Command Line

Command Line Lecture

The TSL command line lecture course is designed to help a COMPLETE beginner get to grips with the command line. We run this course periodically and provide the course notes and slides below should you need them in a hurry.

Slides from Command Line Course

Come and see us for a one-to-one walkthrough of this content

If you want more information and some excellent training videos on this topic, then see the content embedded below and provided by our friends at Software Carpentry. These are a great bunch of educators with many years experience and some wonderful materials. T here are even more at The Software Carpentry Shell Lessons Page.

Command Line Quickies

So you need a quick reminder of the basic command line stuff, no problem, we all need cheat sheets!

Here are some command-line quickies for the following topics, they’re all at this user on youtube.

Short video on how to navigate the command line with ls and cd

Using the cd command and tab completion on the command line

Less and pipes – reading files and redirecting output

Using ls to get useful information about files and directories

How to make and remove directories on the command line

How to delete, copy and rename or move files



Perl, the daddy of all bioinformatics languages and one of the most-widely used. Perl (which doesn’t stand for anything, by the way) has a long, low learning curve and a huge set of libraries that make it quickly useful in all sorts of situations. All of these make it a great language to start with if you haven’t programmed before and an easy one to pick up if you already have some experience.

Here is a video of the beginner’s Perl training course. Try and remember that programming is a practical skill that comes with practice, so be assured that it gets more and more obvious and much easier the more you do. Don’t worry too much if the first time through this material you don’t get everything. That’s why the video, and the bioinformatics team are here. Come by and ask us if you have any questions.

Here is a PDF of the course slides

Here is the course worksheet

Here are the answers

Here are some great training videos!

Perl Intro

Working With Variables

Conditions and Arithmetic

Arrays and Loops

So what happened to the long training video? The hour long one that had Dan in?

Good question. That video served us well but has passed its usefulness. It was loooong. An hour long which we found meant that people got bored waiting or searching for the bit of information they wanted. It was hard to update because it was an hour long, we had to do the whole thing from scratch if we wanted to make a single change. So it has gone in favour of these short, focussed and more accessible mini-vids on specific topics. We don’t make these, but they are the official Perl videos.


Yes, it is named after Monty Python’s Flying Circus

And yes, the documentation and examples across the internet are full of references to Spam, Knights who say “Ni” and Holy Hand-grenades of Antioch, which is either hilarious or tedious depending on whether you think Python-eque humour is cutting edge or is solely for peoples Dads.

Nonetheless, its a fantastic language. Inspired by Perl amongst others it is finding great utility in bioinformatics particularly as a tool for dealing with next-generation sequence associated data.

It does have a higher learning curve than Perl though and some of the design concepts can be initially confusing. For this reason we do a kind of ‘conversion course’ for Python. Once you have a little experience with programming come on our Python course (slides attached) for an introduction.

I don’t want to wait – show me the funny

Python has a large background in computer science and physics (Monty Python fans, perhaps?) so there are actually quite a lot of resources around the ‘Net for this already. My favourite is at Codecademy and it’s really worth a look even for the absolute beginner.