Sunday, January 17, 2010

Installation HOWTO for CDK-Taverna in Taverna 1.7.2

Thomas made a new release of CDK-Taverna for the Taverna 1.7.2 release, which is great news as the previous release was for Taverna 1.7.1.

He asked me to test it, and I installed a fresh Taverna install and the new plugin. After that, I used the MyExperiment plugin to download one of the CDK-Taverna workflows Thomas has on MyExperiment, and tuned it a bit to use some local input instead of the database. I took some screenshots while at it, and will use those now to talk you through the installation of Taverna and the CDK-Taverna plugin.

Download Taverna
Taverna 1.7.2 can be downloaded from this download page, but I took the Linux version from the SourceForge download site. I cannot detail the OS/X or Windows installation, but on Linux you simply unzip the downloaded file, and you're ready to go:
$ cd taverna-1.7.2/
$ sh
Plugin Installation
Plugins can be installed using with the Plugin manager which can be accessed via the Tools menu:

Clicking the Find New Plugins takes you to a second dialog listing known plugin sites, and the default download has several already:

The CDK-Taverna update site is available at, and we can make Taverna aware of this update site by clicking the Add Plugin Site button:

After filling out these values and approving it with the OK button, it will show up on the dialog showing all available plugins, where you need the check the check box in front of the CDK-Taverna plugin name, as done in this screenshot:

You can then hit the Install button after which the plugin will be downloaded:

After it is done downloading the plugin, you can close the Plugin Sites and Plugin Manager dialogs. I shutdown and restarted Taverna with sh, but not entirely sure this is needed. After that, the CDK nodes showed up in the list of Taverna processors:

MyExperiment Plugin
Using the same Taverna Plugin Manager you can also install the MyExperiment plugin that allows you to search, browse, preview and download Taverna workflows from the MyExperiment website from within Taverna itself. I installed the plugin, and then used it to search for CDK workflows (and downloaded a QSAR workflow):

This about everything to get you going. It's not particularly rocket science, but I guess this howto is useful as you get to see what you should expect when setting up a CDK-Taverna environment. If you have further questions, please leave those in the comments section, and I'll try to merge in answers where possible, or otherwise in the reactions too.