On 18/02/2011 19:12, Luciana Gomes wrote: > Hello, > Hello > I'd like to know if the work-in-progress 'workflow components' will be > useful to wrap a local application (suppose a command-line app) into a > component, without transforming it to a web-service. Will it be possible?
What you need will be included in Taverna 2.3 using a new type of service called an "external tool" that builds upon work developed as part of the KnowARC project. You will be able to describe how the application/tool is called and its parameters. In 2.3, the tool can then be run either locally or via ssh to another machine. The way of calling the tool is extensible and there is already a mechanism for running it on a grid, but that will not (for time reasons) be included in Taverna 2.3. It's likely that the grid invocation will be made available as a plugin, and probably an Amazon cloud plugin a bit later. There will be a way to describe tools for individual services and to have sharable registries of tools. You can install a plugin for Taverna 2.2 that shows a very early version of the external tool service. The user interface has changed a lot since and the plugin does not allow easy definition of tools. There is a wiki page describing how to write the XML files that describe the tools. See http://www.mygrid.org.uk/dev/wiki/display/developer/Calling+external+commands+from+Taverna At a recent Debian Med meeting, Hajo Krabbenhoft (who wrote the external tool service) wrote a translator from the description files that Soaplab uses into the descriptions used by the external tool service. With the help of Peter Rice from the EBI he tested this with the descriptions of EMBOSS. Hajo also implemented a registry where you will be able to upload descriptions. I have mainly been testing the external tool service with some Perl scripts written by Paul Fisher, whose workflows you may have seen on myExperiment. A similar mechanism to the external tool service is already being used by GIMIAS - see http://cilab2.upf.edu/gimias2/ Longer term, we aim to be able to take Galaxy tool descriptions and have Taverna be able to call Galaxy tools as services. There is related work done by Kostas Karasavvas from NBIC, that is much further advanced, to be able to have Taverna workflows called as Galaxy tools. He will be giving a presentation about that work soon. "Workflow components" are a way of creating more user-friendly wrappers for services so that they can work together well and are properly described. The workflow component work will be in Taverna 3. What you want will be in 2.3. If you want any more information, please let me know. If you also have some example tools that you'd like to be used as test cases, it will be much appreciated. > Thanks Alan ------------------------------------------------------------------------------ The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/
