The home directory path will look different on different operating systems. On Linux it may look like /home/nelle, and on Windows it will be similar to C:\Documents and Settings\nelle or C:\Users\nelle. (Note that it may look slightly different for different versions of Windows.) In future examples, we’ve used Mac output as the default – Linux and Windows output may differ slightly, but should be generally similar.To understand what a ‘home directory’ is, let’s have a look at how the file system as a whole is organized. For the sake of this example, we’ll be illustrating the filesystem on our scientist Nelle’s computer. After this illustration, you’ll be learning commands to explore your own filesystem, which will be constructed in a similar way, but not be exactly identical.On Nelle’s computer, the filesystem looks like this:
At the top is the root directory that holds everything else. We refer to it using a slash character, /, on its own; this is the leading slash in /Users/nelle.
Inside that directory are several other directories: bin (which is where some built-in programs are stored), data (for miscellaneous data files), Users (where users’ personal directories are located), tmp (for temporary files that don’t need to be stored long-term), and so on.
We know that our current working directory /Users/nelle is stored inside /Users because /Users is the first part of its name. Similarly, we know that /Users is stored inside the root directory / because its name begins with /.
Slashes
Notice that there are two meanings for the / character. When it appears at the front of a file or directory name, it refers to the root directory. When it appears inside a path, it’s just a separator.
Underneath /Users, we find one directory for each user with an account on Nelle’s machine, her colleagues imhotep and larry.
The user imhotep’s files are stored in /Users/imhotep, user larry’s in /Users/larry, and Nelle’s in /Users/nelle. Because Nelle is the user in our examples here, this is why we get /Users/nelle as our home directory. Typically, when you open a new command prompt you will be in your home directory to start.
Now let’s learn the command that will let us see the contents of our own filesystem. We can see what’s in our home directory by running ls:
Applications Documents Library Music Public
Desktop Downloads Movies Pictures
(Again, your results may be slightly different depending on your operating system and how you have customized your filesystem.)
ls prints the names of the files and directories in the current directory. We can make its output more comprehensible by using the -F option (also known as a switch or a flag) , which tells ls to classify the output by adding a marker to file and directory names to indicate what they are:
- a trailing
/ indicates that this is a directory
@ indicates a link* indicates an executable
If your screen gets too cluttered, you can clear your terminal using the clear command. You can still access previous commands using ↑ and ↓ to move line-by-line, or by scrolling in your terminal.
Here, we can see that our home directory contains only sub-directories. Any names in your output that don’t have a classification symbol, are plain old files.
Exploring Other Directories
Not only can we use ls on the current working directory, but we can use it to list the contents of a different directory. Let’s take a look at our Desktop directory by running ls -F Desktop, i.e., the command ls with the -F option and the argument Desktop. The argument Desktop tells ls that we want a listing of something other than our current working directory:
Your output should be a list of all the files and sub-directories in your Desktop directory. On many systems, the command line Desktop directory is the same as your GUI Desktop. Take a look at your Desktop to confirm that your output is accurate. As you may now see, using a bash shell is strongly dependent on the idea that your files are organized in a hierarchical file system. Organizing things hierarchically in this way helps us keep track of our work: it’s possible to put hundreds of files in our home directory, just as it’s possible to pile hundreds of printed papers on our desk, but it’s a self-defeating strategy.
Now that we know the data-shell directory is located in our Desktop directory, we can do two things.
First, we can look at its contents, using the same strategy as before, passing a directory name to ls:
$ ls -F Desktop/data-shell
creatures/ molecules/ notes.txt solar.pdf
data/ north-pacific-gyre/ pizza.cfg writing/
Second, we can actually change our location to a different directory, so we are no longer located in our home directory.
The command to change locations is cd followed by a directory name to change our working directory. cd stands for ‘change directory’, which is a bit misleading: the command doesn’t change the directory, it changes the shell’s idea of what directory we are in. The cd command is akin to double clicking a folder in a graphical interface to get into a folder.
Let’s say we want to move to the data directory we saw above. We can use the following series of commands to get there:
$ cd Desktop
$ cd data-shell
$ cd data
These commands will move us from our home directory into our Desktop directory, then into the data-shell directory, then into the data directory. You will notice that cd doesn’t print anything. This is normal. Many shell commands will not output anything to the screen when successfully executed. But if we run pwd after it, we can see that we are now in /Users/nelle/Desktop/data-shell/data. If we run ls -F without arguments now, it lists the contents of /Users/nelle/Desktop/data-shell/data, because that’s where we now are:
/Users/nelle/Desktop/data-shell/data
amino-acids.txt elements/ pdb/ salmon.txt
animals.txt morse.txt planets.txt sunspot.txt
We now know how to go down the directory tree (i.e. how to go into a subdirectory) but how do we go up (i.e. how do we leave a directory and go into its parent directory)? We might try the following:
-bash: cd: data-shell: No such file or directory
But we get an error! Why is this?
With our methods so far, cd can only see sub-directories inside your current directory. There are different ways to see directories above your current location; we’ll start with the simplest.
