src/hg/utils/automation/doHgNearBlastp.pl 1.7

Index: src/hg/utils/automation/doHgNearBlastp.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/doHgNearBlastp.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/utils/automation/doHgNearBlastp.pl	5 Mar 2009 18:37:03 -0000	1.6
+++ src/hg/utils/automation/doHgNearBlastp.pl	8 Jun 2009 18:41:32 -0000	1.7
@@ -247,9 +247,9 @@
 _EOF_
     ;
   close($fh);
   &HgAutomate::run("chmod a+x $bossScript");
-  &HgAutomate::run("ssh -x $distrHost nice $bossScript");
+  &HgAutomate::run("$HgAutomate::runSSH $distrHost nice $bossScript");
 }
 
 sub formatSequence {
   # Run formatdb on the specified query ($scratchDir should be cluster-mounted)
@@ -273,9 +273,9 @@
 _EOF_
     ;
   close($fh);
   &HgAutomate::run("chmod a+x $bossScript");
-  &HgAutomate::run("ssh -x $distrHost nice $bossScript");
+  &HgAutomate::run("$HgAutomate::runSSH $distrHost nice $bossScript");
 } # formatSequence
 
 sub runPairwiseBlastp {
   # Do a pairwise blastp cluster run for the given query.  
@@ -318,9 +318,9 @@
 _EOF_
     ;
   close($fh);
   &HgAutomate::run("chmod a+x $bossScript");
-  &HgAutomate::run("ssh -x $clusterHub $bossScript");
+  &HgAutomate::run("$HgAutomate::runSSH $clusterHub $bossScript");
 } # runPairwiseBlastp
 
 
 sub dbToPrefix {
@@ -363,9 +363,9 @@
   &HgAutomate::run("chmod a+x $bossScript");
 
   return if ($opt_noLoad);
 
-  &HgAutomate::run("ssh -x $dbHost nice $bossScript");
+  &HgAutomate::run("$HgAutomate::runSSH $dbHost nice $bossScript");
 } # loadPairwise
 
 
 sub recipBest {
@@ -392,12 +392,12 @@
 
 sub cleanup {
   # Remove what we added in $scratchDir.
   foreach my $db (@_) {
-    &HgAutomate::run("ssh -x $distrHost rm -rf $scratchDir/$db.split");
-    &HgAutomate::run("ssh -x $distrHost rm -rf $scratchDir/$db.formatdb");
+    &HgAutomate::run("$HgAutomate::runSSH $distrHost rm -rf $scratchDir/$db.split");
+    &HgAutomate::run("$HgAutomate::runSSH $distrHost rm -rf $scratchDir/$db.formatdb");
   }
-  &HgAutomate::run("ssh -x $distrHost rmdir $scratchDir");
+  &HgAutomate::run("$HgAutomate::runSSH $distrHost rmdir $scratchDir");
 } # cleanup
 
 sub celebrate {
   # Hooray, we're done.
@@ -474,9 +474,9 @@
 ($CONFIG) = @ARGV;
 &parseConfig($CONFIG);
 
 # Split target fasta.
-&HgAutomate::run("ssh -x $distrHost mkdir $scratchDir");
+&HgAutomate::run("$HgAutomate::runSSH $distrHost mkdir $scratchDir");
 my $tFasta = $dbToFasta{$tDb};
 &splitSequence($tDb, $tFasta);
 
 # Self blastp.