workflow-to-galaxy tool generator

Authors

Konstantinos Karasavvas, Finn Bacall

Gem Version

0.3.4

Contact

[email protected], [email protected]

Licence

MIT (See LICENCE or www.opensource.org/licenses/mit-license)

Copyright

© 2010 Netherlands Bioinformatics Centre, The Netherlands

Synopsis

This script requires a Taverna2 workflow URL as input and generates a Galaxy tool (a UI XML definition plus a script) that will enable the execution of this workflow through Galaxy. The tool's description is as good as the description provided in the workflow itself. Currently, the myExperiment workflow repository is used to access workflow information via its REST API but a workflow description from a file is also supported.

The name is workflow-to-galaxy rather than t2-workflow-to-galaxy because it is possible that it will support other workflow management systems in the future.

Installation

[sudo] gem install workflow-to-galaxy

Usage

workflow_to_galaxy [options] <myExperiement-workflow> | <t2flow-file>

Generates a Galaxy tool (a UI xml definition plus a script) for the specified Taverna2 workflow, where <myExperiment-workflow> is the full URL of the workflow in the myExperiment website. Alternatively a t2flow file can be passed for workflows not in myExperiment. Available options are:

-o OUTPUT, --output=OUTPUT  The file name(s) of the generated tool. If it is not specified then the workflow's name will be used.

-s SERVER, --server=SERVER  The taverna server that the script will request execution from. If it is not specified then "http://localhost:8980/taverna-server" will be used.

-t,        --t2flow         The workflow is a t2flow file.

Example

Let's say we want to install the taverna2 workflow www.myexperiment.org/workflows/74.html from myExperiment repository:

$ workflow_to_galaxy  -s http://localhost:8980/taverna-server  http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_781733.t2flow?version=5

References

Taverna-Galaxy

trac.nbic.nl/elabfactory/wiki/eGalaxy

Galaxy

galaxy.psu.edu

Taverna2

www.taverna.org.uk

myExperiment

www.myexperiment.org

Semantic Versioning

This module uses semantic versioning concepts from semver.org/.