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.

Clone the GATK4 repository.

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

Load the Java module.
```
module load java/jdk-1.8.0_112
```
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
```
Move your compile files to the path where you want GATK4.
```
mv gatk/ /your/path/
```
Create the module.

Module Files¶

Apolo II¶

GATK4-4.1.0.0¶

#%Module1.0####################################################################
##
## module load gatk4/4.1.0.0
##
## /share/apps/modules/gatk4/4.1.0.0
## Written by Manuela Carrasco Pinzon
##

proc ModulesHelp {} {
     global version modroot
     puts stderr "Sets the environment for using GATK4\
                  \nin the shared directory /share/apps/gatk4/4.1.0.0/"
}

module-whatis "(Name________) gatk4"
module-whatis "(Version_____) 4.1.0.0"
module-whatis "(Compilers___) java 1.8"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/gatk4/4.1.0.0/
set         version       4.1.0.0
set         sys           x86_64-redhat-linux

conflict gatk
module load java/jdk-1.8.0_112
 

prepend-path    PATH                    $topdir
prepend-path    PATH                    $topdir/libexec

prepend-path    MANPATH                 $topdir/share/man