You will need a terminal program to access the server. This is already available on Mac and Linux, and can be found by searching for ‘Terminal’.
If you do not already have access to a Mac/Linux terminal, for this course you will only need an interface to interact with the server in which we will work: Gemini. An easy way to do this is installing MobaXTerm:
If you have any problems, don’t hesitate to ask the teachers for help.
From the Terminal, you can access the Linux environment for this course, which will take place at the University server Gemini. You can access Gemini through SSH (Secure Shell protocol), which allows connecting securely to a remote server. In the command line, do:
$ ssh username@gemini.science.uu.nl
Replace “username” by your UU username. After you do this, you will need to input your password. Welcome to Gemini!
In order to access the software you will need for this course, you need to run the following command:
$ course b-b3bcg20
Remind yourself of how to work in a linux environment. Check where you currently are by running:
$ pwd
And check what files are available to you by doing:
$ ls -l
You will see the folder “data_bb3bcg20”. Light blue means that it is a ‘soft link’ to a different location, but you can treat this as a regular folder. Check the contents of this folder by doing:
$ ls -l data_bb3bcg20/
Lastly, generate your own work environment in your home directory:
$ mkdir GenomeBioinformatics/
You are all set!
If you would like a quick refresher on some basic linux commands, take a look at the following sites: