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.

Overview

In this chapter we explain what high-performance computing is and, at a very high level, how it is used.

This documentation doesn’t cover everything. You’ll need some basic Linux skills and how to get around using a terminal. This section has suggested reading and covers the conventions of this documentation.

How do request an account? How do I connect? What if I forgot my password? This section covers the basics and a bit more. Read this for a head start.

The queueing system is a central part of any high-performance computing system. Here you learn the most common commands and how to work with both interactive and batch jobs.

These are instructions for the users who are working in a closed zone (primarily iPSYCH). If you are not working in a closed zone you can skip this part.

Most likely you’ll need to install software. Here’s a complete guide to using the Conda package manager for managing all of your software needs.

In this section you learn where to store your data, how backup works and how to get data in and out of GenomeDK.

How do I request a project folder? How many resources am I using? How do I keep an eye on what other members of my project are doing? In this section we aim to answer these questions.

Knowledge is power and so is your data. Therefore you should take great care when handling your data. In this section you’ll learn how to organize your project so that your work becomes more reproducible, easier to navigate, and easier to clean up.

Some software is… special. In this section we cover how to do specific things with specific pieces of software that are commonly used.

Finally, here’s an overview of the commands used in this documentation.