1.2 Navigating the filesystem

In this section, you will learn about the structure of the Linux filesystem, and some basic commands for navigating the filesystem: pwd, ls, cd, mkdir

Exercise - Basic filesystem navigation

First, check where you are currently located in the filesystem with the pwd (“print working directory”) command:

pwd

Next, list the contents of the directory you are in:

ls

To create a new directory inside our current directory, run mkdir and specify a name for the new directory, like

mkdir new

You can change directory by running cd and specifying the directory you want to change to. For example, to change to the directory you’ve just created, run

cd new

and then use

pwd

again to verify your current working directory.

Exercise - Relative and absolute paths

You may have noticed that when you run the pwd command, it gives you a full path with several directory names separated by a / character. This is a full path. For example, after running the commands above, I would see the following output for pwd:

/users/ff524/new

When you run commands that involve a file or directory, you can always give a full path, which starts with a / and contains the entire directory tree up until the file or directory you are interested in. For example, you can run

cd /users/ff524

to return to your home directory. Alternatively, you can give a path that is relative to the directory you are in. For example, when I am inside my home directory (/users/ff524 - yours will be different), which has a directory called new inside it, I can navigate into the new directory with a relative path:

cd new

or the absolute path:

cd /users/ff524/new

The concepts and commands in this section will be essential for future lab assignments. They will be especially important when you use scp to retrieve data from your experiments - you will need to be able to find out the absolute path of the file you want to retrieve, so that you can use it in your scp command.

Some useful shortcuts for navigating the filesystem:

• Running cd with no argument takes you to your home directory.
• The shorthand .. refers to “the directory that is one level higher” (can be used with cd and with other commands).
• The shorthand ~ refers to the current user’s home directory (can be used with cd and with other commands).
• After navigating to a new directory with cd, you can then use cd - to return to the directory you were in previously.

Try these commands. Before and after each cd command, run pwd to see where you have started and where you ended up after running the command.

cd       # takes you to your home directory
cd ..    # takes you one directory "higher" from where you were before
cd ~     # takes you to your home directory
cd ../.. # takes you two directories "higher" from where you were before
cd -     # takes you to the directory you were in before the last time you ran "cd"

Then, return to your home directory.