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We could avoid having to specify the Galaxy job conf by reading galaxy.yml and parsing the job conf out of there. However, adding this functionality directly to TPV (including automatically locating galaxy.yml) is reinventing a wheel (and a rather complicated and messy one) that is already done by Gravity and Galaxy itself. Ideally we would separate this out into a library that all 3 projects could then use.
The dry-run is not going to work for more complex custom rules because we are mocking Galaxy objects that won't have all of the attributes that a custom rule might access (e.g. object_store). We can look at a couple of things, including Galaxy's IntegrationTestCase and the minimal app that celery workers load.
There is currently no way to specify any tool param values or input sizes when performing a dry run. EDIT: --input-size added to Add a tpv dry-run subcommand #52.
The text was updated successfully, but these errors were encountered:
Add explanation for which destination was chosen and why. eg:
RESULT for .....
--------------------------------------------------------------------------------------
DESTINATION
final: condor_tpv
matched(with ranks): condor_tpv(1), singularity(2), interactive(3)
--------------------------------------------------------------------------------------
PARAMS
cores: 8 (min of tool: 10, user: 8, role: 9)
mem: ....
...
Additionally an explanation of how the rank was calculated in this specific case, would be helpful to debug errors in the configuration and check if it works as intentioned.
From the comments on #52 and #48:
galaxy.yml
and parsing the job conf out of there. However, adding this functionality directly to TPV (including automatically locatinggalaxy.yml
) is reinventing a wheel (and a rather complicated and messy one) that is already done by Gravity and Galaxy itself. Ideally we would separate this out into a library that all 3 projects could then use.object_store
). We can look at a couple of things, including Galaxy's IntegrationTestCase and the minimal app that celery workers load.or input sizeswhen performing a dry run. EDIT:--input-size
added to Add atpv dry-run
subcommand #52.The text was updated successfully, but these errors were encountered: