NAVIGATING UNIX/LINUX TERMINAL

The Unix/Linux terminal (also known as the command line or shell) is a powerful text-based interface that allows users to interact with the operating system directly. Through simple commands, you can manage files, install software, automate tasks, and execute scripts efficiently. It is an essential tool for bioinformatics, system administration, and development.

15 Simple Terminal Commands for Beginners

1. 1. pwd – Print Working Directory

   Displays the full path of the current directory you are in.

   pwd

    

   2. ls – List Files and Directories

   Lists the files and folders in the current directory.

   ls           # Basic listing

   ls -l        # Detailed view with permissions, size, and date

   ls -a        # Includes hidden files

    

   3. cd – Change Directory

   Used to navigate between directories.

   cd /home/user/Documents   # Move to a specific directory

   cd ..                     # Move up one directory level

   cd ~                      # Return to the home directory

    

   4. mkdir – Make Director

   Creates a new folder or directory.

   mkdir new_folder

    

   5. rmdir / rm -r – Remove Directory

   Deletes a directory.

   rmdir empty_folder        # Removes an empty directory

   rm -r folder_name         # Removes a non-empty directory recursively

    

   6. cp – Copy Files or Directories

   Copies files or entire folders to a new location.

   cp file1.txt file2.txt          # Copy a file

   cp -r folder1/ folder2/         # Copy a folder and its contents

    

   7. mv – Move or Rename Files

   Moves files to a new location or renames them.

   mv oldname.txt newname.txt      # Rename a file

   mv file.txt /home/user/Desktop  # Move a file to another directory

    

   8. rm – Remove Files

   Deletes files permanently from the system.

   rm file.txt

   rm *.txt     # Remove all text files in a directory

    

   9. cat – View File Content

   Displays the content of a text file.

   cat filename.txt

    

   10. head / tail – View Sections of a File

   Shows the beginning or end of a file.

   head filename.txt      # Display first 10 lines

   tail filename.txt      # Display last 10 lines

    

   11. grep – Search Text Patterns in Files

   Finds specific text or patterns in files.

   grep "keyword" file.txt             # Search for a keyword

   grep -r "sequence" /home/user/data  # Recursive search in a directory

    

   12. find – Locate Files

   Searches for files or directories by name or type.

   find /home/user -name "*.fasta"    # Find all FASTA files

    

   13. chmod – Change File Permissions

   Grants or restricts file access and execution permissions.

   chmod +x script.sh     # Make a script executable

    

   14. history – Display Command History

   Shows the list of recently executed commands.

   history

    

   15. man – Access Manual Pages

   Displays detailed documentation for any terminal command.

   man ls

   man awk