Prerequisites
From GSA
The GATK was designed and is intended for use on Linux (and other POSIX compatible) platforms. We do not currently support running it on a Windows platform.
The GATK is a Java-based tool; to run the GATK from one of our binary releases, you'll need a JRE 1.6 compatible JVM installed. To develop walkers for the GATK, you'll need the Java 1.6 JDK and Ant 1.7.1 (or greater). For testing of our latest releases, we use the following JVM/JRE:
java version "1.6.0_16" Java(TM) SE Runtime Environment (build 1.6.0_16-b01) Java HotSpot(TM) 64-Bit Server VM (build 14.2-b01, mixed mode)
Please be aware that at this time we only support the Sun/Oracle Java JDK; OpenJDK is not supported.
Of note, we have experienced issues with earlier versions of the JIT compiler on our Linux-amd64 machines. If the GATK crashes with a segmentation fault (An unexpected error has been detected by Java Runtime Environment), please update your JRE/JVM and try running the package again.
Within the Broad Institute
To load the JVM and ant into your current environment, use dotkit:
use -q Java-1.6 use -q Ant-1.7
External to the Broad Institute
Download the Sun JDK, version 1.6 from the following location:
Download ant from the Apache project.
