Setting-up
Before we start tutorial, we need to set up our work environment. In particular, we need to:
access files prepared for the tutorial and keep folder structures organised - we have prepared scripts to set this up for you for most of the labs;
if you work without access to Uppmax: check the dependencies
Using computational resources
We have booked 5 cores on Rackham per course participant. To run the tutorial in the interactive mode log on to Rackham and run interactive command:
ssh -Y <username>@rackham.uppmax.uu.se
interactive -A naiss2023-22-673 -p core -n 5 -t 08:00:00
This command gives you access to 5 cores for eight hours or until 17:00, whichever comes first.
Please make sure you do it only ONCE per day, as by repeating this command you will use up resources reserved for others.
Check which node you were assigned
squeue -u <username>
And connect to your node with
ssh -Y <nodename>
If you lose connection to the server during a tutorial, please connect again to Rackham and do ssh -Y <nodename> again. You will reconnect to your set of cores.
Directory structure
There are many files which are part of the data set as well as there are additional files with annotations that are required to run various steps in this tutorial. Therefore saving files in a structured manner is essential to keep track of the analysis steps (and always a good practice). We have preset data access and environment for you.
Commands and modules
Many commands are quite long as there are many input files as well as several parameters to set up. Consequently a command may span over several lines of text. The (backslash character \ indicates to the interpreter that the command input will continue in the following line, not executing the command prematurely.
Hint
To see all options for applications used throughout the class type command -h to view usage help.
You will notice that you will load and unload modules practically before and after each command. This is done because there are often dependency conflicts between the modules used in this exercise. If not unloaded, some modules will cause error messages from the module system on Rackham. More on module system used on Uppmax.
Hint
The commands in this tutorial contain paths as we set them up in the setup steps for each tutorial. If you change file locations, you will need to adjust paths to match these changes when running commands.
Software Dependencies
If you have no access to Uppmax, where all software is preinstalled, you can configure your own system to follow the exercises.
The dependencies are listed in Dependencies.