Butlin:Unix for Bioinformatics - basic tutorial

Before you jump into this tutorial

• Your command line prompt will end with a $ sign. So a $ sign in this tutorial tells you to type the stuff that comes after the $ sign into your command line.

• The words folder and directory mean the same thing. So I use them interchangeably.

• Linux is Unix re-coded under an open-source licence, the same way as R is a re-coded version of S. Here, when I use the term Unix, I refer to all Unix-like computing environments, i. e. the original Unix that comes with Macs as well as most Linux flavours.

• The practical part of the workshop will be done on the computer cluster of the University of Sheffield called Iceberg. It has scientific Linux installed. You will log into your own accounts on Iceberg.

• If you have never used a Unix command line, we suggest you concentrate on the boldly printed text in the first two sections in this module. Make sure you get through them in time so that you are fit to do the rest of the workshop.

• There are still small (hopefully not large) bugs lurking in this protocol. Please help improve it by adding comments.

Iceberg - making first contact

Access with the programme PuTTY

If PuTTY can’t be found on your computer, go to section 1.2 Access via an internet browser.

Chose “iceberg” and press “Open”.

Type in the login name that you have been given, hit Enter, then type in the password and hit Enter.

Access via an internet browser

If PuTTY is not installed, you have to use an internet browser to access Iceberg.

Follow the link “Connect to Iceberg now!” on this site.