Pre-course Information


There are a few things to do *before* the course starts. Please read carefully and follow the instructions so we can have a good start to the course. Contact us in case anything is unclear.

Computational Resources

During the course we will be using Uppsala University’s high performance computer cluster (UPPMAX). We will be using Rackham and Pelle. Note that the instruction below to connect to Rackham is essentially the same for Pelle.

Register at SUPR

A SUPR/NAISS account is needed to use UPPMAX resources. If you do not already have one, please register for an account at SUPR/NAISS and then you must accept the user agreement either online or in paper form. For those within Swedish academia, it is recommended to register with your SWAMID. If you don’t have a SWAMID connected account, you will have to send in your signed user agreement in paper form together with a copy of your passport. Note that this manual process can take a week or more. You can follow this detailed instruction. Once you have a SUPR/NAISS account, please request membership to the project UPPMAX 2025/2-309.

Apply for an UPPMAX user account

After you have been added to a SUPR project, you can now apply for a user account in UPPMAX if you do not have an existing account yet. This will be the account you use to log in to UPPMAX so it is not the same as your SUPR account. Note that it might take up to 2 working days for your account to be created. You will then receive 2 emails with information on how to login to UPPMAX. To apply, please follow this instruction.

Set-up your UPPMAX 2-factor authentication

Please follow the instruction here.


Connect to UPPMAX cluster Rackham

There are three ways to connect to Rackham: a text-based SSH connection from a terminal, a graphical remote desktop using a Thinlinc client on your laptop and a remote desktop environment via a web browser.

SSH connection using a terminal

A straightforward way to connect to Rackham is through a terminal using ssh -X or ssh -Y connection.

  • For Linux users, use Terminal (included by default).

  • For Mac users, use Terminal (included by default). You need to also install XQuartz to enable X11 forwarding from a terminal, i.e., to run graphical applications on a remote server while displaying them on your laptop. After installing XQuartz, restart your laptop.

  • For Windows system, we recommend using MobaXterm. Please install the program and not use the portable version. MobaXterm also has a built-in X11 and an integrated SFTP file browser to transfer data between the remote cluster and your computer. After installing MobaXterm, restart your laptop.

Other SSH clients and X-servers for MacOS and Windows are described here.

GUI desktop using ThinLinc locally

You can also connect to Rackham via a graphical remote desktop using a local ThinLinc client on your laptop. Thinlinc is useful if you need to view images or documents in GUI programs without having to first download the image/document to your own computer first. Since it is using graphics, it will require you to have an internet connection that is good and stable.

GUI desktop using ThinLinc in a web browser

Lastly, you can connect to Rackham using a remote desktop environment via a web browser at https://rackham-gui.uppmax.uu.se/. This is the easiest option as no software installation is needed but it will give you the slowest connection. It will require you to have an internet connection that is good and stable. For this option, you have to set up your UPPMAX two factor authorization (2FA). See how to get an UPPMAX 2FA.


This tutorial will guide you to connect to Rackham using the three methods as described above. For Windows users with MobaXterm, please follow this instruction.


Some useful tutorials:


Check configuration and X11 forwarding

After you complete setting-up and you receive a notification from SUPR that your account have been added to the course allocation

  • open a Terminal

  • login by typing this command ssh -X [username]@rackham.uppmax.uu.se

  • type id in the command line

  • copy the output of the command and email back (to the course organisers at edu.epigenomics@nbis.se)

  • type xclock

If X11 forwarding is enabled then a window with a clock should pop up on your desktop machine.

Install Tools

Software Dependencies

The exercise on WGBS can be executed locally in your laptop using R and RStudio. If you prefer to run R scripts in your laptop, you can configure your own system to follow the exercises:

Both of these work on computers running Linux, Windows and Macintosh operating systems. RStudio is a set of tools as well as an editor that facilitates the use of R (R ICE). Over the last years it has become a very popular tool and in many ways become a de-facto standard for working with R.

Note that on same operative systems it will be easier to install and run R and RStudio if you are administrator of your own computer and hence are allowed to install software on your machine. If you do not have these privileges please ask your system administrator to install the latest version of R and RStudio.

The R packages that you need to install are listed in below. Note that the R and R-package versions follow the setup that is pre-installed in Rackham. You are free to install the latest versions.

Requirements for WGBS labs (all of these are R packages).

Software

Version

R

4.0.0

methylKit

1.14.2

genomation

1.20.0

GenomicRanges

1.40.0



Further optional preparations

For those of you wanting to start ahead and/or brush up on various skills before the course.

Computer skills