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mvdbeek
aadab95bde
CI (integration shard 1) hit the uninstall-resurrect again: after
uninstall_repository, GET /api/tools/{guid} still returned the tool. The
log shows the interleaving - the reload_toolbox queued by the preceding
install's conf write executed while the uninstall was mid-flight, and its
rebuild (including a potentially long inline index populate) ran with no
synchronization against remove_tool_by_id.
Two halves:
1. _get_new_toolbox now builds and swaps the new toolbox under
app._toolbox_lock, the lock remove_tool_by_id and
invalidate_index_cache already hold. Whichever side wins, the other
sees a consistent world: removal-first means the rebuild reads the
already-cleaned index and conf; rebuild-first means the removal runs
against the swapped-in box. The lock is an RLock, so the populate
broadcast delivered inline on the same thread re-enters safely.
2. remove_tool_by_id also cleans the CURRENT app.toolbox when it is a
different object than self - a rebuild that won the race swapped in a
box built from the pre-removal index, and cleaning the superseded
instance alone would leave the live box serving the uninstalled tool.
Verified: new unit test (swapped-in box cleaned), 45 lazy unit tests,
fastp shed-install + repository-uninstall integration tests in lazy mode
(the lock's deadlock canary - install triggers watcher reload + inline
populate under the lock), tox lint/format/mypy.
.. 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>`_ .