|Version 5 (modified by kostas.karasavvas@…, 5 years ago)|
Enacting Taverna workflows through Galaxy
The diversity and availability of bioinformatics tools have been increased in the recent years. Some tools deal with the same problem using a different approach, others provide different access mechanisms to the same resources while others provide aggregation mechanisms to make use of a number of tools in a uniform way. For the latter, software pipelining systems, are becoming the norm in bioinformatics. Widely used examples of such systems are Galaxy1, a web-portal and framework, and Taverna2, a workflow management system. The goal of both of these systems is to provide a platform that bioinformaticians and biologists can use to describe their experiments in a number of well described processing steps, i.e. workflows.
However, the approach used is different. In Galaxy the focus is on an intuitive and easy to use user interface, a web-based portal, to aggregate several bioinformatics tools and expose them in a uniform way. Taverna is a workflow management system that allows for the orchestration of (primarily) Web Services. It provides good extensibility points to add new functionality (called shims and plugins). It offers a powerful and flexible workflow language that allows for the description of complex workflows that include repetitions, conditionals and other well understood programming language constructs.
Both of the above mentioned systems provide a wide range of functionality out of the box. There is some overlap but the real added value would be if we could combine that functionality and try to get the best of both systems. This work aims to bridge the two by allowing the more expressive but complex Taverna workflows to execute via the simple and intuitive interface that Galaxy offers. To this end we built a Galaxy tool generator that given a Taverna workflow description and a Taverna server3 it constructs a Galaxy tool to enable the enactment of that workflow via Galaxy.
This generator is available in a workflow repository, myExperiment4,5, and it will generate the Galaxy tool behind the scenes. The bioinformatician will just browse the myExperiment repository to identify Taverna workflows that are of interest to him/her and he will be able to download them as Galaxy tools which can then be installed into Galaxy server the usual way.
There are plans to further automate this procedure by accessing the myExperiment site as Galaxy external interface, which will dynamically add the workflows as new tools in Galaxy.
1. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team. Genome Biology, Vol. 11, No. 8., 2010
2. Taverna: a tool for building and running workflows of services. Duncan Hull, Katy Wolstencroft, Robert Stevens, Carole Goble, Mathew R. Pocock, Peter Li, Tom Oinn. Nucleic acids research, Vol. 34, Web Server issue, pp. W729-W732, 2006
4. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic acids research, Vol. 38 (suppl 2): W677-W682, 2010.
Kostas Karasavvas (kostas.karasavvas@…)
Marco Roos (m.roos1@…)
(16.5 KB) - added by kostas.karasavvas@…
4 years ago.
Generates the Galaxy tool from a Taverna2 workflow (myExperiment) URL or from t2flow file.
(19.5 KB) - added by kostas.karasavvas@…
4 years ago.
Given a myExperiment URL of a Taverna2 workflow it provides a workflow object with everything needed to generate the Galaxy tool. Uses myExperiments REST API. Also contains the Taverna workflow classes to be used without myExperiment.