There is a shortcut in the shell to move up one directory level that looks like this:
.. is a special directory name meaning “the directory containing this one”, or more succinctly, the parent of the current directory. Sure enough, if we run pwd after running cd .., we’re back in /Users/nelle/Desktop/data-shell:
/Users/nelle/Desktop/data-shell
The special directory .. doesn’t usually show up when we run ls. If we want to display it, we can add the -a option to ls -F:
./ .bash_profile data/ north-pacific-gyre/ pizza.cfg thesis/
../ creatures/ molecules/ notes.txt solar.pdf writing/
-a stands for ‘show all’; it forces ls to show us file and directory names that begin with ., such as .. (which, if we’re in /Users/nelle, refers to the /Users directory) As you can see, it also displays another special directory that’s just called ., which means ‘the current working directory’. It may seem redundant to have a name for it, but we’ll see some uses for it soon.
Note that in most command line tools, multiple options can be combined with a single - and no spaces between the options: ls -F -a is equivalent to ls -Fa.
Other Hidden Files
In addition to the hidden directories .. and ., you may also see a file called .bash_profile. This file usually contains shell configuration settings. You may also see other files and directories beginning with .. These are usually files and directories that are used to configure different programs on your computer. The prefix . is used to prevent these configuration files from cluttering the terminal when a standard ls command is used.
Orthogonality
The special names . and .. don’t belong to cd; they are interpreted the same way by every program. For example, if we are in /Users/nelle/data, the command ls .. will give us a listing of /Users/nelle. When the meanings of the parts are the same no matter how they’re combined, programmers say they are orthogonal: Orthogonal systems tend to be easier for people to learn because there are fewer special cases and exceptions to keep track of.
These then, are the basic commands for navigating the filesystem on your computer: pwd, ls and cd. Let’s explore some variations on those commands. What happens if you type cd on its own, without giving a directory?
How can you check what happened? pwd gives us the answer!
It turns out that cd without an argument will return you to your home directory, which is great if you’ve gotten lost in your own filesystem.
Let’s try returning to the data directory from before. Last time, we used three commands, but we can actually string together the list of directories to move to data in one step:
$ cd Desktop/data-shell/data
Check that we’ve moved to the right place by running pwd and ls -F
If we want to move up one level from the data directory, we could use cd ... But there is another way to move to any directory, regardless of your current location.
So far, when specifying directory names, or even a directory path (as above), we have been using relative paths. When you use a relative path with a command like ls or cd, it tries to find that location from where we are, rather than from the root of the file system.
However, it is possible to specify the absolute path to a directory by including its entire path from the root directory, which is indicated by a leading slash. The leading / tells the computer to follow the path from the root of the file system, so it always refers to exactly one directory, no matter where we are when we run the command.
This allows us to move to our data-shell directory from anywhere on the filesystem (including from inside data). To find the absolute path we’re looking for, we can use pwd and then extract the piece we need to move to data-shell.
/Users/nelle/Desktop/data-shell/data
$ cd /Users/nelle/Desktop/data-shell
Run pwd and ls -F to ensure that we’re in the directory we expect.
Two More Shortcuts
The shell interprets the character ~ (tilde) at the start of a path to mean “the current user’s home directory”. For example, if Nelle’s home directory is /Users/nelle, then ~/data is equivalent to /Users/nelle/data. This only works if it is the first character in the path: here/there/~/elsewhere is not here/there/Users/nelle/elsewhere.
Another shortcut is the - (dash) character. cd will translate - into the previous directory I was in, which is faster than having to remember, then type, the full path. This is a very efficient way of moving back and forth between directories. The difference between cd .. and cd - is that the former brings you up, while the latter brings you back. You can think of it as the Last Channel button on a TV remote.
How to put this to use in a research project:
In our first class, we discussed how a student–let’s call her Nelle, wanted to analyze all the proteins found in a garbage island floating in the ocean. Nelle names her directories ‘year-month-day’, with leading zeroes for months and days, because the shell displays file and directory names in alphabetical order. If she used month names, December would come before July; if she didn’t use leading zeroes, November (‘11’) would come before July (‘7’). Similarly, putting the year first means that June 2012 will come before June 2013.
Each of her physical samples is labelled according to her lab’s convention with a unique ten-character ID, such as ‘NENE01729A’. This is what she used in her collection log to record the location, time, depth, and other characteristics of the sample, so she decides to use it as part of each data file’s name. Since the assay machine’s output is plain text, she will call her files NENE01729A.txt, NENE01812A.txt, and so on. All 1520 files will go into the same directory.
Now in her current directory data-shell, Nelle can see what files she has using the command:
$ ls north-pacific-gyre/2012-07-03/
This is a lot to type, but she can let the shell do most of the work through what is called tab completion. If she types:
and then presses Tab (the tab key on her keyboard), the shell automatically completes the directory name for her:
If she presses Tab again, Bash will add 2012-07-03/ to the command, since it’s the only possible completion. Pressing Tab again does nothing, since there are 19 possibilities; pressing Tab twice brings up a list of all the files, and so on. This is called tab completion, and we will see it in many other tools as we go on.
Key Points
- The file system is responsible for managing information on the disk.
- Information is stored in files, which are stored in directories (folders). Directories can also store other directories, which forms a directory tree.
cd changes the current working directory.ls prints a listing of a specific file or directory; ls on its own lists the current working directory; or you can pass in an argument with a directory name.pwd prints the user’s current working directory./ on its own is the root directory of the whole file system.- A relative path specifies a location starting from the current location.
- An absolute path specifies a location from the root of the file system.
- Directory names in a path are separated with
/ on Unix, but \ on Windows.
.. means ‘the directory above the current one’; . on its own means ‘the current directory’.
