Linux for Scientists [EL016]

Detailed information about this course:

Description

In this course, students will learn how to work with the command line interface of a (remote) computer running a Linux/UNIX operating system. Many scientists in, for example, the fields of genetic epidemiology, bioinformatics and machine learning run large analyses on Linux servers and many software packages and pipelines are developed only for Linux.

After an introduction to some history and basic concepts, students will learn how to find their way around the system and several commands for file and directory manipulation will be discussed. Subsequently, we will cover how to edit files on the server as well as how to redirect input and output of commands and how to use this to create pipelines. At the end of day one, this is followed by the use of more advanced text processing utilities like 'sed' and 'awk'.

The second day of the course teaches how to write Bash shell scripts to automate tasks. This knowledge is then used when discussing the Sun Grid Engine job queue system in use on for example the epib-genstat servers.

The course will focus on providing hands-on experience, so those who have been using a Linux system for a longer time will be able to skip the parts they already feel comfortable with and move on to more advanced concepts like regular expressions, version control and advanced use of a text editor.

Objectives

After completing this course, the students should be able to efficiently use a Linux system and its tools to:

• manage your project data from the command line (i.e. without having to copy files back and forth to the server);
• reformat output from previous analyses and use this as input for a subsequent analysis step;
• write scripts that automate repetitive tasks;
• efficiently run time-consuming analyses like a GWAS without overloading the server.
  

Assessment

Assignment(s)