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galaxyproject / pulsar

Distributed job execution application built for Galaxy
https://pulsar.readthedocs.io
Apache License 2.0
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Implement job and tool stdio separation #318

Closed mvdbeek closed 1 year ago

mvdbeek commented 1 year ago

and always set up job i/o redirection on the pulsar side. Since pulsar stdio is broken prior to this on 23.0 this is maybe a good time to make the switch. Seems like this detail should be controlled on pulsar, not Galaxy.

mvdbeek commented 1 year ago

hmm, 20 new test errors for the framework tests against the master branch (22.05). I guess that was to be expected, but it's no good that dev seem to time out on the parallelism tests

jmchilton commented 1 year ago

Feel free to just increase that complexity threshold if it is a complex thing to "fix".

mvdbeek commented 1 year ago

Alright, the directory metadata variant framework tests pass completely! And the extended metadata tests seem to just have an issue with the stdio redirection.

mvdbeek commented 1 year ago

I've deployed this as https://pypi.org/project/pulsar-galaxy-lib/0.15.0.dev2/ for testing on the Galaxy side (https://github.com/galaxyproject/galaxy/pull/15915)