UNIX command line and scripting

The first part of this course introduces the UNIX command line on a Linux or Mac. The second part provides a basic introduction to string searches and scripting with AWK and BASH. It is aimed at colleagues who are going to run analysis programs on their own or wish to use computing clusters.

Topics

Out of scope

This course focuses on the basics of using the UNIX command line. This course will not teach you statistics or bioinformatics.

Prerequisites

Programming experience is not required but desirable. The ability to type with a low error rate is necessary, because this is a hands-on training.

Windows software

If you bring a Windows laptop to the training, please install the following programs:

Mac software

If you bring a Mac laptop to the training, please install the following program:

Practical information

Number of participants: minimum 5, maximum 10.

Length: The course takes two half-days, from 09:00 to 13:00 on the first half-day and 09:00 to 14:00 on the second day.