Linux for Scientists: what to do at the black screen

This course aims to teach users of a Linux/UNIX system how to work with the command line interface. After an introduction to some history and basic concepts the basic commands for file and directory manipulation will be discussed. Subsequently, the students will learn how to manage processes as well as input and output redirection, followed by more advanced text processing utilities like ‘sed’ and ‘gawk’. The second half of the course shows 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 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.

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.

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