On 10/17/2014 02:47 PM, John Chilton wrote:
In theory GALAXY_SLOTS is now always set unless Galaxy is pretty old -
I still think it is important for tools to specify defaults using the
\${GALAXY_SLOTS:-4} idiom so that tools themselves don't have explicit
dependencies on the Galaxy runtime and in case new resource managers
or job runners come along that don't set this.

That said - I figured someday someone would ask this question so there
is indeed undocumented magic to determine if the number of slots has
been configured explicitly to 1 or if that is just the fallback
because it was left unspecified or Galaxy didn't know how to determine
it from the resource manager.

The magic environment variable is GALAXY_SLOTS_CONFIGURED - if that is
set and GALAXY_SLOTS is 1 - Galaxy believes that the number of
requested cores is truly and explicitly 1. If GALAXY_SLOTS is 1 and
GALAXY_SLOTS_CONFIGURED is not set - Galaxy is just supplying the
default of 1 to the tool because it doesn't know what else to do. (1
is used by the local runner if local_slots is not set i job_conf or
used by all the other job runners if they cannot figure out what the
environment is requesting).

I don't know how actionable it is from a tool author perspective - but
I did think it was important to track it. Hope this helps.


Hi John,

This is great ! I think it is very actionable for my case. I would just overwrite my tool's internal configuration with GALAXY_SLOTS if it is set and if GALAXY_SLOTS > 1 or (GALAXY_SLOTS == 1 and GALAXY_SLOTS_CONFIGURED is set).

Much better than having to guess for the == 1 case, thanks!

Have a nice weekend,
Wolfgang

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