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mvdbeek
57901fcd0e
``add_to_tool_panel`` now writes ``shed_tool_conf.xml`` *before* loading items into the toolbox, then calls ``galaxy.tool_source_store.populator.populate_for_paths`` on the new tool file paths. The populator writes ``StoredToolSource`` + ``ToolIndexEntry`` + the whoosh index for each path and broadcasts ``reload_tool_source_cache`` so peer Galaxy processes refresh. After the populator returns, the in-process toolbox's ``invalidate_index_cache`` is called synchronously so this process sees the new entries immediately (the install API response can't wait for AMQP loopback). Commit 11's stub-registration runs inside that call. ``load_item`` is still invoked per elem so the in-memory ``_tool_panel`` and ``_integrated_tool_panel`` get the standard panel bookkeeping — ``create_tool``'s index lookup now succeeds (commit 10's raise stays quiet) because the populator just wrote the entry. New helper ``_collect_new_tool_paths`` walks ``elem_list``, flattening ``<section>`` children, and returns absolute paths matching what ``discover_tools`` yields after the conf is on disk.
.. 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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: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>`_ .