The Filesystem

Overview

Teaching: 0 min
Exercises: 0 min

Questions

• Key question

Objectives

• Navigate the Unix file system

• Understand and use file paths and relative paths

• Keyboard shortcuts to make work more efficiently at the command line

The Unix directory file structure (a.k.a. where am I?)

As you’ve already just seen, you can move around in different directories or folders at the command line. Why would you want to do this, rather than just navigating around by clicking on folders as you might usually do.

When you’re working with bioinformatics programs, you’re working with your data and it’s key to be able to have that data in the right place and make sure the program has access to the data. Many of the problems people run in to with command line bioinformatics programs is not having the data in the place the program expects it to be.

Moving around the file system

Let’s practice moving around a bit.

We’re going to work in that dc_sample_data directory.

First we did something like go to the folder of our username. Then we opened ‘dc_sample_data’ then ‘data’

Let’s draw out how that went.

Now let’s draw some of the other files and folders we could have clicked on.

This is called a hierarchical file system structure, like an upside down tree with root (/) at the base that looks like this.

That (/) at the base is often also called the ‘top’ level.

When you are working at your computer or log in to a remote computer, you are on one of the branches of that tree, your home directory (/home/dcuser)

Now let’s go do that same navigation at the command line.

Type:

 cd

This puts you in your home directory. This folder here.

Now using cd and ls, go in to the ‘dc_sample_data’ directory and list its contents.

Let’s also check to see where we are. Sometimes when we’re wandering around in the file system, it’s easy to lose track of where we are and get lost.

Now let’s see what directory you’re currently in.

Type:

 pwd

This stands for ‘print working directory’. The directory you’re currently working in.

What if we want to move back up and out of the ‘data’ directory? Can we just type cd dc_sample_data? Try it and see what happens.

To go ‘back up a level’ we need to use ..

Type:

 cd ..

Now do ls and pwd. See now that we went back up in to the ‘dc_sample_data’ directory. .. means go back up a level.

Exercise

Now we’re going to try a hunt. Find the hidden directory in dc_sample_data, list its contents, 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

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 the home directory if you are not already there.

Type:

cd

Then enter the command:

ls dc_sample_data

This will list the contents of the dc_sample_data directory without your having to navigate there.

The cd command works in a similar way.

Try entering:

cd
cd dc_sample_data/untrimmed_fastq

and you will jump directly to untrimmed_fastq without having to go through the intermediate directory.

Exercise

List the contents of the directory containing the ‘SRR097977.fastq’ file. Do this from your home directory without leaving that directory.

Full vs. Relative Paths

The cd command takes an argument which is the directory name. Directories can be specified using either a relative path or a full 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. Now, enter the pwd command and you should see:

/home/dcuser

which is the full name of your home directory. This tells you that you are in a directory called dcuser, 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: dcuser is a directory in home which is a directory in /.

Now enter the following command:

cd /home/dcuser/dc_sample_data/.hidden

This jumps to .hidden. Now go back to the home directory (cd). We saw earlier that the command:

cd dc_sample_data/.hidden

had the same effect - it took us to the hidden directory. But, instead of specifying the full path (/home/dcuser/dc_sample_data/data), we specified a relative path. In other words, we specified the path relative to our current directory. A full path always starts with a /. A relative path does not.

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 just 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.

Exercise

Now, list the contents of the /bin directory. Do you see anything familiar in there? How can you tell these are programs rather than plain files?

Saving time with navigation shortcuts and tab completion

Navigational Shortcuts

There are some shortcuts which you should know about. Dealing with the home directory is very common. So, in the shell the tilde character, “”~””, is a shortcut for your home directory. Navigate to the dc_sample_data directory:

cd
cd dc_sample_data

Then enter the command:

ls ~

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

The shortcut .. always refers to the directory above your current directory.

Thus:

ls ..

prints the contents of the /home/dcuser/dc_sample_data directory.

You can chain these together like so:

ls ../../

prints the contents of /home/dcuser which is your home directory. Finally, the special directory . always refers to your current directory. So, ls, ls ., and ls ././././. all do the same thing, they print the contents of the current directory. This may seem like a useless shortcut right now, but we’ll see when it is needed in a little while.

To summarize, while you are in the shell directory, the commands ls ~, ls ~/., ls ../../, and ls /home/dcuser all do exactly the same thing. These shortcuts are not necessary, they are provided for your convenience.

Tab Completion

Navigate to the home directory. Typing out directory names can waste a lot of time. When you start typing out the name of a directory, then hit the tab key, the shell will try to fill in the rest of the directory name.

For example, type:

cd

to get back to your home directy, then enter:

cd dc_<tab>

The shell will fill in the rest of the directory name for dc_sample_data. Now go to dc_sample_data/untrimmed_fastq.

Type:

ls SR<tab><tab>

When you hit the first tab, nothing happens. The reason is that there are multiple directories in the home directory which start with SR. Thus, the shell does not know which one to fill in. When you hit tab again, the shell will list the possible choices.

Tab completion can also fill in the names of programs. For example, enter e<tab><tab>. You will see the name of every program that starts with an e. One of those is echo. If you enter ec<tab> you will see that tab completion works.

Key Points

• First key point.