Basic Linux Commands

OS, Kernel & Shell

Operating System
System software - manages hardware and software resources
Types - Unix, Unix-like, Microsoft Windows, BSD, etc.
Eg: Windows 11, Linux (Unix-like), MacOS (Unix)
Linux is mostly open source and has many variations - Distributions or Distros - Red Hat (Commercial), Fedora, Debian, Ubuntu, Android, Mint, ChromeOS, etc.
Ubuntu is debian based distro developed by Canonical Ltd. and it has many variants - Lubuntu, Xubuntu, Ubuntu Budgie, Ubuntu Mate, UbuntuDDE, etc.
Fedora is the upstream source for RHEL (Red Hat Enterprise Linux)

Kernel
A computer program at the core of an OS (a portion of OS code), resides in the memory and provides interactions between hardware and software components.
Responsible for executing the programs and allocation of memory, resources, etc.
Types - Monolithic kernels (Linux), Microkernels (Minix 3), Hybrid Kernels (Windows, MacOS), etc.

Shell
An interface between user and kernel.
It allows a user to give commands to the kernel and receive responses from it.
Execute programs and utilities on the kernel.
Types - Bourne Shell (sh - developed by Steve Bourne, AT&T Bell Labs), GNU Bash, C Shell (csh), Korn Shell (ksh), Z Shell (zsh)

Bash

  • GNU Bourne-Again Shell
  • Designed based on the Bourne Shell (sh)
  • Unlike sh, it allows to recall the previous commands and edit them, if required.
  • Adds useful features from various shells like ksh and csh
  • Path: /bin/bash
  • Shortcut to open Terminal: Ctrl + Alt + T
Linux Terminal Window

Basic Commands

Command Description
pwd Print working directory - gives the path of current working directory, where the terminal is open
~ Home directory
/ Root directory
ls Lists contents of the current directory
-l Long list format output
-a All contents including the hidden items
-t List as per the time modified
-h Human readable memory units. Used along with -l
Item permissions - drwxr-xr-x - can be modified with chmod
cd Change directory
Use "TAB" key to autocomplete
.. Parent directory
mkdir Make Directory
touch Create new file
cp Copy a file from source to destination
mv Move a file from source to destination
Also used for renaming files
rm Delete a file
-dir Remove an empty directory (Alternative command: rmdir)
-r Remove directories and their contents recursively
head View the first 10 lines of a file
-n Specify the number of lines to display
tail View the last 10 lines of a file
-n Specify the number of lines to display
cat View the full contents of a file
Also used to concatenate (merge) multiple files into one
split Split files based on a specific number of lines (default is 1000 lines per file)
-l 4 Splits with 4 lines per output file
Redirection > Redirects its input into a new file. Always overwrites an existing file
< Reads from a file and uses it as input
>> Same function but appends to a file, instead of overwriting
| Chain multiple commands
echo Prints an input to the terminal
-e Enables backslash compatibility
--help Shows the instructions on how to use a command
history Displays the terminal history.
Otherwise, Up (↑) and Down (↓) arrows can be used to navigate through the previous commands one at a time
clear Clears the terminal screen
which Displays path of a command
-a To see all the installations/paths of that command
wc Gives line count, word count, and character count by default
-l only line count
-w only word count
-m only character count
grep Checks for an input PATTERN and displays the lines having that PATTERN
-i case insensitive
-c counts the lines having that PATTERN
sed Replaces certain pattern with another pattern
Eg: sed -i 's/:/_/g' Contigs.fasta
-i in-place substitution (Substitution occurs in the original file itself)
's/:/_/g' Substitute ":" with "_" in all instances
lscpu Details of the system processor
wget
curl		 Download content from internet using terminal
Installing Software Packages Ubuntu: sudo apt install package_name
Fedora: sudo dnf install package_name