4. Using the command line

In this section, you will find an overview of the Linux command line, the shell and terminal programs, some commonly used commands, and a sample exercise.

• 4.1. Shell and Terminal
  • 4.1.1. The shell prompt
• 4.2. An overview of commands
  • 4.2.1. Command options
  • 4.2.2. Getting help on using commands
  • 4.2.3. date — display current date and time
  • 4.2.4. cd — change directory
  • 4.2.5. mkdir — create new directory
  • 4.2.6. rmdir — remove empty directory
  • 4.2.7. ls — list files
  • 4.2.8. cp — copy files
  • 4.2.9. cat — display contents of files or combine them
  • 4.2.10. less — view and navigate file contents
  • 4.2.11. head — print first few lines of a file
  • 4.2.12. tail — print last few lines of a file
  • 4.2.13. mv — move a file or directory
  • 4.2.14. rm — remove files or directories
  • 4.2.15. echo — display text or values of variables
• 4.3. Other useful commands
  • 4.3.1. df — report disk usage
  • 4.3.2. du — estimate disk usage of files or directories
  • 4.3.3. find — search for files
  • 4.3.4. free — view free and used memory
  • 4.3.5. locate — find files using their names
  • 4.3.6. which — locate a command
• 4.4. Editing text files using nano
  • 4.4.1. Create new file
  • 4.4.2. Pasting text from clipboard
  • 4.4.3. Saving changes
  • 4.4.4. Exit nano
• 4.5. Exercise — using the command-line
  • 4.5.1. Summary of steps
  • 4.5.2. Get sample data
  • 4.5.3. Install NCBI BLAST+ package
  • 4.5.4. Download query sequence
  • 4.5.5. Download protein sequence database
  • 4.5.6. Search database using query sequence
• 4.6. Notes
  • 4.6.1. Adding directories to PATH
  • 4.6.2. Dealing with spaces in file names