Course Overview
This course covers the basic usage of the Linux Command Line Shell. Knowledge of how to interact with the shell is necessary to interact with most high performance computing (HPC) environments.
The understanding and usage of Linux Command Line Shell is crucial in HPC usage for scientific software tools to analysis large datasets that are too big to generally open on a graphical user interface systems, such as Windows or MacOS.
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.
This course is a prerequisite for all the following other bioinformatics courses, such as RNA-Seq and Sequence Analysis, within this training website.
Goals of this course
- Have some idea of the architecture of the Linux operating system.
- Have some understanding of the organisation of the file system on Linux.
- Understand the reasons why we need to use the command line shell
- Work with the filesystem using the shell Run commands and understand how their output can be usefully redirected
- Write simple scripts
- Understand the general structure of Linux commands.
- Be able to do pivotal things like view and edit the contents of files, copy and move files.
- Have an overview of how computers are used to analyse data.
A quick introduction to Linux/Unix Command line Shell
In part one, I will introduce command line shell: What it is and why we use it. During this session we will get our first view in Unix command line and see the difference between a Linux graphical user interface and the command line. I will work up to navigation of files and start looking into directories.
A quick introduction to Linux/Unix Command line Shell
In part two, I will go further in depth in navigating files and directories/folders. We again see the difference between the Linux graphical user interface and the command line. You will find out how you work with files and how to find your way between directories in the Unix command line. Subsequently, I will go further into how to create new files and directories and how to change these with a diverse range of commands. Once we mastered these commands, we briefly discuss pipes and wildcards that you can use to run multiple commands at once and read and write from multiple files. All these commands that you learned in these two parts are tools will then be applied in an example of sequence analysis.
