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John Chilton
7de2d1e329
--buffer-size="$GALAXY_MEMORY_MB_PER_SLOT"M is a no-op on the default deployment. MEMORY_STATEMENT_TEMPLATE.sh explicitly unsets the variable when it can't derive a positive value, so on the local runner it's absent and GNU sort accepts --buffer-size=M silently (exit 0, no stderr, no cap). Emit the flag only when there's a value rather than defaulting to an invented number, which would be worse than no cap on a big-memory node. GALAXY_MEMORY_MB rather than the per-slot variant: the two sorts now run sequentially, one process at a time with the whole job's memory available, so a per-slot budget combined with --parallel=$GALAXY_SLOTS under-budgets by a factor of GALAXY_SLOTS. Also register comp1 1.0.2 -> 1.0.3 in WORKFLOW_SAFE_TOOL_VERSION_UPDATES. The bump touches only <requirements> and <command>; the inputs are unchanged, so the update is workflow-safe. Without the entry _stock_tool_source_for returns None for workflows pinned to 1.0.2. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
.. 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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: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>`_ .