mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-30 18:13:23 +08:00
Nicola Soranzo
65519718b3
Example traceback for test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_dynamic_output_collections :
galaxy.web.framework.decorators: ERROR: Uncaught exception in exposed API method:
Traceback (most recent call last):
File "/opt/galaxy/lib/galaxy/web/framework/decorators.py", line 260, in decorator
rval = func( self, trans, *args, **kwargs)
File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 182, in create
return self.__api_import_new_workflow( trans, payload, **kwd )
File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 374, in __api_import_new_workflow
workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds )
File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 1111, in _workflow_from_dict
publish=publish
File "/opt/galaxy/lib/galaxy/managers/workflows.py", line 165, in build_workflow_from_dict
missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] )
KeyError: 'name'
.. figure:: https://wiki.galaxyproject.org/Images/GalaxyLogo?action=AttachFile&do=get&target=galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy is available via `https://galaxyproject.org/ <https://galaxyproject.org/>`__
.. image:: https://img.shields.io/badge/questions-galaxy%20biostar-blue.svg
:target: https://biostar.usegalaxy.org
:alt: Ask a question
.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat with us
.. image:: https://readthedocs.org/projects/galaxy/badge/?version=master
:target: https://galaxy.readthedocs.org/en/master/
:alt: Documentation Status
.. 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 2.6 or 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
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 Galaxy
wiki:
https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
Not all dependencies are included for the tools provided in the sample
``tool_conf.xml``. A full list of external dependencies is available at:
https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
Issues
======
Issues can be submitted to trello via the `galaxyproject
website <https://galaxyproject.org/trello>`__ and viewed on the `Galaxy
Trello Board <https://trello.com/b/75c1kASa/galaxy-development>`__.
Alternatively you can `create an issue <https://github.com/galaxyproject/galaxy/issues>`__
through GitHub interface.
Galaxy Development
==================
Galaxy welcomes new development! There is extensive documentation on developing
with Galaxy on the `wiki <https://wiki.galaxyproject.org/Develop>`__.
Source Repository
-----------------
Galaxy development has moved to `Github
<https://github.com/galaxyproject/galaxy>`__.
**Developers** should develop against the ``dev`` branch in the Github
repository.
**Deployers** can continue to pull Galaxy changes from Bitbucket without
interruption. Alternatively, deployers can track the ``master`` branch in
Github.
Syncing a Fork
--------------
If you fork Galaxy to work on it, you may be interested in keeping your copy
up to date with respect to the main repository. Github has `good documentation
<https://help.github.com/articles/syncing-a-fork/>`__ on this.
.. code:: console
$ git remote add upstream https://github.com/galaxyproject/galaxy
$ git fetch upstream
$ git checkout dev
$ git merge upstream/dev