d -p /scratch/tmp doWindowMasker.XXXXXX` +set tmpDir = `mktemp -d -p $tmpDir doWindowMasker.XXXXXX` chmod 775 \$tmpDir set inputTwoBit = $unmaskedSeq cp windowmasker.counts \$tmpDir pushd \$tmpDir twoBitToFa \$inputTwoBit \$fa \$windowMasker -ustat windowmasker.counts -sdust true -input \$fa -output windowmasker.intervals perl -wpe \'if \(s\/^\>lcl\\\|\(\.\*\)\\n\$\/\/\) { \$chr = \$1\; } \\ if \(\/^\(\\d+\) \- \(\\d+\)\/\) { \\ \$s=\$1\; \$e=\$2+1\; s\/\(\\d+\) \- \(\\d+\)\/\$chr\\t\$s\\t\$e\/\; \\ }\' windowmasker.intervals > windowmasker.sdust.bed popd cp \$tmpDir/windowmasker.sdust.bed . rm -rf \$tmpDir _EOF_ );