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mvdbeek
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Data managers can record absolute paths below $out_file.extra_files_path, while bundle writing runs on the job handler after that directory has been collected into the object store. Relativizing against dataset.extra_files_path then escapes with '..' and leaves the compute-side path in the bundle index. The job working directory is already known. For outputs_to_working_directory, reconstruct the exact compute-side extra-files root with the same uuid-keyed output-path rule used during command construction, then pass that per-output root to bundle writing. For other outputs, retain the dataset extra-files path. This restores ordinary os.path.relpath containment checks, including '.' for the extra-files root itself, instead of inferring the root from a matching directory component. It handles split job/object-store prefixes and id-keyed object stores without changing the bundle format or sending anything to the compute node. Regression tests cover the split-prefix case, uuid-keyed compute paths on id-keyed stores, the root directory, and nested dataset-like directory names.
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: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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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>`_ .