mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 10:24:38 +08:00
Nicola Soranzo
314ca33509
Fix https://github.com/galaxyproject/galaxy/issues/12412 . We have a dependency on `Tempita` (through `sqlalchemy-migrate`), which is abandonware and uses the `use_2to3=True` option of `setup()` in its `setup.py` . The new Setuptools v58.0.0 removed support for 2to3 during builds: https://github.com/pypa/setuptools/blob/main/CHANGES.rst#v5800 As a result Tempita is installed at even older version and importing it raises a SyntaxError. For Galaxy as a full application this has been solved by creating a wheel on https://wheels.galaxyproject.org . But the `galaxy-data` package (which also depends on `sqlalchemy-migrate`) cannot automatically install the tempita-0.5.2 wheel from our alternative package index when installed via `pip install galaxy-data` as there is no syntax to specify that. I've therefore resurrected Tempita from the Bitbucket Mercurial repo (thanks to Software Heritage backups! https://bitbucket-archive.softwareheritage.org/projects/ia/ianb/tempita.html ), converted to a GitHub repo and updated its code to Python 3.6 with 2to3 and pyupgrade.
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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 3.6 . To check your Python version, run:
.. code:: console
$ python -V
Python 3.6.10
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>`_ .