Dear Peter,

As the author of several tool wrappers, I've been asking for a Galaxy
wide mechanism for Galaxy to tell the tool how many threads it can
use, for example via an environment variable. The value could then
be set with a general default, per runner default, or even per tool
using the existing runner configuration under [galaxy:tool_runners]
in universe_wsgi.ini

This would be a possibility. Another would be to communicate the number of 
threads the other way.
So the tool tells the runner how many threads. And the runner knows how to 
handle this.
I can imagine universe_wsgi.ini having such lines:

ncbi_blastp_wrapper  = drmaa://-V -pe smp $GALAXY_THREADS

and then $GALAXY_THREADS is changed for the value given by the wrapper.
Thinking again this is probably not goint to work because the runner comes first and the wrapper after. My idea was that the wrapper could decide what recources to request. So I could use lower memory settings for small mapping jobs ...

In your example, and others like the BWA and BLAST+ wrappers where
the tool XML is hard coded to 8 threads, you would probably want to
use a custom runner in universe_wsgi.ini setting the cluster submission
to request that many slots/CPUs.

A list of all these wrappers on the Wiki would be nice.

regards, Andreas

Andreas Kuntzagk


Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany
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