Too bad there aren't any really good options. I will use the environment
variable approach for the query size limit. 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.

@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.


On 16 June 2014 09:08, Peter Cock <> wrote:

> On Mon, Jun 16, 2014 at 4:18 AM, John Chilton <> wrote:
> > Hello Jan,
> >
> > Thanks for the clarification. Not quite what I was expecting so I am
> > glad I asked - I don't have great answers for either case so hopefully
> > other people will have some ideas.
> >
> > For the first use case - I would just specify some default input to
> > supply to the input wrapper - lets call this N - add a parameter to
> > the tool wrapper "--limit-size=N" - test that and then allow it to be
> > overridden via an environment variable - so in your command block use
> > "--limit-size=\${BLAST_QUERY_LIMIT:N}". This will use N is not limit
> > is set, but deployers can set limits. There are a number of ways to
> > set such variables - DRM specific environment files, login rc files,
> > etc.... Just this last release I added the ability to define
> > environment variables right in job_conf.xml
> > (
> ).
> > I thought the tool shed might have a way to collect such definitions
> > as well and insert them into package files - but Google failed to find
> > this for me.
> Hmm. Jan emailed me off list earlier about this. We could insert
> a pre-BLAST script to check the size of the query FASTA file,
> and abort if it is too large (e.g. number of queries, total sequence
> length, perhaps scaled according to the database size if we want
> to get clever?).
> I was hoping there was a more general mechanism in Galaxy -
> after all, BLAST is by no means the only computationally
> expensive tool ;)
> We have had query files of 20,000 and more genes against NR
> (both BLASTP and BLASTX), but our Galaxy has task-splitting
> enabled so this becomes 20 (or more) individual cluster jobs
> of 1000 queries each. This works fine apart from the occasional
> glitch with the network drive when the data is merged afterwards.
> (We know this failed once shortly after the underlying storage
> had been expanded, and would have been under heavy load
> rebalancing the data across the new disks.)
> > Not sure about how to proceed with the second use case - extending the
> > .loc file should work locally - I am not sure it is feasible within
> > the context of the existing tool shed tools, data manager, etc.... You
> > could certainly duplicate this stuff with your modifications - this
> > how down sides in terms of interoperability though.
> Currently the BLAST wrappers use the *.loc files directly, but
> this is likely to switch to the newer "Data Manager" approach.
> That may or may not complicate local modifications like adding
> extra columns...
> > Sorry I don't have great answers for either question,
> > -John
> Thanks John,
> Peter
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