The Unix Shell

Creating Things

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

$ pwd

/Users/nelle/2015-12-15-southampton/novice/shell/test_directory

$ ls -F

creatures/  molecules/           pizza.cfg
data/       north-pacific-gyre/  solar.pdf
Desktop/    notes.txt            writing/

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

$ mkdir thesis

As you might (or might not) 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

creatures/  north-pacific-gyre/  thesis/
data/       notes.txt            writing/
Desktop/    pizza.cfg
molecules/  solar.pdf

However, there’s nothing in it yet:

$ ls -F thesis

Let’s change our working directory to thesis using cd, then use VSCode to create a text file called draft.txt, and save it in the directory:

We launch VSCode, select the New File option:

New File

Then type a few lines of text into the file:

Typing Text

Then go to file, save as, and navigate to your new thesis directory (in the workshop directory, under novice, shell, test_directory then thesis) and save new file as draft.txt.
Now we’ve saved the file, we can use ls to see that there is a new file in the directory called draft.txt:

$ ls

draft.txt

We can use the shell on its own to take a look at its contents using the cat command (which stands for “concatenate”):

$ cat draft.txt

This is a regular text editor
with some extra features.

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

Let’s re-create that file and then move up one directory using cd ... If you kept thesis.txt open in VSCode after deleting the file, you should just be able to re-save it in the same location with File->Save. We can check it out:

$ pwd

/Users/nelle/2015-12-15-southampton/novice/shell/test_directory/thesis

$ ls

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 only works on files, not directories. The right command is rmdir, which is short for “remove directory”. It doesn’t work yet either, though, because the directory we’re trying to remove isn’t empty:

$ rmdir thesis

rmdir: failed to remove `thesis': Directory not empty

This little safety feature can save you a lot of grief, particularly if you are a bad typist. To really get rid of thesis we must first delete the file draft.txt:

$ rm thesis/draft.txt

The directory is now empty, so rmdir can delete it:

$ rmdir thesis

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

$ pwd

/Users/nelle

$ mkdir thesis

As before, if you kept thesis.txt open in VSCode after deleting directory, you should just be able to re-save it in the same location after re-creating the directory! We can check this out:

$ ls thesis

draft.txt

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

quotes.txt

Just for the sake of inconsistency, mv also works on directories — there is no separate mvdir command.

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

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 thousands of 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 (we can get to this command by pressing the up arrow twice).

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

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

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.

$ pwd
/Users/jamie/data
$ ls
proteins.dat
$ mkdir recombine
$ mv proteins.dat recombine
$ cp recombine/proteins.dat ../proteins-saved.dat
$ ls

$ ls -F
analyzed/  fructose.dat    raw/   sucrose.dat

$ ls -F
analyzed/   raw/
$ ls analyzed
fructose.dat    sucrose.dat

$ mkdir backup
$ cp thesis/citations.txt thesis/quotations.txt backup

$ ls -F
intro.txt    methods.txt    survey.txt
$ cp intro.txt methods.txt survey.txt