Linux_Commands.md

The command prompt

When you open a terminal you are presented with a command prompt, waiting for you to input a command. It will look something like this:

username@computer-name:~$ |

It gives you information about:

• Your username

• The name of your computer

• The location in your filesystem (~ indicates your home directory) A separator, usually $ symbol

• The prompt (often blinking) waiting for your command input

Using user commands

Using sudo

Navigating the filesystem

The location of files in Unix is represented as a file path. For example:

/home/participant/Documents

Indicates the “Documents” folder of a user called “participant”. The first / at the beginning of the path indicates the root (or start) of the filesystem.

Paths can be specific in two ways:

Absolute path: specify the full path starting from the root. These paths always start with /.

Relative path: specify the path starting from your current location. For example, if you are located in /home/participant, the path Documents/resources would be equivalent to /home/participant/Documents/ resources. Relative paths never start with /.

Here are some key commands to navigate the filesystem:

• Up Arrow: Will show your last command
• Down Arrow: Will show your next command
• Tab: Will auto-complete your command
• Ctrl + L: Will clear the screen
• Ctrl + C: Will cancel a command
• Ctrl + R: Will search for a command
• Ctrl + D: Will exit the terminal

Some of the commands to know for navigation:

• pwd prints your current directory
• cd changes directory
• ls lists files and folders
• * is known as a “wildcard” and can be used to match multiple files

Here are some key commands to create directories and investigate the content of text files:

• mkdir creates a directory
• head prints the top lines of a file
• tail prints the bottom lines of a file
• less opens the file in a viewer
• wc counts lines, words and characters in a file
• grep prints lines that match a specified text pattern

Print working directory

pwd # Print the current working directory

The wildcard * can be used to match files that share part of their name. For example:

ls reference/*.fasta

Only matches the files with .fasta extension.

Using ls

Using cd

Using rm

Using rmdir

Using cat

Using grep

Using touch

Using weget

Using echo

Using zip tools

Clear the terminal screen

clear # Clear the terminal screen

Kill a process by name

kill process_name # Kill a process by name

kill -9 process_name # Force kill a process by name