Il giorno gio, 13/06/2013 alle 18.06 +0100, Peter Cock ha scritto: 
> On Thu, Jun 13, 2013 at 6:02 PM, Nicola Soranzo <sora...@crs4.it> wrote:
> >>
> >> There are two issues here, one that we would like to be able to
> >> handle multi-threading better via Galaxy configuration on a
> >> per-tool level, but for now it must often be hard coded or
> >> done via tool-specific environment variables.
> >
> > Regarding the configuration of multi-threading for BLAST+ tools, instead
> > of hardcoding "-num_threads 8" in the XML files, I'd like to do
> > implement something like this:
> >
> > http://toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/rev/cca0838c1597
> >
> > What do you think? Should I prepare a pull request to discuss at
> > GCC2013?
> 
> That's a sensible idea, something like $BLASTTHREADS as
> an environment variable?

I was thinking something like BLAST_SITE_OPTIONS='-num_threads 8', which
could also include other parameters (e.g. memory limits) in the future.

> I'd still prefer something built into Galaxy like $THREADS or
> $GALAXYTHREADS or whatever which can be sets with a
> default value and adjusted in the per-tool job runner setup
> (e.g. send BLAST jobs to this cluster queue with 16 threads).
> 
> This is definitely a good general topic for the tool authors
> and/or BLAST wrapping BoF sessions at the conference:
> http://wiki.galaxyproject.org/Events/GCC2013/BoF/ToolDevelopers
> http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyBlast
> 
> Peter


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