Before setting up Hadoop-1.2.1 cluster, all nodes should be configured first. It can be done by following steps in given link: http://www.michael-noll.com/tutorials/running-hadoop-on-ubuntu-linux-single-node-cluster/
Hadoop multi node cluster setup is done by following this link: http://www.michael-noll.com/tutorials/running-hadoop-on-ubuntu-linux-multi-node-cluster/
Download Eclipse IDE for java EE Developers by following this link: http://www.eclipse.org/downloads/eclipse-packages/
Download hadoop plugin by following this link:Download
Configure the hadoop plugin with eclipse by following this link: https://www.youtube.com/watch?v=-001hhMk11M&index=12&list=PL2jvR2CemrGomVj6pTLd6726b7CyXGpgc
Start Hadoop Daemons.
Import Pharmahadoop in Eclipse.
Fill the details which are specified by "<>" symbol in java files. Input file must be in SDF format and the query file must be in xml format.
To run programme do right click from main (Driver method) programme and run application as Java application.