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mvdbeek
caea1912b9
GalaxyAppConfiguration materializes every schema option, so the hasattr/getattr guards around tool_configs, shed_tool_config_file, migrated_tools_config, root, tool_search_index_dir and use_lazy_toolbox were dead (StandaloneInstallationTarget's Config stub gains the use_lazy_toolbox attribute the real config carries). The tool_source_url getattr had no matching schema option — the default sqlalchemy store is now disk-path only; full URLs remain available via named tool_source_stores entries. getattr(entry, "source_path") was hiding a real gap: ToolIndexEntry never carried the field, so LazyTool.config_file always materialised. The populator now stamps source_path onto every entry. discover.py's duplicated _looks_like_a_tool is replaced by the real galaxy.tool_util.loader_directory.looks_like_a_tool (threading enable_beta_tool_formats), and the works-without-galaxy fallback for MODEL_TOOLS_PATH is gone — the populator always runs with galaxy importable.
.. 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/>`__.
.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter
.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat on irc
.. image:: https://img.shields.io/badge/release-documentation-blue.svg
: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>`_ .