Problem installing GATK

Question

[j.e.kelly]

Hi all,

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 /usr/local/bin.

I have entered the command : export PATH=$PATH:/usr/local/bin/gatk-4.1.0.0/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: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/bin/gatk-4.1.0.0/gatk.

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.

Thanks.

Answer 1

[WouterDeCoster]

in the $PATH environmental variable you should add the directory of the wrapper script, not the wrapper script itself.

Often it's also a better idea to create a symlink, rather than adding more and more directories to $PATH, e.g.:

ln -s /usr/local/bin/gatk-4.1.0.0/gatk /usr/local/bin/