mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
mvdbeek
b1361c8e79
in tool schema. New lxml is more strict when validating
the xml schema and fails with
```
lxml.etree.XMLSchemaParseError: complex type 'Output': The content model is not determinist., line 5329
```
this is because `filter` and `discover_datasets` are present in
OutputDataElement and OutputCollectionElement, making
```
<xs:sequence>
<xs:group ref="OutputDataElement" minOccurs="0" maxOccurs="unbounded" />
<xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
```
not deterministic.
In any case this isn't an accurate model of what is allowed and parsed,
as you can't use collection-specific discover_datasets options outside
of a dataset collection.
I **think** that the reason for adding
OutputCollectionElement to the sequence is that you can have a `data`
element nested in a `collection` element.
To continue allowing this and making it more precise I've added an
additional `OutputCollectionDataElement` type that is allowed within
`collection`. This then should allow us to remove
`OutputCollectionElement` from the `OutputData` type.
A quick test against IUC and devteam revealed no problem with this
approach per se, however it showed that https://github.com/galaxyproject/tools-iuc/blob/aa8360cb3ec9faf1488938a430855977632706ff/tools/krakentools/extract_kraken_reads.xml#L145
uses `change_format` which is not implemented for collections.
.. 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 3.7 . To check your Python version, run:
.. code:: console
$ python -V
Python 3.7.6
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>`_ .