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Implement external Galaxy engine. #781

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merged 7 commits into from Mar 13, 2018

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jmchilton commented Feb 26, 2018

This work is focused on getting the "test" and "run" commands for Galaxy tools and workflows to be able to target already running Galaxy servers, though it should enable other combinations of artifacts and commands such as serving workflows and various CWL artifact operations against that fork of Galaxy.

The tool piece of this requires an unreleased version of galaxy-lib (galaxyproject/galaxy-lib#91) and development APIs in Galaxy for external tool testing (galaxyproject/galaxy-lib#103).

Implements #592.
Implements #508.

@jmchilton jmchilton referenced this pull request Mar 7, 2018

Open

External Tool Test Follow Up Work #5651

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@jmchilton jmchilton force-pushed the jmchilton:external_engines branch from 5012549 to 6c056f1 Mar 7, 2018

jmchilton added a commit to jmchilton/galaxy-lib that referenced this pull request Mar 7, 2018

Provide more test data when running verify_tool.
This is information Planemo generates from Galaxy's XUnit report and inserts back into the result JSON, with this change I think one can simply run ``planemo test_reports result.json`` on the result of the driver script here to generate Planemo-style reports for tool test runs.

```
pip install galaxy-lib
galaxy-tool-test -u http://localhost:8080 -a dccd838ad8f46637e0d7661d849806a1 -k dccd838ad8f46637e0d7661d849806a1 -t inputs_as_json -j output.json
planemo test_reports --test_output output.html --test_output_markdown output.md output.json
```

Requires some small changes to Planemo's test_reports command contained within galaxyproject/planemo#781.
Implement external Galaxy engine.
This work is focused on "test" and "run" commands for Galaxy tools and workflows, though it should enable other combinations of artifacts and commands such as serving workflows and various CWL artifact operations against that fork of Galaxy.

The tool piece of this requires an unreleased version of galaxy-lib (galaxyproject/galaxy-lib#91) and unmerged Galaxy modifications to expose a APIs for external tool testing (galaxyproject/galaxy#5545). Workflows are oddly enough likely closer to working with this WIP.

Implements #592.
Implements #508.

@jmchilton jmchilton force-pushed the jmchilton:external_engines branch from 6c056f1 to d7a7124 Mar 12, 2018

jmchilton added some commits Mar 12, 2018

@jmchilton jmchilton merged commit 3ad944d into galaxyproject:master Mar 13, 2018

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@bgruening bgruening changed the title [WIP] Implement external Galaxy engine. Implement external Galaxy engine. Mar 13, 2018

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