(moved to galaxy-dev)

Nate Coraor wrote, On 06/02/2011 01:31 PM:
> Peter Cock wrote:
>> On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>>> pbs.py then knows to translate '<resource type="cores">8</resource>' to
>>> '-l nodes=1:ppn=8'.
>>> Your tool can access that value a bunch, like $__resources__.cores.
>>> The same should be possible for other consumables.

Just a thought here:

The actual parameters that are passed to the scheduler are not necessarily 
Meaning, at least with SGE, specifying the number of cores can be:
 qsub -pe threads=8
 qsub -pe cores=8
 qsub -pe jiffies=8

and same thing for memory limitation (e.g. "-l virtual_free=800M").

The reason is that those resources (e.g. "threads", "cores", "virtual_free") 
are just identifiers, and they are created and configured by whomever installed 
SGE - they are not built-in or hard-coded).

So just be careful in your design/implementation when automatically translating 
XML resources to hard-coded parameters.

If you do hard-code them, just make sure the specifically document it (i.e. 
Galaxy expect the SGE threads parameter to be "-pe threads=8" and nothing else).

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