Navigating Files and Directories

Overview

Teaching: 30 min
Exercises: 20 min

Questions

• How can I perform operations on files outside of my working directory?

• What are some navigational shortcuts I can use to make my work more efficient?

Objectives

• Use a single command to navigate multiple steps in your directory structure, including moving backwards (one level up).

• Perform operations on files in directories outside your working directory.

• Work with hidden directories and hidden files.

• Interconvert between absolute and relative paths.

• Employ navigational shortcuts to move around your file system.

Moving around the file system

We’ve learned how to use pwd to find our current location within our file system. We’ve also learned how to use cd to change locations and ls to list the contents of a directory. Now we’re going to learn some additional commands for moving around within our file system.

Use the commands we’ve learned so far to navigate to the shell_data/untrimmed_fastq directory, if you’re not already there.

$ cd
$ cd shell_data
$ cd untrimmed_fastq

Notice that your prompt changes each time you “cd” into another directory. This is very helpfu for keeping track of where you are.

What if we want to move back up and out of this directory and to our top level directory? Can we type cd shell_data? Try it and see what happens.

$ cd shell_data

-bash: cd: shell_data: No such file or directory

Your computer looked for a directory or file called shell_data within the directory you were already in. It didn’t know you wanted to look at a directory level above the one you were located in.

We have a special command to tell the computer to move us back or up one directory level.

$ cd ..

Now we can use pwd to make sure that we are in the directory we intended to navigate to, and ls to check that the contents of the directory are correct.

$ pwd

/home/user/shell_data

$ ls

sra_metadata  untrimmed_fastq

From this output, we can see that .. did indeed take us back one level in our file system.

You can chain these together like so:

$ ls ../../

prints the contents of /home.

Finding hidden directories

First navigate to the shell_data directory. There is a hidden directory within this directory. Explore the options for ls to find out how to see hidden directories. List the contents of the directory and identify the name of the text file in that directory.

Hint: hidden files and folders in Unix start with ., for example .my_hidden_directory

Solution

First use the man command to look at the options for ls.

$ man ls

The --all option causes ls to “not ignore entries starting with .” This is the option we want. The short form is -a.

$ ls --all

.  ..  .hidden	sra_metadata  untrimmed_fastq

The name of the hidden directory is .hidden. We can navigate to that directory using cd.

$ cd .hidden

And then list the contents of the directory using ls.

$ ls

youfoundit.txt

The name of the text file is youfoundit.txt.

The ls command comes with many other useful options, such as sorting by size or modification time. Take a moment to peruse some of these options. Don’t worry about remembering the flags, just make a mental note of what is possible, in case you need it in the future.

Examining the contents of other directories

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.

$ cd

Then enter the command:

$ ls shell_data

sra_metadata  untrimmed_fastq

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

The cd command works in a similar way.

Try entering:

$ cd
$ cd shell_data/untrimmed_fastq

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

Navigating practice

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

Solution

$ cd
$ ls shell_data/untrimmed_fastq/

SRR097977.fastq  SRR098026.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.

$ cd  
$ pwd  

You will see:

/home/user

This is the full name of your home directory. This tells you that you are in a directory called user (where user is your Garvan ID), 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: user is a directory in home which is a directory in /. More on root and home in the next section.

Now enter the following command (again, substitute user for your Garvan ID):

$ cd /home/user/shell_data/.hidden

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

$ cd

You can also navigate to the .hidden directory using:

$ cd shell_data/.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 home directory. The second uses a relative path, giving only the address from the working directory. A full path always starts with a /. A relative path does not.

Take a moment to let that sink in. Two of the most common problems with specifying file paths are 1) forgetting to start an absolute path with / and 2) starting a path with / when you actually wanted to specify a relative path. The best way to avoid these errors is to rely on tab completion every time you enter a path. It’s quicker, you’ll avoid typos AND you will avoid confusion between absolute and relative paths (because tab completion won’t work if you use / incorrectly, reminding you to double-check).

A relative path is like getting directions from someone on the street. They tell you to “go right at the stop sign, and then turn left on Main Street”. That works great if you’re standing there together, but not so well if you’re trying to tell someone how to get there from another country. A full path is like GPS coordinates. It tells you exactly where something is no matter where you are right now.

You can usually use either a full path or a relative path depending on what is most convenient. If we are in the home directory, it is more convenient to enter the full path. If we are in the working directory, it is more convenient to enter the relative path since it involves less typing.

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.

Relative path resolution

Using the filesystem diagram below, if pwd displays /Users/thing, what will ls ../backup display?

1. ../backup: No such file or directory
2. 2012-12-01 2013-01-08 2013-01-27
3. 2012-12-01/ 2013-01-08/ 2013-01-27/
4. original pnas_final pnas_sub

Solution

1. No: there is a directory backup in /Users.
2. No: this is the content of Users/thing/backup, but with .. we asked for one level further up.
3. No: see previous explanation. Also, we did not specify -F to display / at the end of the directory names.
4. Yes: ../backup refers to /Users/backup.

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 the 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/user and cd / will take you to /. Navigate to the shell_data directory:

$ cd
$ cd shell_data

Then enter the command:

$ ls ~

bio  course  data  r_data  shell_data

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.

Tree view

There is a very useful utility available on Wolfpack called tree that uses ASCII art to display the structure of the current directory as well as its subdirectory. Try the following:

$ cd ~
$ tree -L 3

Caution: By default, tree displays all of the directories below the current directory, as well as all the subdirectories of those directories and all their subdirectories, and so on all the way down to the lowest level. Depending on where you are in the filesystem, that could produce more output than is really helpful. It is usually a good idea to use the -L flag to only display a few “levels”.

Note: By default, tree doesn’t follow symbolic links. We’ve made quite liberal use of symbolic links for this workshop by placing the real data files on /share/ScratchGeneral/ and linking to these files from your home directory. You can instruct tree to follow symbolic links using the -l flag (that’s lowercase “l”).

$ cd ~/course
$ tree -l -L 3

sshfs

All the command line has many advantages, sometimes it is easier to browse the filesystem using familiar graphical interfaces. sshfs (Mac) and sshfs-win (Windows) are tools that allow you to “mount” the volumes on the cluster with the filesystem on your laptop so that you browse files and directories in much the same way as you would “mount” a USB stick or external drive. Using Finder or File Explorer to visually check the results of your operations can be helpful as you work through this course. See this Confluence page for details.

Key Points

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

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

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