Hi Nate,

> Hi Björn,
> 
> Are you certain that SGE is responsible?  I ran in to the same thing with 
> bowtie2 with other runners.  
> The double semicolon is invalid syntax in Bourne-compatible shells and so the 
> tool ought to be fixed not to produce them (it happens under certain 
> combinations of options).  
> Have you noticed this happening with any other tools?

Yes, but only with tools from the toolshed and there I poked people to
remove the trailing semicolon from the wrapper. From my observation the
tool does not produce double semicolons. Only one at the end, but the
Job scheduler adds one, resulting in a double one with invalid syntax.

I can't see where bowtie is producing a double semicolon. I really think
SGE is adding one. At least I restructured the semicolons (attached) and
it worked for us.

Thanks Nate,
Bjoern

> --nate
> 
> On Oct 11, 2013, at 8:57 AM, John Chilton wrote:
> 
> > This sounds like a good way to solve the problem, I guess I would modify
> > 
> > 
> > On Thu, Oct 10, 2013 at 6:10 PM, Björn Grüning
> > <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> >> 
> >> 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
> >> 
> >> 
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> 


Attachment: bowtie2_wrapper.xml
Description: XML document

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