Installing Java Software

Synopsis

Google the package: for example GATK (You may  need to create an account with the Broad institute) to find the download link. A common scenario is the JAR file will be stored in a zip or tar.gz collection of files. After downloading you can invoke the JAR file with a compatible version of Java loaded as a module.

Example GATK

wget https://github.com/broadinstitute/gatk/releases/download/4.6.1.0/gatk-4.6.1.0.zip

unzip gatk-4.6.1.0.zip

mkdir ~/.local/gatk

mv gatk-4.6.1.0 ~/.local/gatk/4.6.1.0

Invocation

Invoke using full path:

module load Java/17

java -jar ~/.local/gatk/4.6.1.0/gatk-package-4.6.1.0-local.jar -h