Linux/Mac command line tutorial

Table of contents

• Introduction to Linux
  • Introduction
  • File system overview
  • Key features of Linux
  • The terminal and the shell
• Command line overview: the essentials
  • Some commands to start with
  • Moving on the command line
  • List files and directories
  • File permission system
  • Useful commands
  • Pipes
  • Remote access
• Bash and shell scripting with bash
  • Introduction
  • Example of shell script

Introduction to Linux

Introduction

The linux philosophy: Many small programs that work together efficiently, with as goal usability and maintainability

Linux is a kernel, the operating system is GNU. But when people say Linux, they mean Linux Kernel + GNU-utils, which are a set of programs that are very well known and widely used, such as ls. There are also other kernels such as the BSD kernel, with a similar set of tools comparable to the GNU-utils.

The Kernel manages:

• System hardware such as the CPU and other input/output (IO)
• File system
• Processes scheduling

File system overview

Key features of Linux

• Comes with a package manager which installs and updates software from trusted sources. Updating the system is very easy.
• Very flexible: You can install desktops, GUI’s, window managers etc on top of linux
• Lightweight: You can make it as lightweight or bloated as you want
• Free and open source

The terminal and the shell

• The terminal is program that outputs text to user. Examples are: allacrity, iterm2, urxvt, st, putty and many more.
• Inside the terminal runs a shell, which is its own program which has certain functionalities such as: variables, functions, auto-completion.
• Examples of shells are: csh, zsh, bash, fish, bash is the most common, and often the one you encounter when you log onto a server.
• The shell runs as a REPL (Read Evaluate Print Loop, same as a console in R). It reads your input and evaluates it, prints the output, and lets you type in a new command.

Command line overview: the essentials

Some commands to start with

Moving on the command line

Tip: Press tab to auto-complete commands or paths when typing out paths.

List files and directories

File permission system

Useful commands

Pipes

Extremely useful and often used. Can be used to chain programs together that are on PATH variable (run echo $PATH so see all the directories that bash can use programs from, run env to see all variables that are currently in the bash environment)

use | to stream the output of a program to the input of a program

use >> for appending to a file
echo "I want to append my file with this string" >> myfile

use > for overwriting the file, it gives no warnings
echo "I want to overwrite my file with this string" > myfile

use < for reading from a file
less < bigFile.txt

Remote access

Bash and shell scripting with bash

Introduction

Bash is often the default shell when you log onto a system. The config file of bash is stored in a file called ~/.bashrc, when starting up a terminal with bash as the shell, the contents in ~/.bashrc are loaded (sourced), in your ~/.bashrc you can set your own settings.

Bash has its own programming language, which is very similar to but not the same as the programming languages of other shells. Bash has support for variables, functions and control flow statements. Writing a script using a shell script language, is called shell scripting. The combination of shell scripting and pipes is very powerful and can be used to write short and powerful programs. The power lies in the fact that you can create an new programs by combining other programs that are in the /bin directory (or one of the other directories on the PATH variable)

Use aliases to create your own shortcuts (run your shortcuts as if they are programs in the /bin folder). Aliases are very powerful, they can refer to scripts that do non-trivial things. Example: alias tu='top -o %CPU'. You can put these aliases in your ~/.bashrc so they are sourced when you start your shell session.

Example of shell script

Bash has its own scripting language, below is an example of a shell script:

#!/bin/bash

# The first line of the script tells the OS
# that the script has the be execute with bash.
# Bash is also a program. Try executing bash inside bash.

# Define the variable COUNTER and set to 1
COUNTER=1

while true; do

    # Append a string to the file called counter.log
    echo "Dit is mijn counter: ""$COUNTER" >> counter.log

    # Add one to counter
    COUNTER=$((COUNTER+1))

    # Let the CPU sleep for half a second
    sleep 0.5;

done & echo "Process has been send to the background, please kill me! run: kill ""$!"

# Note: the ampersand sends a program to the background and frees up the terminal. 
# Do not forget to kill it

To run this script, make it executable: chmod +x ./myscript.sh. Then you can run the program as follows: $ /path/to/myscript.sh. This script is appending a new line to a file called counter.log, a file which has been created by the script in the folder from where the script is run. Try executing tail -f counter.log on the file to see what happens. To see what the -f flag is doing, run: man tail.

See this overview for more an extensive overview of bash.

Tip: You can run shell commands from with python and R (In R this can be done with the system() function)