jstjohn / gatk

GATK Official Release Repository

Green lab fork of GATK

Installation

1. Follow the steps on Broad's GATK building Queue from source wiki.
2. Follow the steps for setting up InteliJ Idea to work with Sting/queue.

Installation issues

One gotcha I ran into is with the following InteliJ step:

Back in the Project Structure window, under the Module 'Sting' , on the Sources tab make sure the following folders are selected

I found that the previous step which said to uncheck all but the java/src directory resulted in only that directly being listed as a source directory. The fix here is when you do this step to "make sure" these folders are selected, just navigate to the folders on the right side of the screen, right click on them, and select source or test from the dropdown. This adds the required files to the IDE.