Introduction to Linux Command Line

Linux is an operating system with a powerful command line interface that is widely used for biological data analysis and in server and cluster systems. A knowledge and understanding of how to interact effectively with the command line is essential when using many popular bioinformatics software packages, efficiently performing repetitive computational tasks, and working in high-performance computing cluster environments.

This course will provide an introduction to the most basic linux commands and by the end of the course the participants should be confident and competent in navigating around a linux filesystem, performing basic file operations and finding help on the command line. Most of the skills taught are also applicable to the Mac OS X operating system, which has a very similar and powerful command line interface.

This course is aimed at users who haven’t used the Linux command line before. In the first part of the course, the participants will get a short introduction to the general Linux filesystem layout and then learn about the most important commands to find help (man, apropos), move around the filesystem and find out where they are (cd, pwd, hostname), organize and manage files and directories (cp, mv, mkdir, rmdir) and permissions (ls, chmod, chown, chgrp).

The second part of the course will deal with viewing files (less, cat), extracting data from files (grep, head, tail) and introduce to some useful terminal tools (reset, clear), remote login (ssh) and the most important environment variables ($HOME, $PATH).

Topics explicitely not covered are: Editors, desktop tools, multimedia, scripts and control statements, background jobs.

Tutors: Toby Hodges (Bio-IT, Zeller Team) & Holger Dinkel (Bio-IT, Gibson Team)
Course Goals: Enable users to navigate the filesystem, manage files and directories and do simple data extraction from textfiles on the commandline
Prerequisites: None
Duration: 2 x 3-4 hours