https://github.com/stain/workflow-to-galaxy

cloned from https://trac.nbic.nl/svn/elabfactory/galaxy-taverna/workflow-to-galaxy/
https://github.com/stain/workflow-to-galaxy

Last synced: about 1 month ago
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cloned from https://trac.nbic.nl/svn/elabfactory/galaxy-taverna/workflow-to-galaxy/

• Host: GitHub
• URL: https://github.com/stain/workflow-to-galaxy
• Owner: stain
• License: other
• Created: 2014-12-09T10:24:23.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2014-12-09T10:28:43.000Z (about 10 years ago)
• Last Synced: 2024-11-05T13:13:11.288Z (3 months ago)
• Language: Ruby
• Homepage: https://trac.nbic.nl/elabfactory/wiki/eGalaxy
• Size: 156 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • Changelog: CHANGES
  • License: LICENSE

Awesome Lists containing this project

README

        
= workflow-to-galaxy tool generator

Authors::     Konstantinos Karasavvas, Finn Bacall

Gem Version:: 0.3.4

Contact::     mailto:[email protected], mailto:[email protected]

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

Copyright::   (c) 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]  | 

Generates a Galaxy tool (a UI xml definition plus a script) for the

specified Taverna2 workflow, where  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 http://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:: https://trac.nbic.nl/elabfactory/wiki/eGalaxy

Galaxy::         http://galaxy.psu.edu

Taverna2::       http://www.taverna.org.uk

myExperiment::   http://www.myexperiment.org

== Semantic Versioning

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