Creating, moving, and deleting files and directories

I'm going to be working mainly in the Desktop directory -- recommend that people follow along.

Creating an empty file

Lets create an empty file using the touch command. Enter the command:

$ touch testfile

Then list the contents of the directory again using ls. You should see that a new entry, called testfile, exists. It does not have a slash at the end, showing that it is not a directory. The touch command just creates an empty file.

Some terminals can color the directory entries in this very convenient way. In those terminals, use ls -G instead of ls if you are on a Mac or ls --color if you run on Windows. Now your directories, files, and executables will have different colors.

Now if you use the command ls -l you will notice that testfile has a size of zero. OK then, let's get rid of testfile. To remove a file, just enter the command:

$ rm -i testfile

When prompted, type:

$ y

The rm command can be used to remove files. The -i adds the "are you sure?" message. If you enter ls again, you will see that testfile is gone.

Warning: The shell does not have a recycling bin. So any file removed with rm is gone forever. Use with caution. Remember the -i argument

If you want to create a file with some text, say notes about what you are doing, you'll need to use a text editor. The one we'll be using here is nano.

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 Unix systems (such as Linux and Mac OS X), many programmers use Emacs or Vim (both of which are completely unintuitive, even by Unix standards), or a graphical editor such as Gedit. On Windows, you may wish to use Notepad++.

No matter what editor you use, you will need to know where it searches for and saves files. If you start it from the shell, it will (probably) use your current working directory as its default location. If you use your computer's start menu, it may want to save files in your desktop or documents directory instead. You can change this by navigating to another directory the first time you "Save As..."

To create a new file and open nano, type

$ nano notes.txt

Pause to make sure this worked for everyone, especially Windows users who may not have installed nano.

Now, type a line of text, something like "This is where I am keeping my notes." To exit, hit Ctrl-X, then Y (to save), then Enter.

Now use ls to view the contents of your desktop. Do you see the file you created? (Does anyone not see it?)

Exercise: View the contents of the file you just created within your terminal (hint: we learned a command for viewing the contents of a file in the last section). Then, open the file, add some more text to it, save it, and exit.

Manipulating the file system

Make directories with mkdir. This will create a new directory within the current directory.

$ mkdir swc-wsu

You can create as many folders as you like in a single call.

$ mkdir directory_name_1 directory_name_2 directory_name_3

To copy and move files, we use the commands cp and mv, followed by the file you want to copy/move, and then the location that you want to copy/move it to.

$ cp file1 file2
$ mv file1 file2

So if I am in my data directory and I want to copy or move one of the data files to my desktop, I would do. (Do these, then show them on the Desktop. Do rm ~/Desktop/car-speeds.csv in between.)

$ cp gapminder.csv swc-wsu/
$ mv gapminder.csv swc-wsu/

cp and mv can also rename files. If you want to rename a file in place, just do:

$ mv file_oldname file_newname

When we moved gapminder.csv to the swc-wsu folder, if we'd wanted to rename it at the same time we could have done:

$ cp gapminder.csv swc-wsu/gapminder-2.csv

Both cp and mv can be used with directories in addition to files.

See the man command to get help on options you can use with these commands.

Remove files with rm.

Let's try out some of the commands above

First create a temporary directory on your desktop. Ask for people to call out commands to make directory and navigate into it.

$ cd ~/Desktop
$ mkdir scratchpad
$ cd scratchpad

Make a few directories inside scratchpad

$ mkdir dir1 dir2 dir3
$ cp ~/Desktop/swc-data/*.png .

Use ls to view the contents of the current directory. What just happened? (Ask for a volunteer)

This is our first introduction to wildcards, which I'm going to talk a bit more about later. The *.png is telling the computer to match anything that ends in .png, which in this case is all of the figures from Karl's ggplot2 lesson.

Now try and remove scratchpad.

rm scratchpad

What just happened? If you want to remove everything within scratchpad no matter what, you will need to add the -r argument to function rm

rm -r scratchpad

One could also create lots of subdirectories at once using curly brackets expansions (not entirely sure if this works on Windows).

mkdir temp
cd temp
ls
mkdir dir-{0..10}
ls
rm -r temp

|-- swc-wsu/
|-- |-- data/
|-- |-- |-- (data here)
|-- |-- figures/
|-- |-- |-- (figures here)
|-- |-- notes/
|-- |-- R/
|-- |-- |-- (R scripts here)
|-- |-- swc-wsu.Rproj

Note that this will break read.csv in your R script go to RStudio and demonstrate, then use relative paths to fix loading of data

It is a good idea to keep all the materials for a given project or analysis organized. Separating data (raw vs cleaned), scripts, figures, and manuscript text in a logical project structure will help you and your collaborators understand what is

Acknowledgments: these lessons were adapted by Kara Woo from materials by Diego Barneche.