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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
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dynamic variables priority order is incorrect #277

Closed nsheff closed 3 years ago

nsheff commented 4 years ago

In my hands, if I include a dynamic variables script, then these variables are treated as a lower priority than elements in the divvy config package.

I think the dynamic variables should have a higher priority than elements in the divvy config package.

stolarczyk commented 4 years ago

I can't reproduce this or I just don't understand the problem. What do you mean by "divvy config package"?

When I use the dynamic variables feature, the selected values are used correctly by divvy in the submission scripts. By looking at the relevant lines I see that whatever is returned by choose_resource_package (dynamic variables are given priority there) method is only overwritten by the CLI resources specification:

https://github.com/pepkit/looper/blob/0c5f94c54b086232e538571a37111526cef94d80/looper/conductor.py#L406-L409

nsheff commented 4 years ago

I put 'partition: largemem' in dynamic variables, they are submitted to 'standard' anyway because of this line:

https://github.com/pepkit/divcfg/blob/98ba06587d49f4cc9f630cd7d157fb81a16c95c9/uva_rivanna.yaml#L19

the dynamic variable should have precedence.

stolarczyk commented 4 years ago

should be fixed now