I am not using job splitting, because I am implementing this for a client
with a small (one machine) galaxy setup.

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.

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


On 17 June 2014 21:55, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> On Tue, Jun 17, 2014 at 4:57 PM, Jan Kanis <jan.c...@jankanis.nl> wrote:
> > Too bad there aren't any really good options. I will use the environment
> > variable approach for the query size limit.
>
> Are you using the optional job splitting (parallelism) feature in Galaxy?
> That seems to be me to be a good place to insert a Galaxy level
> job size limit. e.g. BLAST+ jobs are split into 1000 query chunks,
> so you might wish to impose a 25 chunk limit?
>
> Long term being able to set limits on the input file parameters
> of each tool would be nicer - e.g. Limit BLASTN to at most
> 20,000 queries, limit MIRA to at most 50GB FASTQ files, etc.
>
> > For the gene bank links I guess modifying the .loc file is the least
> > bad way. Maybe it can be merged into galaxy_blast, that would at
> > least solve the interoperability problems.
>
> It would have to be sufficiently general, and backward compatible.
>
> FYI other people have also looked at extending the blast *.loc
> files (e.g. adding a category column for helping filter down a
> very large BLAST database list).
>
> > @Peter: One potential problem in merging my blast2html tool
> > could be that I have written it in python3, and the current tool
> > wrapper therefore installs python3 and a host of its dependencies,
> > making for a quite large download.
>
> Without seeing your code, it is hard to say, but actually writing
> Python code which works unmodified under Python 2.7 and
> Python 3 is quite doable (and under Python 2.6 with a few
> more provisos). Both NumPy and Biopython do this if you
> wanted some reassurance.
>
> On the other hand, Galaxy itself will need to more to Python 3
> at some point, and certainly individual tools will too. This will
> probably mean (as with Linux Python packages) having double
> entries on the ToolSehd (one for Python 2, one for Python 3),
>
> e.g ToolShed package for NumPy under Python 2 (done)
> and under Python 3 (needed).
>
> Peter
>
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