Skip to main content

Technology and Tooling

The Bash shell

Files and Dir... [bash]

Technology and Tooling

The Bash shell

Pipes and Fil... [bash]

Creating Things
This material was originally taken from training materials developed by the University of Southampton Research Software Group, which are based on the Software Carpentries course "Version Control with Git".

This material was originally taken from training materials developed by the University of Southampton Research Software Group, which are based on the Software Carpentries course "Version Control with Git".

Creative Commons License

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/shell-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 ~/shell-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.

Which Editor?

When we say, "nano is a text editor," we really do mean "text": it can only work with plain character data, not tables, images, or any other human-friendly media. We use it in examples because almost anyone can drive it anywhere without training, but please use something more powerful for real work.
On Windows, you may wish to use Notepad++. A more powerful example is Microsoft's VSCode. It's a fairly standard text editor that can be installed on Windows, Mac or Linux but also has some handy features like code highlighting that make it easy to write scripts and code. Similar editors exist like Atom, a highly customisable text editor which also runs on these platforms.
Your choice of editor will depend on the size of project you're working on, and how comfortable you are with the terminal.
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:
Nano in action
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

Deleting Is Forever

The Bash shell doesn't have a trash bin that we can recover deleted files from. 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.
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/shell-novice/test_directory/thesis
nano draft.txt
ls
draft.txt
cd ..
pwd
/Users/nelle/shell-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

With Great Power Comes Great Responsibility

Removing the files in a directory just so that we can remove the directory quickly becomes tedious. Instead, we can use rm with the -r flag (which stands for "recursive"):
rm -r thesis
This removes everything in the directory, then the directory itself. If the directory contains sub-directories, rm -r does the same thing to them, and so on. It's very handy, but can do a lot of damage if used without care.

Renaming and moving files and directories

Let's create that directory and file one more time.
pwd
/Users/user/shell-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.
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

Renaming Files

Suppose that you created a .txt file in your current directory to contain a list of the statistical tests you will need to do to analyze your data, and named it: statstics.txt
After creating and saving this file you realize you misspelled the filename! You want to correct the mistake, which of the following commands could you use to do so?
  1. cp statstics.txt statistics.txt
  2. mv statstics.txt statistics.txt
  3. mv statstics.txt .
  4. cp statstics.txt .

Moving and Copying

What is the output of the closing ls command in the sequence shown below?
pwd
/Users/jamie/data
ls
proteins.dat
mkdir recombine
mv proteins.dat recombine
cp recombine/proteins.dat ../proteins-saved.dat
ls
  1. proteins-saved.dat recombine
  2. recombine
  3. proteins.dat recombine
  4. proteins-saved.dat

Organising Directories and Files

Jamie is working on a project and she sees that her files aren't very well organized:
ls -F
analyzed/  fructose.dat    raw/   sucrose.dat
The fructose.dat and sucrose.dat files contain output from her data analysis. What command(s) covered in this lesson does she need to run so that the commands below will produce the output shown?
ls -F
analyzed/   raw/
ls analyzed
fructose.dat    sucrose.dat

Copy with Multiple Filenames

What does cp do when given several filenames and a directory name, as in:
mkdir backup
cp thesis/citations.txt thesis/quotations.txt backup
What does cp do when given three or more filenames, as in:
ls -F
intro.txt    methods.txt    survey.txt
cp intro.txt methods.txt survey.txt