I am currently experiencing a problem with installing the GATK. I have followed the instructions on the quick start guide but seem to have a problem with the wrapper script. I have downloaded the package and it is stored within the directory
I have entered the command :
export PATH=$PATH:/usr/local/bin/gatk-18.104.22.168/gatk into the terminal as instructed. I have then checked if the gatk wrapper script has been added to my path with the command echo
$PATH, and indeed it is. The path was displayed was the following:
Upon trying to invoke the GATK with the command:
./gatk --help, this fails and I get the message
'No such file or directory'. I was wondering if anyone could aid in troubleshooting this? I have an the correct versions of Java and Python outlined in the requirements section.