Computational Techniques for Life Sciences

Looking and Moving Around

On a Windows or Mac desktop, our present location determines what files and folders we can access. I can “see” my present location visually with the help of the graphic interface - I could be looking at my Desktop, or the contents of a folder, for example. In a Linux command-line interface, we lack the same visual queues to tell us what our location is. Instead, we use a command - pwd (print working directory) - to tell us our present location. Try executing this command on Lonestar5:

$ pwd
/home1/03439/wallen 

This home location on the Linux filesystem is unique for each user, and it is roughly analogous to C:\Users\username on Windows, or /Users/username on Mac.

To see what files and folders are available at this location, use the ls (list) command:

$ ls

I have no files or folders in my home directory yet, so I do not get a response. We can create some folders using the mkdir (make directory) command. The words ‘folder’ and ‘directory’ are interchangeable:

$ mkdir folder1
$ mkdir folder2
$ mkdir folder3

$ ls
folder1  folder2  folder3

Now we have some folders to work with. To “open” a folder, navigate into that folder using the cd (change directory) command. This process is analogous to double-clicking a folder on Windows or Mac:

$ pwd
/home1/03439/wallen
$ cd folder1
$ pwd
/home1/03439/wallen/folder1

Now that we are inside folder1, make a few sub-folders:

$ mkdir subfolderA
$ mkdir subfolderB
$ mkdir subfolderC
$ ls
subfolderA  subfolderB  subfolderC

Use cd to Navigate into subfolderA, then use ls to list the contents. What do you expect to see?

$ cd subfolderA
$ pwd
/home1/03439/wallen/folder1/subfolderA
$ ls

There is nothing there because we have not made anything yet. Next, we will navigate back to the home directory. So far we have seen how to navigate “down” into folders, but how do we navigate back “up” to the parent folder? There are different ways to do it. For example, we could specify the complete path of where we want to go:

$ pwd
/home1/03439/wallen/folder1/subfolderA
$ cd /home1/03439/wallen/folder1
$ pwd
/home1/03439/wallen/folder1/

Or, we could use a shortcut, .., which refers to the parent folder - one level higher than the present location:

$ pwd
/home1/03439/wallen/folder1
$ cd ..
$ pwd
/home1/03439/wallen

We are back in our home directory. Finally, use the rmdir (remove directory) command to remove folders. This will not work on folders that have any contents (more on this later):

$ mkdir junkfolder
$ ls 
folder1 folder2 folder3 junkfolder
$ rmdir junkfolder
$ ls
folder1 folder2 folder3

A bonus command available on some Linux operating systems is called tree. (This is not found on your cheat sheet. Consider writing it in.) The tree command displays files and folders in a hierarchical view. Use another Linux shortcut, ., to indicate that you want to list files and folders in your present location.

$ tree .
.
|-- folder1
|   |-- subfolderA
|   |-- subfolderB
|   `-- subfolderC
|-- folder2
`-- folder3

Exercise

1. Navigate to your home directory
2. Make a new folder called challenge01
3. Navigate into that new folder
4. Make 5 sub folders called a, b, c, d, e
5. Wihin each of those sub folders, make 5 sub folders called 1, 2, 3, 4, 5
6. Navigate back to your home directory and print a hierarchical view of the challenge01 folder
7. Advanced Linux users: can you do this on one line?

Click here for solution

Review of Topics Covered