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mvdbeek
9a12b3aaed
test_repository_uninstall kept resurrecting the tool after all index-level fixes. Local repro + probes showed removal completed on the right toolbox but two in-memory paths still served the tool: - The materialise LRU is keyed by whatever id the caller resolved with, so the same tool sits under both its guid and its short id; the guid-prefix purge left the short-id entry behind. Purge by cached tool identity instead. - _tools_by_old_id is keyed by old_id — the SHORT id for a shed guid — and super().remove_tool_by_id deletes from it by object identity only, which misses when the bucket holds an earlier registration (stub or materialised instance) than _tools_by_id. The leftover resurfaced through the eager get_tool fall-through. Scrub every object belonging to the removed guid; sibling installs sharing the short id survive. Verified locally: the full TestRepositoryInstallIntegrationTestCase passes 3/3 consecutive lazy runs (install, uninstall, update).
.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
: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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:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter
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:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat on irc
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:target: https://docs.galaxyproject.org/en/master/
:alt: Release Documentation
.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
:target: https://travis-ci.org/galaxyproject/galaxy
:alt: Inspect the test results
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>`_ .