GATK Queue support¶

We have code that integrates GATK Queue with Arvados, creating child jobs for each work unit spawned by GATK Queue. Source is on GitHub

Build process:

1. Install Maven, dependencies, and plug-ins: sudo aptitude install openjdk-7-jdk maven libmaven-jar-plugin-java libmaven-shared-jar-java libmaven-compiler-plugin-java
2. Build and install the Arvados Java SDK. In arvados/sdk/java, run: mvn package -Dmaven.test.skip=true && mvn install -Dmaven.test.skip=true
3. Build GATK Queue. In gatk-protected, run: mvn package

If it succeeds, you'll have target/Queue.jar. Our GATK Queue jobs to date run that jar from a collection, so arv keep put it where you need it.