Problem installing GATK
1
0
Entering edit mode
2.7 years ago
j.e.kelly • 0

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.

GATK script software error Ubuntu • 1.4k views
ADD COMMENT
0
Entering edit mode
2.7 years ago

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/
ADD COMMENT

Login before adding your answer.

Traffic: 1072 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6