8dddffded74dff5108fa03a4e64d7e9f4040cd47 hiram Tue Nov 23 07:24:49 2021 -0800 fixup bcsh->bash script name refs #28457 diff --git src/hg/utils/automation/doCpgIslands.pl src/hg/utils/automation/doCpgIslands.pl index b4c24d6..b674f3f 100755 --- src/hg/utils/automation/doCpgIslands.pl +++ src/hg/utils/automation/doCpgIslands.pl @@ -131,31 +131,31 @@ # * step: cpg [workhorse] sub doCpg { # Set up and perform the cluster run to run the CpG function on the # hard masked sequence. my $paraHub = $bigClusterHub; my $runDir = $buildDir; # Second, make sure we're starting clean. if (-e "$runDir/cpglh.result") { die "doCpg: looks like this was run successfully already " . "(cpglh.result exists). Either run with -continue makeBed or some later " . "stage, or move aside/remove $runDir/ and run again.\n"; } &HgAutomate::mustMkdir($runDir); my $whatItDoes = "Run /hive/data/staging/data/cpgIslandExt/cpglh on masked sequence."; - my $bossScript = newBash HgRemoteScript("$runDir/doCpg.bcsh", $workhorse, + my $bossScript = newBash HgRemoteScript("$runDir/doCpg.bash", $workhorse, $runDir, $whatItDoes); $bossScript->add(<<_EOF_ export twoBit=\"$maskedSeq\" twoBitToFa \$twoBit stdout | maskOutFa stdin hard stdout \\ | /hive/data/staging/data/cpgIslandExt/cpglh /dev/stdin 2> cpglh.stderr \\ > cpglh.result _EOF_ ); $bossScript->execute(); } # doCpg ######################################################################### # * step: make bed [workhorse] sub doMakeBed {