Dear all,

some SGE instances will add automatically an semicolon add the end of
each command, resulting in a disrupted job, because ';;' are not
allowed.

The latest changes to the Bowtie2 wrapper resulting in such a case and a
crash in our instance. An easy solution would be to fix the wrapper and
omitting the trailing ';' but maybe its better to fix it once for all in
the corresponding tools code, patched attached.

I'm not familiar with other Job schedulers so I'm seeking for
comments ... it there any disadvantage of removing trailing ';' from the
command line?

Ciao,
Bjoern

diff -r 384240b8cd29 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py	Fri Oct 04 16:11:45 2013 -0400
+++ b/lib/galaxy/tools/__init__.py	Thu Oct 10 22:08:56 2013 +0200
@@ -2677,6 +2677,9 @@
             command_line = fill_template( self.command, context=param_dict )
             # Remove newlines from command line, and any leading/trailing white space
             command_line = command_line.replace( "\n", " " ).replace( "\r", " " ).strip()
+            # Remove trailing semicolon
+            # Some SGE versions add automatically an semicolon at the end, which will result in an ';;' - SGE error
+            command_line = command_line.rstrip(';')
         except Exception:
             # Modify exception message to be more clear
             #e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ), )
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