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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