mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
Nicola Soranzo
48a01454e4
Pinning to the version that was current when https://github.com/galaxyproject/galaxy/pull/12435 was merged to fix the following traceback with rich 12.1.0: ``` 2022-04-04T14:16:19.5073158Z File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tools/data/__init__.py", line 21, in <module> 2022-04-04T14:16:19.5073535Z import refgenconf 2022-04-04T14:16:19.5074393Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/__init__.py", line 6, in <module> 2022-04-04T14:16:19.5074853Z from .populator import looper_refgenie_populate 2022-04-04T14:16:19.5075535Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/populator.py", line 9, in <module> 2022-04-04T14:16:19.5075970Z from . import refgenconf 2022-04-04T14:16:19.5076607Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/refgenconf.py", line 27, in <module> 2022-04-04T14:16:19.5077091Z from rich.progress import BarColumn, Progress, TextColumn 2022-04-04T14:16:19.5077768Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/progress.py", line 43, in <module> 2022-04-04T14:16:19.5078272Z from .console import Console, JustifyMethod, RenderableType, Group 2022-04-04T14:16:19.5078956Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/console.py", line 46, in <module> 2022-04-04T14:16:19.5079437Z from ._log_render import FormatTimeCallable, LogRender 2022-04-04T14:16:19.5080105Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/_log_render.py", line 5, in <module> 2022-04-04T14:16:19.5124479Z from .text import Text, TextType 2022-04-04T14:16:19.5130069Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/text.py", line 5, in <module> 2022-04-04T14:16:19.5134858Z from rich.emoji import EmojiVariant 2022-04-04T14:16:19.5139847Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/emoji.py", line 4, in <module> 2022-04-04T14:16:19.5144648Z from .jupyter import JupyterMixin 2022-04-04T14:16:19.5147478Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/jupyter.py", line 4, in <module> 2022-04-04T14:16:19.5150060Z from .segment import Segment 2022-04-04T14:16:19.5152862Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/segment.py", line 19, in <module> 2022-04-04T14:16:19.5155442Z from .cells import ( 2022-04-04T14:16:19.5158112Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/cells.py", line 6, in <module> 2022-04-04T14:16:19.5159612Z from ._lru_cache import LRUCache 2022-04-04T14:16:19.5161691Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/_lru_cache.py", line 8, in <module> 2022-04-04T14:16:19.5163233Z from typing_extensions import OrderedDict 2022-04-04T14:16:19.5165289Z ImportError: cannot import name 'OrderedDict' from 'typing_extensions' (/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/typing_extensions.py) ```
.. 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 3.6 . 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>`_ .