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?

--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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