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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