Quick Unix/Linux command line shell

The key to power bioinformatics

The command line shell is the main way to interact with most powerful computing systems and bioinformatics tools. This course provides what you need to get going with the shell.

Next session: October 2020

Instructors

Matthew Hartley
Burkhard Steuernagel

Audience

For those new to the command line shell with a need to use it.

Overview

Many bioinformatics applications and pipelines require knowledge of the unix command line shell. In particular, High Performance Computing (HPC) systems work with a command line interface. In addition, the shell provides a powerful tool for saving time and making computational work reproducible. This course is intended for those with no previous experience of the command line shell, and aims to enable attendees to use command line applications.

Schedule

Day1

9:30	Start
11:00	Coffee break
13:00	End

Learning outcomes

By the end of the course you should be able to:

Understand the reasons why we need to use the command line shell, and advantages to doing do.
Work with the filesystem using the shell
Run commands and understand how their output can be usefully redirected
Write simple scripts

Pre-requisites

None

Full course syllabus

Introduction
Navigating files and directories
Working with files and directories
Pipes and filters
Loops
Shell scripts
Finding things

Course materials

Course book