Navigating the Filesystem

reading

We will loosely follow the Software Carpentry lesson on Navigating Files and Directories

You are also encouraged to work through it on your own outside of class.

Filesystem terminology

We’ll use the following terms throughout here:

• filesystem : the collection (and organization) of all of the files stored on your computer.

• file : a single unit containing a collection of data

• directory : (also known as a folder) a collection of files and directories

• home directory : your default directory. When you first open a shell on your computer, this is where you are.

Directory structure

First, let’s figure out where we are. The “print working directory” command does this for us:

pwd

You’ll see something like this:

/home/mzingale/shell-lesson-data

We call this full string the path. Notice a few things:

• Forward slashes, /, are used to separate the path into parts.

• The path begins with a /—we call this the root directory of the filesystem.

• Your username is in the path.

Going home

Each of us has a home directory. This is the location in the filesystem where you have permission to read, write, and modify files. It is also the location in the filesystem that you start in when you first log in or open a shell.

Changing to your home directory

If we use the cd command without any arguments, it will take us home:

cd
pwd

This gives:

/home/mzingale

Tip

Your home directory is special that we have a shortcut for it, ~, so we can also do:

cd ~

We can use ~ as the starting point for changing directories. E.g., each of these will put us in the shell-lesson-data/ directory from wherever we are on the filesystem:

cd
cd shell-lesson-data

cd ~/shell-lesson-data

Absolute vs. relative path

Notice that the path to (my copy of) shell-lesson-data may be written either as:

• /home/mzingale/shell-lesson-data/ (absolute path)

• ~/shell-lesson-data/ (relative path)

Each of these specifies the same location, one as an absolute path (this will always begin at the root of the filesystem, /, and the other a relative path.

Listing directory contents

The ls command lists the contents of a directory. Starting in shell-lesson-data/, if we do:

ls

we will see:

exercise-data  north-pacific-gyre

These are 2 sub-directories (directories beneath shell-less-data/. We can make this a little more clear by adding the -F flag:

ls -F

Then we see:

exercise-data/  north-pacific-gyre/

This now adds a / to the end of any directories in the listing.

We use sub-directories to help organize our files. Our complete project has the structure:

shell-lesson-data
├── exercise-data
│   ├── alkanes
│   │   ├── cubane.pdb
│   │   ├── ethane.pdb
│   │   ├── methane.pdb
│   │   ├── octane.pdb
│   │   ├── pentane.pdb
│   │   └── propane.pdb
│   ├── animal-counts
│   │   └── animals.csv
│   ├── creatures
│   │   ├── basilisk.dat
│   │   ├── minotaur.dat
│   │   └── unicorn.dat
│   ├── numbers.txt
│   └── writing
│       ├── haiku.txt
│       └── LittleWomen.txt
└── north-pacific-gyre
    ├── goodiff.sh
    ├── goostats.sh
    ├── NENE01729A.txt
    ├── NENE01729B.txt
    ├── NENE01736A.txt
    ├── NENE01751A.txt
    ├── NENE01751B.txt
    ├── NENE01812A.txt
    ├── NENE01843A.txt
    ├── NENE01843B.txt
    ├── NENE01971Z.txt
    ├── NENE01978A.txt
    ├── NENE01978B.txt
    ├── NENE02018B.txt
    ├── NENE02040A.txt
    ├── NENE02040B.txt
    ├── NENE02040Z.txt
    ├── NENE02043A.txt
    └── NENE02043B.txt

More options

ls has a lot of options. We can see the manual page for ls by doing:

man ls

The options include some that sort the listing, others that show different sets of information, and more.

A helpful option is -a, which shows all the files in a directory. Let’s look. Doing:

ls -a

Shows:

.  ..  .DS_Store  exercise-data  north-pacific-gyre

Note

man ls shows that we can do either -a or --all, i.e., a short option or a long option. When typing commands on the commandline, we usually use the short options, to save keystrokes. But these are equivalent.

We can combine the short option -a with the -F option we saw previously:

ls -aF

gives:

./  ../  .DS_Store  exercise-data/  north-pacific-gyre/

Now we see the “hidden files”—those that begin with a ., and we see two special “files”, . and ..—these are helpful for navigation.

. and ..

Every directory contains the special directories . and ..:

• . refers to the current directory

• .. refers to the directory immediately above the one you are in.

For instance, starting in ~/shell-lesson-data, if we do:

pwd
ls -aF .
ls -aF ..

Then the output would look like:

[mzingale@portal shell-lesson-data]$ pwd
/home/mzingale/shell-lesson-data
[mzingale@portal shell-lesson-data]$ ls -aF .
./  ../  .DS_Store  exercise-data/  north-pacific-gyre/
[mzingale@portal shell-lesson-data]$ ls -aF ..
./             .bashrc   .emacs.d/         __MACOSX/              .Xauthority
../            .cache/   .gnuplot_history  .mozilla/              .zshrc
.bash_history  .config/  hello*            shell-lesson-data/
.bash_logout   .emacs    hello.cpp         shell-lesson-data.zip
.bash_profile  .emacs~   .lesshst          .ssh/

Try it…

Let’s use cd to move up and down through our project’s directory structure.

Moving through the hierarchy

Let’s start at our home directory and navigate to ~/shell-lesson-data/exercise-data/alkanes/. We can do this one directory at a time:

cd shell-lesson-data
cd exercise-data
cd alkanes

or all at once:

cd shell-lesson-data/exercise-data/alkanes/

Tip

You can use the “Tab” key to autocomplete directory and file names once you type enough to be unique.

Try doing: cd shel and hitting “Tab”

Last directory

A final shortcut for navigating directories is doing cd -. This switches to the previous directory we were in. So for instance, doing:

cd
cd shell-lesson-data/exercise-data/alkanes/
cd
cd -

would bring us back to shell-lesson-data/exercise-data/alkanes/.

Summary

We learned the following commands:

• pwd : print working directory (where you currently are in the file system)

• ls : list the contents of a directory

• cd : change directory

There are a few special directories that always exist the help us navigate:

• . : the current directory

• .. : one directory above us

• ~ : our home directory

The / character has 2 roles:

• The / directory is the root of the filesystem

• A path uses / to separate directory names