Introduction to the Command Line for Genomics: Glossary

The shell gives you the ability to work more efficiently by using keyboard commands rather than a GUI.

Useful commands for navigating your file system include: ls, pwd, and cd.

Most commands take options (flags) which begin with a -.

Tab completion can reduce errors from mistyping and make work more efficient in the shell.

The /, ~, and .. characters represent important navigational shortcuts.

Hidden files and directories start with . and can be viewed using ls -a.

Relative paths specify a location starting from the current location, while absolute paths specify a location from the root of the file system.

You can view file contents using less, cat, head or tail.

The commands cp, mv, and mkdir are useful for manipulating existing files and creating new directories.

You can view file permissions using ls -l and change permissions using chmod.

The history command and the up arrow on your keyboard can be used to repeat recently used commands.

grep is a powerful search tool with many options for customization.

>, >>, and | are different ways of redirecting output.

command > file redirects a command’s output to a file.

command >> file redirects a command’s output to a file without overwriting the existing contents of the file.

command_1 | command_2 redirects the output of the first command as input to the second command.

Scripts are a collection of commands executed together.

Loops make commands to be repeated multiple times.

Spend the time to organize your file system when you start a new project. Your future self will thank you!

Always save a write-protected copy of your raw data.