Documentation

It’s time to get your feet wet and learn how to use GenomeDK! The documentation is organized such that it can be used in two ways:

  • You can read it from beginning to end like a book to familiarize yourself with GenomeDK and learn how to do basic things like submitting a job and working with projects.
  • You can use it as a reference to look up the solution for specific questions you may have, such as what is the command for requesting a new project folder? Or, how do I get passwordless authentication working?

If you’re new to GenomeDK you will most likely want to read the documentation as a book. As you become more experienced you will more often use it as a reference.

Before you start reading the documentation and using GenomeDK, there’s a few things that you should know.

Conventions

You will be jumping a lot between different computers. This includes your own computer, the frontend node, and various compute nodes.

Commands that need to be run on your own computer will look like this:

[local]$ echo hello

Note that the prompt says local in square brackets. When you need to run a command on the frontend node, the prompt will instead say:

[fe-open-01]$ echo hello

Here, fe-open-01 is the name of the frontend node. If you need to run a command on a compute node that you started an interactive job on (more about this later), it will be shown like this:

[cn-1004]$ echo hello

In this case the compute node is cn-1004.

Learning to use the shell

When interacting with GenomeDK you will be using a shell on a Linux/UNIX system. If you are not familiar with these concepts we recommend the Shell novice tutorial from Software Carpentry.

If you are affiliated with Aarhus University or the Central Denmark Region (RM), there’s also excellent local training and consultancy initiatives available at:

If your research group, company or department needs training for GenomeDK specifically, we also offer workshops based on your needs.