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Jump into the terminal#

Select File -> New -> Terminal, or click the Terminal icon on the launcher pane. You'll get a new terminal tab in the activity bar, and find yourself in a bash shell.

Who is jovyan?

Looking at your bash prompt, you'll notice that your username is jovyan (there's a backstory, but it means 'related to Jupyter'). Why is everyone's username the same? Your notebook server is running as a container. The container instance is private and linked to your Bryn user's storage, but the image it runs is the same for everyone. As a result, it is not necessary or desirable to have unique system users.

TLDR: don't worry about it. Inside your notebook server, your username is jovyan

By jove comic

Where am I? Who am I?#

By default, you're in a bash shell running against the base operating system of the climb-jupyterhub container image (which is based on Ubuntu). You'll see in your bash prompt that you're in your home directory (represented by the tilde character ~).

jovyan:~$ pwd

What about sudo?

jovyan doesn't have sudo privileges. This may seem restrictive, but we've pre-configured the climb-jupyter base image with everything you'd likely need sudo for pre-installed. Everything else should be installable via package managers, such as Conda. You'll also be able to run Nextflow against out K8s execution environment 'out-of-the-box'.

How do I install software?#

In the first instance, check out installing software with Conda.

What next?#

You many want to read the reference material on using the Linux command line