Hi Stephan,

I will just quickly answer to your last question. Because, I’m not sure to understand the first part of your message or take the time to :P

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

Perhaps, I didn’t understand your message at all:

In your tool wrapper, you can use "\${GALAXY_SLOTS:-8}" to dynamically set the ressource according to the setting in the job_conf.xml.
Here by default, the job will take 8 CPU (personally, I find that it’s a trap when the administrator/me miss this default value, I prefer to set the default value to 1)

<tool id="my_amazing_wrapper" name="My Amazing" >


     my_amazing_tool -query "$query" […] -num_threads "\${GALAXY_SLOTS:-8}" […]


In your job_conf.xml, you can set per tool a destination. Thus, you can specify the number of CPU/Slot, the memory needed, the queue, the nodes ...

<destinations  default="sge_default">

     <destination id="thread4-men_free10" runner="sge">

           <param id="nativeSpecification">-V -w n -q galaxy.q -R y -pe thread 4 -l mem_free=10G </param>




     <tool id="my_amazing_wrapper" destination="thread4-men_free10"/>


I hope it will help you



Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)

Member of the Workflow4Metabolomics project

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81

Le 12 mars 2016 à 10:36, Stephan Oepen <oe@ifi.uio.no> a écrit :

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/drmaa.py’ via
‘scripts/drmaa_external_runner.py’ 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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