GATK source code debugging

pcdeni

Hi,

I followed the instructions from your guide on how to make GATK from source with IntelliJ IDEA.
My only problem is that GenomeAnalysisTK.jar is not generated, and I don't know which class should I give to the debugger as the main class?

Sheila

@pcdeni
Hi,

You can download the GATK here: https://www.broadinstitute.org/gatk/download/

-Sheila

pcdeni

Dear Sheila,

I downloaded the source code from github.
Then I followed your instructions from guide » developer zone » Setting up your dev environment: Maven and IntelliJ for GATK 3+
And now I have the source code in the IDE, and I can even make it, but if I try to modify something, then I have to set the main class (for ex. for debugging), and I don't know which is the main class, because GenomeAnalysisTK.jar is not among the source files, and there is no corresponding .java or .class file.

Thanks.

Sheila

@pcdeni
Hi,

I hope this will answer your question. I had to ask some of our software engineers @thibault @ronlevine

First you have to build the executable from the source code mvn verify -P!queue
The executable is: target/GenomeAnalysisTK.jar
Then setup IntelliJ: http://gatkforums.broadinstitute.org/discussion/4023/setting-up-your-dev-environment-maven-and-intellij-for-gatk-3
If you are debugging remotely: http://gatkforums.broadinstitute.org/discussion/4712/howto-set-up-remote-debugging-in-intellij

-Sheila