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Implement job and tool stdio separation #318

Merged
merged 10 commits into from
Apr 11, 2023
Merged

Implement job and tool stdio separation #318

merged 10 commits into from
Apr 11, 2023

Commits on Apr 10, 2023

  1. Implement job and tool stdio separation 

    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
    mvdbeek committed Apr 10, 2023
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  2. Test against my fork

    @mvdbeek
    mvdbeek committed Apr 10, 2023
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  3. Import MEMORY_STATEMENT.sh from Galaxy 

    This will write to metadata/memory_statement.log, instead of the working
directory. Fixes a bunch of tests that use metadata collection.
    @mvdbeek
    mvdbeek committed Apr 10, 2023
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  4. More memory statement fixes from upsytream

    @mvdbeek
    mvdbeek committed Apr 10, 2023
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  5. Collect extra_files from galaxy.json

    @mvdbeek
    mvdbeek committed Apr 10, 2023
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  6. Drop continue-on-error for tests that should pass now

    @mvdbeek
    mvdbeek committed Apr 10, 2023
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  7. Decrease complexity

    @mvdbeek
    mvdbeek committed Apr 10, 2023
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  8. Require 23.0 tests to actuall pass

    @mvdbeek
    mvdbeek committed Apr 10, 2023
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  9. Bump up minimum galaxy-util version 

    Should fix galaxyproject#311.
    @mvdbeek
    mvdbeek committed Apr 10, 2023
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  10. Move galaxy framework tests back to upstream dev branch

    @mvdbeek
    mvdbeek committed Apr 10, 2023
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