The Bash Shell

Creating Things

We now know how to explore files and directories, but how do we create them in the first place?

First, let’s check where we are:

$ pwd

/Users/nelle/2020-10-29-socobio-crs/novice/shell/test_directory

If you’re not in this directory, use the cd command to navigate to it as covered in the last lesson, for example:

$ cd ~/2020-10-29-socobio-crs/novice/shell/test_directory

Creating a new directory

Now let’s use ls -F to see what our test directory contains:

$ ls -F

creatures/          molecules/          notes.txt           solar.pdf
data/               north-pacific-gyre/ pizza.cfg           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 - this will show no output:

$ ls -F thesis

Creating a new text file

Now we’ll create a new file using a text editor in this new directory.

Let’s first change our working directory to thesis using cd, and then we’ll use the Nano editor to create a text file called draft.txt, and then save it in that directory.

$ cd thesis
$ nano draft.txt

We add a filename after the nano command to tell it that we want to edit (or in this case create) a file.

Now, let’s type in a few lines of text, for example:

Once we have a few words, to save this data in a new draft.txt file we then use Control-O (pressing Control and the letter O at the same time), and then press Enter to confirm the filename.

Once our file is saved, we can use Control-X to quit the editor and return to the shell. nano doesn’t leave any output on the screen after it exits, but ls now shows that we have created a file called 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 we can use to print the contents of files):

$ cat draft.txt

It's not "publish or perish" any more,
it's "share and thrive".

Deleting files and directories

Now, let’s assume we didn’t actually need to create this file. We can delete it 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

But what if we want to delete a directory, perhaps one that already contains a file? Let’s re-create that file and then move up one directory using cd ..:

$ pwd

/Users/nelle/2020-10-29-socobio-crs/novice/shell/test_directory/thesis

$ nano draft.txt
$ ls

draft.txt

$ cd ..
$ pwd

/Users/nelle/2020-10-29-socobio-crs/novice/shell/test_directory

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

On a Mac, it may look a bit different (rm: thesis: is a directory), but means the same thing.

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 (again, it may look a bit different on a Mac):

$ 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

Renaming and moving files and directories

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

$ pwd

/Users/user/2020-10-29-socobio-crs/novice/shell/test_directory

$ mkdir thesis

Again, put anything you like in this file (note we’re giving the thesis path to nano as well as the draft.txt filename, so we create it in that directory):

$ nano thesis/draft.txt
$ 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 (the file draft.txt in the thesis directory) to thesis/quotes.txt (the quotes.txt again in the thesis directory), 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. Another example of the Bash shell’s pariochial nature!

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

Copying files

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.

Exercises

$ 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

Next: Pipes and Filters