I already fixed it one week ago:

https://bitbucket.org/nsoranzo/galaxy-central-tools/commits/74b5fd2318d33b76382b052eae6a28b035dc075f

but then Ross committed a similar fix to galaxy-central, I merged it in my pull request and then Ross reverted the fix!
This is the reason for rebasing pull request #222 to #234.

Ciao,
Nicola

Il 2013-10-11 16:05 Björn Grüning ha scritto:
Hi Nicola,

interesting you fixed bowtie in the same way than we did. But somehow I
would like to strip a trailing ';' by default in Galaxy, when it does
not break anything else.

Thanks for sharing!
Bjoern

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:


https://bitbucket.org/galaxy/galaxy-central/pull-request/234/bug-fixes-for-3-tools-rebased-222

> 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.

Ciao,
Nicola


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