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Workflow


Taverna Administrators Guide


This Administrator's Guide provides the information and procedures necessary for installing and deploying a Taverna workflow service. The Taverna Workflow Service has two main components: the WSRF wrapper and the workflow engine.

The Taverna 2.0 Workflow Service is a WSRF implementation that wraps the Taverna engine as a WS Resource and exposes the available operations such as Create, Start, getStatus, and getOutput for user-submitted workflows.

The Taverna 2.0 Workflow Engine is what actually runs the workflows once they are submitted to the service.

Contents

Before You Begin


Prerequisite Software and Container Installation

In order to install and run the Taverna 2.0 workflow service, you need to install the caGrid 1.3 prerequisites and configure a container to host the Taverna service. In this guide, a Tomcat container is assumed.

The installation of caGrid 1.3 can occur via the recommended caGrid 1.3 Installer or manual caGrid 1.3 install.

Start Tomcat Container

In order to download and configure the Taverna workflow service with Tomcat, you must start the Tomcat service. Use the following commands to start the Tomcat service:

%> cd $CATALINA_HOME/bin
%> ./startup.sh

As the service starts, you should see lines similar to those shown in the figure below:

When finished, the Tomcat service is started. You can now validate that the service has started using the instructions below.

Validate Tomcat Installation and Service Startup

Once the Tomcat service has started, you can validate proper deployment and startup using your browser.

Assuming that you are using the default 8080 port, enter the following URL into your browser address bar:

http://localhost:8080/

If you are not using the default port, you must change the URL you enter to reflect the port you used to configure Tomcat:

https://localhost:<port_number>/

So for example, if you are using a secure port instead of the default port, the URL you enter may instead be:

https://localhost:8443/

When the URL opens, you should see the following page in your browser window:

Build Taverna Workflow Service

Because you used the Installer or Manual methods identified in the previous steps to install the current caGrid software release, you can skip this section. These methods automatically build the Taverna Workflow Service along with caGrid.

In the event that you want to build caGrid manually, use these commands:

  • Open a terminal and change to caGrid, then run the Ant build

    %> cd $CAGRID_HOME
    %> ant all

This should build the complete CaGrid software release, including the Taverna Workflow Service.

Once the build is complete, you can find the Taverna Workflow Service at $CAGRID_HOME/caGrid/projects/TavernaWorkflowService.

From this point forward, we will refer to this location as $TWS_HOME.

Taverna 2.0 Configuration and Installation


Once the Taverna Workflow Service is built, you must download a local copy of the Taverna 2.0 workflow engine.

The workflow service comes with an Ant target called taverna-package that downloads and installs a local copy of Taverna.

 %> cd $TWS_HOME
%> ant taverna-package

This target downloads the Taverna artifacts from theTaverna Maven Repository and installs it into $TWS_HOME/taverna directory.

NOTE: Ignore the Error messages (java.io.FileNotFoundException) when downloading the Taverna artifacts.

The Taverna engine is installed in the $TWS_HOME/taverna directory by default. If you need to install it to a different location, you can modify the _taverna-build.properties _file located in $TWS_HOME. See Editing taverna-build.properties below.

Currently the above step (ant taverna-package) can only install the Taverna 2.0 version. If you already have Taverna 1.7, you can still continue to use the older version along with the new one.

Editing the service.properties file allows you to use either Taverna installation at any given time. See Editing service.properties for more information.

After the ant target is finished, you should have a directly named $TWS_HOME/taverna/target/repository that contains all of the Taverna artifacts.

This completes the Build and Installation of Taverna Workflow Service and the Taverna 2.0 workflow engine. Simple, right

Editing the taverna-build.properties File (optional)

The taverna-package Ant target downloads the Taverna artifacts from the Taverna Maven Repository and by default installs them to the $TWS_HOME/taverna directory.

If you need to install the Taverna engine to a different location, you can modify the taverna-build.properties file to identify the preferred location for the installation. The taverna-build.properties file is located in the $TWS_HOME directory.

To change the location to which the Taverna artifacts are downloaded and installed, modify the maven.build.dir entry to reflect the appropriate path.

You can then run the command "ant taverna-package" as shown in the configuration and installation section above. The Taverna engine is installed into the directory you identify.

Be advised, that we recommend retaining the default settings for the taverna-build.properties file unless you have a specific reason to change them.

Deploy Taverna Service


Once the Taverna 2.0 Workflow Service and the Taverna 2.0 Workflow Engine are installed, you need to deploy the Taverna service. Deploying the service is simply a matter of letting the service know where the Taverna 2.0 repository is located. This is done in two steps: editing the Taverna 2.0 service.properties file, and then deploying the service in the Tomcat container.

Editing the service.properties File

Before deploying the service in the Tomcat container, you need to edit the service.properties file to set the tavernaDir and baseRepositoryDir entries to point to the corrct locations of the Taverna 2.0 artifacts.

You must use ablosute paths in the file. Do NOT include environment variables in the paths

If you retained the defaults for the caGrid and the Taverna installations, the values for these directory entries would be as follows:

  • tavernaDir = $TWS_HOME/taverna
  • baseRepositoryDir = $TWS_HOME/taverna/target/repository

The figure below shows these values for the directory entries:

Keep in mind that for these instructions, the $TWS_HOME directory is identified as $CAGRID_HOME/caGrid/projects/TavernaWorkflowService, and $CAGRID_HOME is /caGrid-1-0/. If you changed the target directories for the installation of either caGrid or Taverna, be sure to alter the values shown above to reflect the appropriate path(s).

NOTE: If you have both Taverna 1.7 and 2.0 installed, you can use either installation, however you MUST alter the directory entries in this file to point to the installation you want to use.

Running ant deployTomcat

Running the ant deployTomcat command deploys the Taverna Workflow Service in the Tomcat container.

Assuming that you have already set the $CATALINA_HOME environment variable, from within $TWS_HOME, run the following command:

 %> ant deployTomcat
When finished, you should receive a Deploy Successful message.

If you have not set the $CATALINA_HOME environment variable, you must do so prior to this step, being sure the variable points to the location where Tomcat is installed.

Running ant deployGlobus

In order to verify your installation you will need to deploy Taverna to your Globus installation. This will cause the creation of a client that can be used for testing.

 %> ant deployGlobus

Verifying the Installation


Perform the following are the steps to run a workflow:

  1. Download the Taverna test file
    Taverna caDSR Test File
  2. Change directory to Globus
     cd $GLOBUS_LOCATION/bin 
  3. Run the taverna-client against your service

    %> taverna-client -url <url of the service> -scuflDoc <workflow file>

  4. Verify Test Success
    1. Watch the output. There will be 4 steps that look like the following:

      In order to verify proper installation and deployment of the Taverna workflow service ocmponents, open the following URL in a Web browser:

If the validation is successful, pat yourself on the back! You have successfully installed and deployed a Taverna Workflow Service.

Last edited by
Sarah Honacki (1376 days ago)
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