## Wednesday, August 7, 2013

### 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.
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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 https://github.com/Frogee/gatk-protected.git

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:
ant

And everything compiled successfully. From then on, I could move to the dist directory and test out the GATK:
java -jar GenomeAnalysisTK.jar --version