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mvdbeek
bab23839ae
Deletes the three workarounds that existed only because the toolbox and the populator both wrote to the index: - ``_stamp_panel_sections_onto_index`` (~45 lines) — section metadata is now stamped by ``build_index_entry_from_source`` at populator time from ``DiscoveredTool.section_id`` / ``section_name``. - ``_sync_tool_mutations_to_index`` (~32 lines) — conf-level hidden / labels are now captured by ``DiscoveredTool`` and stamped onto the entry at populator time (commit 4). - ``_warn_if_index_misses_panel_tools`` (~44 lines) — the diagnostic is obsolete now that the populator walks the same confs the toolbox walks; coverage is structural, not best-effort. Its replacement is ``reconcile_index`` (commit 6), which prunes orphans rather than just warning about them. Their call sites in ``__init__`` are gone too, and the now-unused ``ToolSection`` import drops with them. ``lazy_toolbox.py`` shrinks from 1455 to 1314 lines. All 21 unit tests in ``test_lazy_tool.py`` still pass.
.. 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: Chat on irc
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:alt: Release Documentation
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: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>`_ .