Gentle introduction

Materials and notes for practicals in Masaryk University course DSIB01 Introduction to Bioinformatics taught in the fall semester 2021/2022


Gentle introduction

When the shell is first opened, you are presented with a prompt, indicating that the shell is waiting for input.

Terminal

$

The shell typically uses $ as the prompt, but may use a different symbol. In the examples for this lesson, we’ll show the prompt as $ . Most importantly: when typing commands, either from these lessons or from other sources, do not type the prompt, only the commands that follow it. Also note that after you type a command, you have to press the Enter key to execute it.

The prompt is followed by a text cursor, a character that indicates the position where your typing will appear. The cursor is usually a flashing or solid block, but it can also be an underscore or a pipe. You may have seen it in a text editor program, for example.

First command

So let’s try our first command, ls which is short for listing.

Terminal

$ ls

When we hit enter, we will get list the contents of the current directory:

Terminal

$ ls

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Command not found

If the shell can’t find a program whose name is the command you typed, it will print an error message such as:

Terminal

$ ks

ks: command not found

This might happen if the command was mis-typed or if the program corresponding to that command is not installed.

Clearing your terminal

If your screen gets too cluttered, you can clear your terminal using the clear command. You can still access previous commands using and to move line-by-line.

Terminal

$ ls

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$ ks

ks: command not found

$ clear

Up to now, we already have our terminal full of information. We use clear command to get back to empty terminal.

Terminal

$


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