mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
mvdbeek
c1261948c2
Fixes
```
Traceback (most recent call last):
File "/Users/mvandenb/.pyenv/versions/3.6.9/bin/planemo", line 11, in <module>
load_entry_point('planemo', 'console_scripts', 'planemo')()
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/click/decorators.py", line 64, in new_func
return ctx.invoke(f, obj, *args, **kwargs)
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/Users/mvandenb/src/planemo/planemo/cli.py", line 190, in handle_blended_options
return f(*args, **kwds)
File "/Users/mvandenb/src/planemo/planemo/commands/cmd_lint.py", line 58, in cli
recursive=kwds["recursive"]
File "/Users/mvandenb/src/planemo/planemo/tool_lint.py", line 33, in lint_tools_on_path
if not lint_tool_source(tool_xml, name=basename(tool_path), **lint_args):
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/galaxy/tool_util/lint.py", line 18, in lint_tool_source
lint_tool_source_with(lint_context, tool_source, extra_modules)
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/galaxy/tool_util/lint.py", line 54, in lint_tool_source_with
lint_context.lint(name, value, tool_source)
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/galaxy/tool_util/lint.py", line 83, in lint
lint_func(lint_target, self)
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/galaxy/tool_util/linters/general.py", line 27, in lint_general
parsed_version = packaging.version.parse(version)
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/packaging/version.py", line 28, in parse
return Version(version)
File "/Users/mvandenb/.pyenv/versions/3.6.9/lib/python3.6/site-packages/packaging/version.py", line 219, in __init__
match = self._regex.search(version)
TypeError: expected string or bytes-like object
```
.. 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-irc.freenode.net%23galaxyproject-blue.svg
:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat on irc
.. 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/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 2.7 To check your python version, run:
.. code:: console
$ python -V
Python 2.7.3
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
Configuration & Tools
=====================
You may wish to make changes from the default configuration. This can be
done in the ``config/galaxy.ini`` file.
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>`_ .
Roadmap
=============================
Interested in the next steps for Galaxy? Take a look at the `roadmap <https://github.com/galaxyproject/galaxy/projects/8>`__.