2ee491feb25f942fad09e7d09e2d7a94ffcd06eb hiram Wed Jun 15 17:12:12 2022 -0700 can not do the faSize measure in the background since the shell may exit before it is done refs #59545 diff --git src/hg/utils/automation/doRepeatMasker.pl src/hg/utils/automation/doRepeatMasker.pl index 216085e..497a1fd 100755 --- src/hg/utils/automation/doRepeatMasker.pl +++ src/hg/utils/automation/doRepeatMasker.pl @@ -567,31 +567,31 @@ ######################################################################### # * step: mask [workhorse] sub doMask { my $runDir = "$buildDir"; &HgAutomate::checkExistsUnlessDebug('cat', 'mask', "$buildDir/$db.sorted.fa.out"); my $whatItDoes = "It makes a masked .2bit in this build directory."; my $workhorse = &HgAutomate::chooseWorkhorse(); my $bossScript = newBash HgRemoteScript("$runDir/doMask.bash", $workhorse, $runDir, $whatItDoes); $bossScript->add(<<_EOF_ export db=$db twoBitMask $unmaskedSeq \$db.sorted.fa.out \$db.rmsk$updateTable.2bit -twoBitToFa \$db.rmsk$updateTable.2bit stdout | faSize stdin > faSize.rmsk$updateTable.txt & +twoBitToFa \$db.rmsk$updateTable.2bit stdout | faSize stdin > faSize.rmsk$updateTable.txt _EOF_ ); $bossScript->execute(); } # doMask ######################################################################### # * step: install [dbHost, maybe fileServer] sub doInstall { my $runDir = "$buildDir"; &HgAutomate::checkExistsUnlessDebug('cat', 'install', "$buildDir/$db.sorted.fa.out"); my $split = ""; $split = " (split)" if ($opt_splitTables); my $whatItDoes = "It loads $db.sorted.fa.out into the$split rmsk$updateTable table and $db.nestedRepeats.bed\n" .