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Allow specifying URL and API key with workflow autoupdate and docs improvements #1237

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May 20, 2022
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Allow specifying URL and API key with workflow autoupdate and docs improvements #1237

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11 changes: 9 additions & 2 deletions docs/autoupdate.rst
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Expand Up @@ -38,16 +38,23 @@ The ``autoupdate`` subcommand can also be used to automatically update workflows

planemo autoupdate workflow.ga

In the basic usage, a local Galaxy instance will be spun up and the workflow uploaded, refactored to include the most recent tool versions, and re-downloaded.
In the basic usage with the above command, a local Galaxy instance will be spun up and the workflow uploaded, refactored to include the most recent tool versions, and re-downloaded.

Workflows can also be updated against an external galaxy, for example:
Workflows can also be updated against an external Galaxy server; see the example below. (Please note the server must be running Galaxy version 21.05 or more recent.)

::

planemo autoupdate workflow.ga --profile usegalaxy-eu

In this case, the workflow returned will contain the most recent tool and subworkflow versions available on that Galaxy server.

An equivalent alternative, if you don't want to use Planemo profiles, is the following:

::

planemo autoupdate workflow.ga --galaxy_url SERVER_URL --galaxy_user_key API_KEY


Implementing an autoupdate CI job
=================================

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2 changes: 2 additions & 0 deletions planemo/commands/cmd_autoupdate.py
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Expand Up @@ -78,6 +78,8 @@ def skip_requirements_option():
@options.report_level_option()
@options.report_xunit()
@options.fail_level_option()
@options.galaxy_url_option()
@options.galaxy_user_key_option()
@command_function
def cli(ctx, paths, **kwds): # noqa C901
"""Auto-update tool requirements by checking against Conda and updating if newer versions are available."""
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