Taverna 1.6 Manual.
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Taverna 1.6 Manual.

Warning

If you are running a version of Taverna later than version 1.6, for example 2.0, then please visit the myGrid site for up-to-date documentation.

Table of Contents

1. Users Guide.
1. Workbench Overview
1.1. Definitions
1.2. Benefits of workflow technology
2. Getting started with Taverna
2.1. Installation
2.1.1. Windows
2.1.2. Linux
2.2. Configuration
2.2.1. Artefact repository location
2.2.2. Proxy configuration
2.2.3. The mygrid.properties file
2.2.4. Default services
2.2.5. Image types and the mysterious 'Error 4'
2.2.6. Setting an alternative location for the 'dot' tool
2.3. Custom perspectives
2.4. Running Taverna
2.4.1. Enacting a predefined workflow
2.4.1.1. Loading a workflow
2.4.1.2. Enacting the current workflow
2.4.1.3. Browsing results
2.4.2. Creating a (very) simple workflow
2.4.2.1. Workflow inputs and outputs
2.4.2.2. A single sequence fetch component
2.4.2.3. Connecting everything together
2.4.2.4. Describing the input
2.4.2.5. Enacting the workflow
3. Workbench windows in detail
3.1. Advanced Model Explorer
3.1.1. Entity table
3.1.1.1. Workflow metadata
3.1.1.2. Worfklow inputs and outputs
3.1.1.3. (Slight digression) - Interesting MIME types for Taverna
3.1.1.4. Connecting workflow inputs to processors
3.1.1.5. Processors (Top level node)
3.1.1.6. Individual processor nodes
3.1.1.7. Data link nodes
3.1.1.8. Control link nodes
3.2. Workflow diagram
3.2.1. Toolbar
3.2.1.1. Diagram Save Options
3.2.2. Diagram configuration
3.2.3. Show types
3.2.4. Expanding nested workflows
3.2.5. Hide boring processors
3.2.6. Port display section
3.2.7. Alignment control
3.2.8. Image navigation, where the 'Fit to window checkbox' gone?
3.2.9. Processor colours
3.3. Available services
3.3.1. Service panel organisation
3.3.2. Adding instances of a service to the workflow
3.3.2.1. Creation using drag and drop
3.3.2.2. Creation using menu options
3.3.2.3. Discovering the service for a given processor
3.3.2.4. Importing a workflow from the service panel
3.3.2.5. Searching over the service panel
3.3.2.6. Fetching service descriptions
3.3.2.7. Populating the services panel
3.4. Enactor launch panel
3.4.1. Enactment status panel
3.4.1.1. Enactment status
3.4.1.2. Processor states
3.4.1.3. Inspecting intermediate results
3.4.1.4. Results browser
3.4.1.5. Process report
4. Scufl language and Workbench features
4.1. Implicit iteration
4.1.1. Implicit iteration over multiple inputs
4.2. Conditional branching
4.3. Beanshell scripting
4.3.1. Creating a new beanshell instance
4.3.2. Defining inputs and outputs
4.3.3. Configuring the script
4.3.4. Sharing and reuse of scripts
4.3.5. Depending on third party libraries
4.3.5.1. Using dependencies
4.3.5.2. Dependency classloaders
4.3.5.3. JNI-based native libraries
4.4. R-scripts with the RShell processor
4.4.1. Introduction and installation
4.4.1.1. Installing on Windows
4.4.2. Using the RServe processor
4.4.3. Connection and advanced port types
4.4.4. Graph output
4.5. Biomart query integration
4.5.1. Describing a Biomart service
4.5.2. Creating a new Biomart query
4.5.3. Configuring filters
4.5.4. Parameterised filters
4.5.5. Configuring attributes
4.5.5.1. Selecting attributes
4.5.5.2. Result modes
4.5.6. Second dataset filters
4.6. Soaplab configuration
4.6.1. Metadata display
4.6.2. Polling
4.7. WSDL processor
4.7.1. WSDL scavenger
4.7.2. XML Splitters
4.7.3. Optional elements in return data
4.7.4. Cyclic references
4.8. Breakpoints - debugging and steering workflow invocation
4.8.1. Breakpoints
4.8.2. Global pause function
4.8.3. Editing intermediate data
4.8.3.1. Effect on LSIDs
4.8.4. Cancelling the workflow
4.9. Executing a workflow without the GUI
5. Taverna plugins
5.1. Semantic search of services with Feta
5.1.1. Creating service search requests
5.1.2. Results displayed and integration into the workflow
5.2. Taverna LogBook
5.2.1. LogBook Wiki
5.3. Taverna Interaction Service
5.3.1. Using the Interaction Service from Taverna
5.4. Taverna Remote Execution
5.4.1. Specifying Remote Execution Servers
5.4.2. Running a workflow remotely
6. Additional optional tools
6.1. API Consumer
6.1.1. Prerequisites
6.1.2. Setup
6.1.3. Usage
6.1.4. Adding methods to API definition
6.1.5. API level metadata.
6.1.6. Saving the API definition file.
6.1.7. Using the API consumer processor from Taverna
6.1.8. A word of advice
6.2. Webservice Data Proxy
6.2.1. Description
6.2.2. Initial Configuration and Installation
6.2.3. Adding Webservices
6.2.4. Configuring Webservices
6.2.5. Referencing in action.
6.2.6. Data dereferencing
6.2.7. Data housekeeping
6.2.8. Current constraints and future work.
6.3. Interaction Service Server
6.3.1. Setup
6.4. Remote Execution Server
6.4.1. Configuring the database
6.4.2. Installation
6.4.3. Administration
6.4.4. Security Considerations
2. Developers Guide.
1. Getting started.
1.1. Subscribing to the mailing lists.
1.2. Getting the Taverna sourcecode.
1.3. Building Taverna with Maven.
2. Extending Taverna using a Service Provider Interface (SPI).
2.1. Available SPI's.
2.2. Declaring your SPI.
3. Creating Plugins.
3.1. Writing the Plugin.
3.2. Publishing the Plugin.
3.2.1. Deploying the Plugin artifact.
3.2.2. Describing the Plugin.
3.2.3. Installing the Plugin.
3.3. Publishing Plugin updates.
4. Using the Taverna API to programmatically execute a workflow
4.1. Initialising the Repository
4.2. Registering the repository with the Taverna SPI registry
4.3. Example application
4.4. Example source code
5. Appendix.
5.1. Useful properties.
5.2. Taverna versioning guidelines.
3. Administrator's Guide
1. Overview
2. What happens when Taverna loads?
3. Runtime configuration of Raven within the Workbench
4. Customising mygrid.properties (and raven.properties, log4j.properties).
5. Summary
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   Chapter 1. Users Guide.