Intro to Unix

An introduction to basic Unix commands and the file system.

The notes below are modified from the excellent Unix Shell tutorial that is freely available on the Software Carpentry website. We highly recommend checking out the full version for further reading. The material is being used here under the terms of the Creative Commons Attribution license.

Working with Files and Directories

We now know how to explore files and directories, but how do we create them in the first place? Let’s go back to our home directory and use ls -F to see what it contains:

$ cd
$ pwd
$ ls -F
config.yaml  examples/  lost+found/  work/  worker-template.yaml

Let’s create a new directory called thesis using the command mkdir thesis (which has no output):

$ mkdir thesis

As you might guess from its name, mkdir means “make directory”. Since thesis is a relative path (i.e., doesn’t have a leading slash), the new directory is created in the current working directory:

$ ls -F
config.yaml  examples/  lost+found/  thesis/  work/  worker-template.yaml

Good names for files and directories

Complicated names of files and directories can make your life painful when working on the command line. Here we provide a few useful tips for the names of your files.

  1. Don’t use whitespaces.

    Whitespaces can make a name more meaningful but since whitespace is used to break arguments on the command line is better to avoid them on name of files and directories. You can use - or _ instead of whitespace.

  2. Don’t begin the name with - (dash).

    Commands treat names starting with - as options.

  3. Stick with letters, numbers, . (period), - (dash) and _ (underscore).

    Many other characters have special meanings on the command line. We will learn about some of these during this lesson. There are special characters that can cause your command to not work as expected and can even result in data loss.

If you need to refer to names of files or directories that have whitespace or another non-alphanumeric character, you should surround the name in quotes ("").

Since we’ve just created the thesis directory, there’s nothing in it yet:

$ ls -F thesis

Let’s change our working directory to thesis using cd. We then create a blank new file called draft.txt using the touch command:

$ cd thesis
$ touch draft.txt

Now we can edit the file in JupyterLab’s text editor. Let’s type in a few lines of text. Once we’re happy with our text, we save the file, and return to the shell.

ls now shows that we have created a file called draft.txt:

$ ls

Let’s tidy up by running rm draft.txt:

$ rm draft.txt

This command removes files (rm is short for “remove”). If we run ls again, its output is empty once more, which tells us that our file is gone:

$ ls

Deleting Is Forever

The Unix shell doesn’t have a trash bin that we can recover deleted files from (though most graphical interfaces to Unix do). Instead, when we delete files, they are unhooked from the file system so that their storage space on disk can be recycled. Tools for finding and recovering deleted files do exist, but there’s no guarantee they’ll work in any particular situation, since the computer may recycle the file’s disk space right away.

Let’s re-create that file and then move up one directory to /home/jovyan using cd ..:

$ touch draft.txt
$ cd ..

If we try to remove the entire thesis directory using rm thesis, we get an error message:

$ rm thesis
rm: cannot remove `thesis`: Is a directory

This happens because rm by default only works on files, not directories.

To really get rid of thesis we must also delete the file draft.txt. We can do this with the recursive option for rm:

$ rm -r thesis

With Great Power Comes Great Responsibility

Removing the files in a directory recursively can be very dangerous operation. If we’re concerned about what we might be deleting we can add the “interactive” flag -i to rm which will ask us for confirmation before each step

 $ rm -r -i thesis
 rm: descend into directory ‘thesis’? y
 rm: remove regular file ‘thesis/draft.txt’? y
 rm: remove directory ‘thesis’? y

This removes everything in the directory, then the directory itself, asking at each step for you to confirm the deletion.

Let’s create that directory and file one more time.

$ mkdir thesis
$ touch thesis/draft.txt
$ ls thesis

draft.txt isn’t a particularly informative name, so let’s change the file’s name using mv, which is short for “move”:

$ mv thesis/draft.txt thesis/quotes.txt

The first parameter tells mv what we’re “moving”, while the second is where it’s to go. In this case, we’re moving thesis/draft.txt to thesis/quotes.txt, which has the same effect as renaming the file. Sure enough, ls shows us that thesis now contains one file called quotes.txt:

$ ls thesis

One has to be careful when specifying the target file name, since mv will silently overwrite any existing file with the same name, which could lead to data loss. An additional flag, mv -i (or mv --interactive), can be used to make mv ask you for confirmation before overwriting.

Just for the sake of consistency, mv also works on directories

Let’s move quotes.txt into the current working directory. We use mv once again, but this time we’ll just use the name of a directory as the second parameter to tell mv that we want to keep the filename, but put the file somewhere new. (This is why the command is called “move”.) In this case, the directory name we use is the special directory name . that we mentioned earlier.

$ mv thesis/quotes.txt .

The effect is to move the file from the directory it was in to the current working directory. ls now shows us that thesis is empty:

$ ls thesis

Further, ls with a filename or directory name as a parameter only lists that file or directory. We can use this to see that quotes.txt is still in our current directory:

$ ls quotes.txt

The cp command works very much like mv, except it copies a file instead of moving it. We can check that it did the right thing using ls with two paths as parameters — like most Unix commands, ls can be given multiple paths at once:

$ cp quotes.txt thesis/quotations.txt
$ ls quotes.txt thesis/quotations.txt
quotes.txt   thesis/quotations.txt

To prove that we made a copy, let’s delete the quotes.txt file in the current directory and then run that same ls again.

$ rm quotes.txt
$ ls quotes.txt thesis/quotations.txt
ls: cannot access quotes.txt: No such file or directory

This time it tells us that it can’t find quotes.txt in the current directory, but it does find the copy in thesis that we didn’t delete.

Key Points

  • cp old new copies a file.

  • mkdir path creates a new directory.

  • mv old new moves (renames) a file or directory.

  • rm path removes (deletes) a file.

  • Use of the Control key may be described in many ways, including Ctrl-X, Control-X, and ^X.

  • The shell does not have a trash bin: once something is deleted, it’s really gone.

  • Depending on the type of work you do, you may need a more powerful text editor than Nano.

Learning More

The goal of this lesson was to familiarize you with the basics of working with files and directories. There is a lot more to the unix shell and filexsystem than what we have covered here! To ge deeper with self study, we recommend the excellent Software Carpentry Unix Shell Lesson, on which the above material was based.