gatk-3.8.def

BootStrap: docker
From: ubuntu:16.04

%labels
Maintainer klein
base.image="ubuntu:16.04"
version="1"
software="GATK"
software.version="3.8-1"

%post
apt-get update
apt-get install -y build-essential wget zlib1g-dev openjdk-8-jdk-headless maven git
apt-get clean && apt-get purge

cd /tmp

git clone https://github.com/broadgsa/gatk-protected.git gatk
cd gatk
git checkout 3.8-1
mvn package
cp target/GenomeAnalysisTK.jar /opt
cd /tmp
rm -r gatk




%runscript
exec java -jar /opt/GenomeAnalysisTK.jar "$@"