Il giorno ven, 11/10/2013 alle 01.10 +0200, Björn Grüning ha scritto: 
> 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.

The Bowtie2 bug may be fixed if my pull request 234 will be merged:

> 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?

That would be sensible too.


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