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mvdbeek
68f579b638
Walking a CVMFS shed conf, the eager _load_tool_tag_set paid two per-tool costs the lazy toolbox doesn't need: an os.path.exists stat (network round trip on CVMFS — minutes over ~10k tools) and, since conf-provided repositories have no install-DB row by design, one 'Attempted to load tool shed tool, but the repository ... was not found in database' warning per tool per boot. Two overridable hooks in AbstractToolBox, both eager-behavior-preserving: _tool_file_on_disk (the existence gate) and _missing_repository_log_level (the warning's severity). LazyToolBox answers both from an identity-cached set of indexed source_paths: the populator established existence when it stored the source and materialisation reads the raw source from the store, so the stat proves nothing; the missing install-DB row is expected, so it logs at debug. Unindexed paths keep exact eager behavior. Claude-Session: https://claude.ai/code/session_018L7ZmCv2ubKA3JNeSL8Pkr
.. 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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:alt: Release Documentation
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: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>`_ .