Compiling and Installing GATK

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following commands to install GATK4:

   unzip gatk-4.0.0.0.zip
   export PATH=/path/to/GATK/gatk-4.0.0.0:$PATH
   gatk -help

3. Install and deploy the Hadoop and Spark services and then start them. For details, see "Compiling and Installing Hadoop and Spark" in Hadoop 3.1.2 + Spark 2.4.4 Porting Guide (CentOS 7.6).