Navigating Files and Directories

Getting started

The first thing we need to do is log in to our cloud instance.

**1. Open the cloudspan folder you created for the course**

Open your file manager and navigate to the cloudspan folder (hint: we recommended you make the folder in your Desktop directory - but you might have made it somewhere else). If you cannot find the folder, you can remind yourself where it is stored by looking at the absolute path you wrote down in the previous episode.

The folder should contain the login key file we downloaded in the previous episode and nothing else.

2. Right-click and open your machine’s command line interface

Now we can open the command line.

Windows users:
- Right click anywhere inside the blank space of the file manager, then select Git Bash Here. A new window will open - this is your command line interface, also known as the shell or the terminal. It will automatically open with your cloudspan directory as the working directory.
Mac users, you have two options:
- EITHER: Open Terminal in one window and type cd followed by a space. Do not press enter! Now open Finder in another window. Drag and drop the cloudspan folder from the Finder to the Terminal. You should see the file path leading to your cloudspan folder appear. Now press enter to navigate to the folder.
- OR: Open Terminal and type cd followed by the absolute path that leads to your cloudspan folder. Press enter.

Reminder: our file structure

Before we start, here’s a reminder of what our file structure looks like as a hierarchy tree:

Keep this in mind as we continue to navigate the file system, and don’t hesitate to refer back to it if needed.

Examining the contents of other directories

In the previous session we learned how to use pwd to find our current location within our file system. We also learned how to use cd to change locations and ls to list the contents of a directory.

By default, the ls commands lists the contents of the working directory (i.e. the directory you are in). You can always find the directory you are in using the pwd command. However, you can also give ls the names of other directories to view. Navigate to your home directory if you are not already there.

Code

cd

Then enter the command:

Code

ls cs_course

Output

data   databases

This will list the contents of the cs_course directory without you needing to navigate there.

The cd command works in a similar way.

Try entering:

Code

cd
cd cs_course/data/

This will take you to the data directory without having to go through the intermediate cs_course directory.

Navigating practice

Navigate to your home directory. From there, list the contents of the illumina_fastq directory.

Solution

Code

cd
ls cs_course/data/illumina_fastq

Output

ERR4998593_1.fastq  ERR4998593_2.fastq

Full vs. Relative Paths

The cd command takes an argument which is a directory name. Directories can be specified using either a relative path or a full absolute path. The directories on the computer are arranged into a hierarchy. The full path tells you where a directory is in that hierarchy. Navigate to the home directory, then enter the pwd command.

Code

cd  
pwd

You will see:

Output

/home/csuser

This is the full name of your home directory. This tells you that you are in a directory called csuser, which sits inside a directory called home which sits inside the very top directory in the hierarchy. The very top of the hierarchy is a directory called / which is usually referred to as the root directory. So, to summarize: csuser is a directory in home which is a directory in /. More on root and home in the next section.

Now enter the following command:

Code

cd /home/csuser/cs_course/.hidden

This jumps forward multiple levels to the .hidden directory. Now go back to the home directory.

Code

cd

You can also navigate to the .hidden directory using:

Code

cd cs_course/.hidden

These two commands have the same effect - they both take us to the .hidden directory. The first uses the absolute path, giving the full address from the root directory /. The second uses a relative path, giving only the address from the working directory. A absolute (full) path always starts with a /. A relative path does not.

You can usually use either a full path or a relative path depending on what is most convenient. If you want to reach a directory further down the same branch as your current working directory, it’s easiest to use the relative path since it involves less typing. If you’re trying to get to a directory in a different branch, it might be more convenient to use the full path instead of navigating “backwards” and then forwards.

Over time, it will become easier for you to keep a mental note of the structure of the directories that you are using and how to quickly navigate amongst them. We will be using the same directory structure for this whole course so navigating it should get easier as you progress.

Relative path resolution

Using the file system diagram below, if pwd displays /home/csuser/cs_course/data/illumina_fastq, what will ls ../nano_fastq display?

Can you explain why?

Blank instance file tree. — Instance file tree.

Solution

Output

ERR5000342_sub12.fastq

The command ls .. moves us up a folder level before we list the contents of nano_fastq.

Navigational Shortcuts

The root directory is the highest level directory in your file system and contains files that are important for your computer to perform its daily work. While you will be using the root (/) at the beginning of your absolute paths, it is important that you avoid working with data in these higher-level directories, as your commands can permanently alter files that the operating system needs to function. In many cases, trying to run commands in root directories will require special permissions which are not discussed here, so it’s best to avoid them and work within your home directory.

Dealing with your home directory is very common. The tilde character, ~, is a shortcut for your home directory. In our case, the root directory is two levels above our home directory, so cd or cd ~ will take you to/home/csuser and cd / will take you to /.

Navigate to the illumina_fastq directory:

Code

cd
cd cs_course/data/illumina_fastq

Then enter the command:

Code

ls ~

Output

bin  cs_course software

This prints the contents of your home directory, without you needing to type the full path.

The commands cd, and cd ~ are very useful for quickly navigating back to your home directory. We will be using the ~ character in later lessons to specify our home directory.