dear colleagues,

at the university of oslo, we develop a galaxy-based portal for
natural language processing (LAP: Language Analysis Portal).  jobs are
submitted to a compute cluster via DRMAA and SLURM.  current
development is against the galaxy release of march 2015.

i am wondering about fine-grained control of job resources.  our goal
is that most users need not look past the ‘Use default job resource
parameters’ toggle in the job configuration dialogue.

as i understand it, i think we can populate the ‘nativeSpecification’
parameter in ‘job_conf.xml’ with SLURM-specific command-line options
to set defaults, for example the project, maximum run-time, number of
cores, memory per core, and such.  i assume these defaults will be
combined with and overwritten by ‘custom’ job resource parameters, in
case any are specified in the job configuration dialogue?

i tried to track the flow of information from
‘lib/galaxy/jobs/runners/’ via
‘scripts/’ into the drmaa-python egg, but i
could not easily work out where the merging of ‘nativeSpecification’
and custom resource parameters happens; presumably at about the same
time as an actual job script file is created, for submission to SLURM?
 could someone point me in the right direction here?

—more importantly, maybe: we would like to establish per-tool resource
defaults.  for example, some of our tools require substantially more
memory per core than others.  i cannot easily find a way of
associating resource default with individual tools.  i looked at the
tool configuration syntax, ‘job_conf.xml.sample_advanced’, and
‘job_resource_params_conf.xml.sample’, as well as at the following
documentation pages:

i am hoping i am overlooking something :-).  is there a way to define
job resource defaults on a per-tool basis?

with warmest thanks in advance, oe
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