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:

• file system : 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 listing

The ls command lists the contents of a directory

We use directories to help organize our files. For our project data, we can see this organization using the tree command:

tree exercise-data

This gives:

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

Organization of Unix filesystem

A standard file system layout is used on Unix-like systems. The important top-level directories are:

• / : the root directory

• /boot : the kernel and files needed to boot the system

• /home : the directories where user data is stored.

• /usr : the location of the a lot of the commands we use

We can go to our home directory by simply doing:

cd

(with no arguments). If we look at this directory with pwd we would see something like:

/home/mzingale

Relative vs. absolute paths

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

Tip

The Unix shell uses tab-completion to make it easier to type. Start typing a path (or command) and then press the Tab key and it will either complete it (if there is a unique file / command) or display the possible completions.

Tip

You can navigate through your history of commands using the up and down arrows.