installation.rst

Tested on (Requirements)

• OS base: CentOS (x86_64) \boldsymbol{\ge} 6.6
• Java 1.8.
• Python \boldsymbol{\ge} 2.6.
• Git \boldsymbol{\ge} 1.8.2 with git-lfs.

Build process

This entry described the installation process of GATK4.

1. Clone the GATK4 repository.

   git clone https://github.com/broadinstitute/gatk

2. Load the Java module.

   module load java/jdk-1.8.0_112

3. Enter the directory and compile it.

   Note

   You can choose tha way to build:

   • ./gradlew bundle or ./gradlew
     • This creates a zip archive in the build/ directory with a name like gatk-VERSION.zip containing a complete standalone GATK distribution, you can also run GATK commands directly from the root of your git clone after running this command.
   • ./gradlew installDist
     • Does a fast build that only lets you run GATK tools from inside your git clone, and locally only (not on a cluster).
   • ./gradlew installAll
     • Does a semi-fast build that only lets you run GATK tools from inside your git clone, but works both locally and on a cluster.
   • ./gradlew localJar
     • Builds only the GATK jar used for running tools locally (not on a Spark cluster). The resulting jar will be in build/libs with a name like gatk-package-VERSION-local.jar, and can be used outside of your git clone.
   • ./gradlew sparkJar
     • Builds only the GATK jar used for running tools on a Spark cluster (rather than locally).

   cd gatk
   ./gradlew installDist

4. Move your compile files to the path where you want GATK4.

   mv gatk/ /your/path/

5. Create the module.

Module Files

Apolo II

.. literalinclude:: src/4.1.0.0
   :language: tcl
   :caption: :download:`GATK4-4.1.0.0 <src/4.1.0.0>`