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Dannon Baker
823d2b6e36
A pass over the rest of the prompt against the actual model turned up several places where it tells the model something that isn't true. The container section promised Galaxy re-resolves a "close, plausible" image to a verified biocontainer, but container_recommendation_enabled is off by default, so the guess is usually what runs -- and the accuracy section right below told the model never to guess. Reworded so the two agree. `help` was described as help text when it wants a HelpContent object; a scalar fails validation, so there's an example now. Collection outputs need discover_datasets rather than from_work_dir, which the generic "one or the other" wording hid. The id pattern is stricter than "lowercase with hyphens" -- it must start with a letter. And GALAXY_SLOTS was promised to equal cores_min, which only holds where the deployment maps it; the local runner falls back to local_slots or 1. Also fixed the critic prompt, which asked for `default` on optional parameters. Scalar inputs use `value` and forbid extras, so acting on that suggestion produced a tool that fails validation.
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:alt: Galaxy Logo
The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.
Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
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Galaxy Quickstart
=================
Galaxy requires Python 3.10 or higher. To check your Python version, run:
.. code:: console
$ python -V
Python 3.10.12
Start Galaxy:
.. code:: console
$ sh run.sh
Once Galaxy completes startup, you should be able to view Galaxy in your
browser at: http://localhost:8080
For more installation details please see: https://getgalaxy.org/
Documentation is available at: https://docs.galaxyproject.org/
Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
Tools
=====
Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.
Issues and Galaxy Development
=============================
Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .