On Wed, Jun 18, 2014 at 12:04 PM, Jan Kanis <jan.c...@jankanis.nl> wrote:
> I am not using job splitting, because I am implementing this for a client
> with a small (one machine) galaxy setup.

Ah - this also explains why a job size limit is important for you.

> Implementing a query limit feature in galaxy core would probably be the best
> idea, but that would also probably require an admin screen to edit those
> limits, and I don't think I can sell the required time to my boss under the
> contract we have with the client.

The wrapper script idea I outlined to you earlier would be the least
invasive (although might cause trouble if BLAST is run at the command
line outside Galaxy), while your idea of inserting the check script into
the Galaxy Tool XML just before running BLAST itself should also
work well.

> I gave a quick try before on making the blast2html tool run in both python
> 2.6 and 3, but I gave up due to too many encoding issues. The client's
> machine has python 2.6. Maybe I should have another look.
>
> Jan

It gets easier with practice - a mixture of little syntax things, and
the big pain about bytes versus unicode (and thus encodings,
and raw versus text mode for file handles).

Peter
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