Some colleagues have been asking about installing and using the fabulous Prokka software on a compute cluster. Without root privledges this can be somewhat tricky if you don’t know where to start. Particularly, on our compute cluster the default Perl version is old, and you don’t have the option to install custom modules due to permissions restrictions. Here’s how you get a working standalone Perl environment that you can update and modify freely and how you install the Prokka perl module dependencies. We’ll be using the glorious Perlbrew.
Setting up PERL5 environment
Installing Prokka dependencies
These are the required perl modules for Prokka
If you are interested in prediciting rRNAs then I would recommend installing the barrnap program
Finally, add barrnap-0.7/bin to your PATH
Installing Prokka itself
Add prokka-1.1X/bin to your PATH
Good to go!