Compile Genome Analysis Toolkit (GATK) from source

07/28/14 Edit: I don't think this post is up to date any more. Word on the street is that they're using something else as the build tool.

I'm planning on using the Broad Institute's Genome Analysis Toolkit (GATK) for some variant calling. The Java source code is available on GitHub, so I forked it over so I could have a look at the code (and play with it one day?). I've never compiled any Java code before, so I figured it was a good time to learn. I was doing this on a brand new workstation in our lab that I'm administrating, so I had to get a few dependencies first:
sudo apt-get install git ant openjdk-7-jre openjdk-7-jdk
Git is a version control software, ant is (from my understanding) a build tool for Java, conceptually similar to GNU make, and, based on the name, I assume the others are Java version 7, the Java Runtime Environment and the Java Development Kit, respectively. Then I cloned my forked repository:
git clone
My best guess is that a build.xml file for ant are conceptually similar to a Makefile for make, although I'm not entirely sure. Changing to the top-level of the cloned directory, I simply ran:
And everything compiled successfully. From then on, I could move to the dist directory and test out the GATK:
java -jar GenomeAnalysisTK.jar --version
Good times ahead.


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