Welcome to WAVES galaxy adapter documentation !¶

ReadME¶

WAVES adaptors classes are aimed to be used inside a WAVES-webapp project, but could be useful elsewhere depending on your requirements

Features¶

Waves Galaxy adapter is a set of classes intended to wrapped remote calculation devices interface into the WAVES unified ServiceRunner API through Galaxy Server (https://usegalaxy.org)

WAVES core package: https://github.com/lirmm/waves-core
GALAXY project: https://galaxyproject.org/
BioBlend galaxy API: https://github.com/galaxyproject/bioblend

Contribute¶

Issue Tracker: https://github.com/lirmm/waves-galaxy/issues
Source Code: https://github.com/lirmm/waves-galaxy

Support¶

If you are having issues, please let us know. We have a mailing list located at: waves-webapp@googlegroups.com

License¶

The project is licensed under the GNU GPLv3 license.

Authors¶

Marc Chakiachvili (LIRMM - UMR 5506 CNRS / UM - France)
Vincent Lefort (LIRMM - UMR 5506 CNRS / UM - France)
Anne-Muriel Arigon Chiffoleau (LIRMM - UMR 5506 CNRS / UM - France)

License (GPLv3)¶

WAVES packages are free software: you can redistribute it and/or modify it under the terms of the GNU General Public License version 3 as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

For more specific details see http://www.gnu.org/licenses, the Quick Guide to GPLv3. in the codebase.

The GNU operating system which is under the same license has an informative FAQ here.

Note to developers¶

We very much appreciate you using our code to do fun and interesting things with. We hope that while doing this you may find and fix bugs or make enhancements that could be useful for the greater community and will makes the developers aware of them by emailing to waves-webapp@googlegroups.com so they can be considered to be added to the original code base.

Installation¶

Add WAVES adaptors to communicate with Galaxy server

Warning

To run WAVES, it is strongly recommended to read dedicated doc: waves-core.

Note

You need to install waves-core packages in your app before running this setup Once created your Django application, with waves-core, simply add waves-galaxy package

Add package to your virtual env

pip install waves-galaxy

1. Configure WAVES¶

You simply enable waves-galaxy adapters in your settings.py file

WAVES_CORE = {
   ...
   'ADAPTORS_CLASSES': (
        ...
        'waves.adaptors.galaxy.tool.GalaxyJobAdaptor',
        'waves.adaptors.galaxy.workflow.GalaxyWorkFlowAdaptor',
    ),
}

Contributing¶

You can contribute to WAVES project(s) with following repositories:

Git source code: https://github.com/lirmm/waves-galaxy
Issue tracker: https://github.com/lirmm/waves-galaxy
Mailing list: waves-webapp@googlegroups.com

Version 1.1.3 - 2018-02-15¶

Integrated tools import from waves-core last version (1.1.9)

Version 1.1.2 - 2014-02-07¶

[Updated] - updated dependency to waves-core 1.1.6

Version 1.1.1 - 2014-10-18¶

Corrected importer / runner for Galaxy Tools

Version 1.1.0 - 2017-09-30¶

Integrated modification issued from waves-core 1.1.2
Added changelog

Version 0.0.3 - 2017-07-07¶

First Ready to play version - detached from waves-core