Taverna to Pig Compiler

Compiling Taverna Workflows to Apache Pig Programs

Introduction

Taverna is an open source and domain-independent Workflow Management System - a suite of tools used to design and execute scientific workflows and aid in silico experimentation. In order to be able to easily scale workflows created with Taverna, this compiler automatically generates a pig script file that can be executed on a Hadoop Cluster.

For more information see https://pig.apache.org/ or http://www.taverna.org.uk/

Usage

This will compile the taverna workflow and generate the pig script and configuration files in the output path.

java -cp target/taverna-to-pig-1.0-SNAPSHOT-withDependencies.jar \ 
  edu.tuberlin.dima.taverna_to_pig.main.TavernaToPigMain \
  -i path_to_taverna_workflow -o path_to_output

To run the pig script in local mode, go inside the path_to_output use the predefined shell script.

sudo chmod +x run.sh
./run.sh

Demo

Prerequisites

• Install Oracle Java (JDK 1.6)
• Install Taverna from http://www.taverna.org.uk/download/workbench/
• Download/install Apache Pig 0.10.1 from http://mirror.dkd.de/apache/pig/pig-0.10.1/

Getting the project

• In Eclipse Check out from SCM: https://github.com/umaqsud/taverna-to-pig.git
• git clone https://github.com/umaqsud/taverna-to-pig.git

Run the Example

java -cp target/taverna-to-pig-1.0-SNAPSHOT-withDependencies.jar \ 
  edu.tuberlin.dima.taverna_to_pig.main.TavernaToPigMain \
  -i src/test/resources/scufl/workflows/scape_ffff/FFFF-Workflows-simple.t2flow -o output

Or in Eclipse, open the Run Configurations

• Create a new one and name it whatever you want
  • As Project choose taverna-to-pig
  • As main class choose edu.tuberlin.dima.taverna_to_pig.main.TavernaToPigMain.java
  • If you want a simple demo, add the program arguments -i src/test/resources/scufl/workflows/scape_ffff/FFFF-Workflows-simple.t2flow -o output
• Click on Run

Extending the Compiler

Currently, the compiler supports workflows with any number of Local Tool Incocations or XPath Services processors, which can be combined in a linear fashion. In the future it shall be possible to extend the compiler easily in order to incorporate further Taverna features.