Pre-course

There are 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 in unclear.

Computational resources

During the course we will be using Uppsala University’s high performance computer (Uppmax) as well as run scripts locally on laptops using R and R-Studio.

To be able to follow exercises we ask you to

  1. configure access to Uppmax
  2. install R and R-Studio on your laptop
  3. install Integrative Genomics Viewer on your laptop

Uppmax

Computational resources are provided by SNIC_UPPMAX. To be able to use them

  1. create a user account (only if you do not already have one)
  2. associate your user account with the course project

Create user account & request membership in the course project (for those new to Uppmax)

This involves few steps. Briefly,

  1. registering at SUPR
  2. accepting the User Agreement
  3. becoming a member in the project (g2018030)
  4. applying for an account at Uppmax

To go through the steps follow the instructions on Uppmax website. While at this keep this information handy:

  • Cluster name: rackham
  • Project ID: g2018030

Request membership in the course project (for those already having Uppmax account)

  1. log in to SUPR
  2. under Projects: Requesting Membership in Projects, request membership in g2018030

Check configuration (everyone)

After you complete setting-up

  • login to rackham.uppmax.uu.se
  • type “id” in the command line
  • copy and email back (course organisers) the output of the command

[A guide on how to log-in for the first time]((http://www.uppmax.uu.se/support/user-guides/guide–first-login-to-uppmax/)

R & R-Studio

We will also be using the latest version of R and R-studio locally. Both of these work on computers running Linux, Windows and Macintosh operative systems. R-studio is a set of tools as well as an editor that facilitates the use of R. 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 R-studio 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 R-studio.

Install R & R Studio

R

Install version 3.5.0 or higher

  1. Go to CRAN
  2. Click on the link corresponding to your operative system
  3. Download the recommended files for your system.
  4. Run the installer or move the downloaded files to suitable place on your computer.

R Studio

Go to the web page rstudio download the installer corresponding to your operative system. Unpack the installer and install the app on a suitable place on your system.

Test installations

If the installation above went without any problem you should be able to fire up R-studio and see something like the following:

IGV

To install, follow the instructions on the IGV website

Further optional preparations

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

Computer skills

ChIP-seq