Introduction

The default configuration of the freefluo workflow enactment engine is for WSFL. Some changes are required to use XScufl.

The installation of freefluo is basically the same whether you are going to be enacting XScufl workflows or WSFL workflows. The basic information is given in the installation and configuration page of the freefluo documentation.

Note that XScufl requires java 1.4.1 and therefore servlet.jar is required.

Common changes for Standalone or Web Services Freefluo

mygrid.properties

You need to edit the mygrid.properties file: see the standalone or web services section below for full details.

taverna jar files

1. Copy taverna-0.1beta4.jar (or the equivalent taverna jar file) to the lib directory. The taverna-0.1beta4.jar file is in the build directory if you have downloaded the taverna source, or in the lib directory if you have the scufl workbench.
2. Copy talisman1.4.5.11.jar (or equivalent) to the lib directory. The talisman1.4.5.11.jar is in the lib directory if you have downloaded the taverna source, or in the lib directory if you have the scufl workbench. (Strictly speaking you do not need this jar file unless you are running XScufl workflows that include talisman processors.)
3. Copy servlet.jar to the lib directory. The servlet.jar file if in the devlib directory if you have downloaded the taverna source, or in the lib directory if you have the scufl workbench.

Changes for Standalone Freefluo

runenactor.bat

Edit the runenactor.bat file in the bin directory so that the three jar files ( taverna-0.1beta4.jar, talisman1.4.5.11.jar, servlet.jar) to the classpath argument.

mygrid.properties

You need to edit the mygrid.properties file:

1. mygrid.workflow.enactor.api.class should be set to uk.ac.soton.itinnovation.taverna.enactor.TavernaWorkflowEnactor
2. The proxy properties: http.proxyHost, http.proxyPort, proxySet, and http.nonProxyHosts all need to be set for your local environment.
3. The provenance and workflow output logging properties are not normally relevant when running the freefluo enactor standalone. The properties mygrid.log.provenance and mygrid.log.output should both be set to false.

Testing

AffyIdToSequence is a simple test workflow. Any valid user.xml file should be acceptable. (There is one in the freefluo samples directory.)

Changes for Web Service Freefluo

runwsclient.bat

Edit the runwsclient.bat file in the bin directory so servlet.jar is added to the classpath argument.

mygrid.properties

You need to edit the mygrid.properties file:

1. mygrid.workflow.enactor.api.class should be set to uk.ac.soton.itinnovation.taverna.enactor.TavernaWorkflowEnactor
2. The proxy properties: http.proxyHost, http.proxyPort, proxySet, and http.nonProxyHosts all need to be set for your local environment.
3. The provenance and workflow output logging properties are not normally relevant when running the freefluo enactor as a web service. (If you are running the workflow from the myGrid workbench then freefluo enactor web service returns the provenance and output data to the workbench which has the responsibility for updating the myGrid Information Repository.) The properties mygrid.log.provenance and mygrid.log.output should both be set to false.

(re)deploy the enactment engine

ant deploy.freefluo.ws.axis (remember to set TOMCAT_HOME)

See freefluo installation and configuration page for details.

copy taverna jar file to axis

1. Copy taverna-0.1beta4.jar to %TOMCAT_HOME%\webapps\axis\WEB-INF\lib
2. Restart tomcat

The documentation says that the file copied to %TOMCAT_HOME%\webapps\axis\WEB-INF\lib should be tavernaenactor-0.1beta4.jar from the taverna source build directory. However the above approach also appears to work.

testing

1. runwsclient <enactor-service-url> (N.B. not the WSDL url)
2. The easiest way is to open the XScufl, input and user files in an editor and use cut and paste (ctrl-v).

AffyIdToSequence is a simple test workflow. Any valid user.xml file should be acceptable. (There is one in the freefluo samples directory.)

Documentation

There is documentation about configuring freefluo for XScufl.

From the taverna web site http://taverna.sourceforge.net

Select User Manual -> Configuring the myGrid Workflow Enactment Engine

However, (at 9th Sept 2003) this refers to an older version of the enactment engine.

Useful links

• Taverna (includes Sculf) http://taverna.sourceforge.net
• Freefluo http://freefluo.sourceforge.net
• XScufl models http://cvs.mygrid.org.uk/scufl

-- MarkGreenwood - 09 Sep 2003