If you see an error: CommandLineGATK : Unsupported major.minor version 51.0), while running new GATK, this means you most likely need newer java. Either:
- Install the latest java with apt-get (if you have root access and Ubuntu/Debian)
sudo apt-get install oracle-java9-installer
ie. if you have your JRE unpacked in ~/src/jre add these lines to your ~/.bashrc:
#java RE export PATH=~/src/jre/bin:$PATH
And open new terminal window.
You can check installed JRE version with
The location of `java` binaries can be checked with