Implement external Galaxy engine.#781
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jmchilton merged 7 commits intogalaxyproject:masterfrom Mar 13, 2018
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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.
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 galaxyproject#592. Implements galaxyproject#508.
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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.