GATK
Web: https://gatk.broadinstitute.org/hc/en-us
Installation
OpenJDK
Web: https://www.openlogic.com/openjdk-downloads
| Version | module | cromwell | Class file version |
|---|---|---|---|
| 8 | 8u382-b05 | cromwell-50.jar | 52 |
| 11 | 11.0.20+8 | cromwell-85.jar | 55 |
| 17 | 17.0.8+7 | cromwell-85.jar | 61 |
e.g., module load ceuadmin/openjdk/17.0.8+7 for Java 17.
GATK
The latest is 4.4.0.0,
wget https://github.com/broadinstitute/gatk/releases/download/4.4.0.0/gatk-4.4.0.0.zip
unzip gatk-4.4.0.0.zip
gatk --list
gatk HaplotypeCaller --help
We proceed to set up a module, to be loaded with module load ceuadmin/gatk/4.4.0.0.
At the time of writing (28/9/2023), gatk --list only works with Java 17.
Python
The dependencies are set up as follows,
module load anaconda/3.2019-10
conda env create -p /usr/local/Cluster-Apps/ceuadmin/gatk/4.4.0.0/anaconda-3.2019-10 -f gatkcondaenv.yml
conda activate /usr/local/Cluster-Apps/ceuadmin/gatk/4.4.0.0/anaconda-3.2019-10
cromwell
Web: https://cromwell.readthedocs.io/en/stable/
It provides support for workflow description language (WDL).
cd $CEUADMIN/gatk/cromwell
wget https://github.com/broadinstitute/cromwell/releases/download/85/cromwell-85.jar
wget https://github.com/broadinstitute/cromwell/releases/download/85/womtool-85.jar
wget https://github.com/broadinstitute/cromwell/releases/download/50/cromwell-50.jar
wget https://github.com/broadinstitute/cromwell/releases/download/50/womtool-50.jar
hello world
The WDL script hello-world.wdl is as follows,
workflow HelloWorld {
call WriteGreeting
}
task WriteGreeting {
command {
echo "Hello World"
}
output {
File outfile = stdout()
}
}
The call is as follows,
#!/usr/bin/bash
export GATK=$CEUADMIN/gatk
export v=4.4.0.0
module load ceuadmin/gatk/4.4.0.0
java -jar ${GATK}/cromwell/cromwell-85.jar run ${GATK}/${v}/tests/hello-world.wdl