Source code and BaseSpace configs for GATK3 Best Practices wrapping App.
Docker container with this sources is at https://hub.docker.com/r/gurevich/gatk3_best_practices/. It is based on ubuntu Docker. Additional installations are (after sudo apt-get update):
- python v2.7 (
sudo apt-get install python) - java v1.7 (
sudo apt-get install openjdk-7-jre-headless) - samtools v.0.1.19 (
sudo apt-get install samtools) - tabix and bgzip (
sudo apt-get install tabix)
Deployment protocol and workflow overview are here.