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 go back to Nelle’s home directory, /Users/nelle, and use ls -F to see what it contains:

$ pwd

/mnt/home/nelle

$ ls -F

avida/    notes.txt

We’re going to repeat a classic Avida experiment on the origin of complex features. Let’s set up a directory structure to keep track of everything.

$ mkdir complex_features_experiment

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

avida/    notes.txt    complex_features_experiment/

However, there’s nothing in it yet:

$ ls -F complex_features_experiment

Let’s change our working directory to complex_features_experiment using cd, then run a text editor called Nano to create a file called notes.txt:

$ cd complex_features_experiment
$ nano notes.txt

Let’s type in a few lines of text, then use Control-O to write our data to disk:

Nano in action

Once our file is saved, we can use Control-X to quit the editor and return to the shell. (Unix documentation often uses the shorthand ^A to mean “control-A”.) 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:

$ ls

notes.txt

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

$ rm notes.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 to /mnt/home/nelle using cd ..:

$ pwd

/mnt/home/nelle/complex_features_experiment

$ nano notes.txt
$ ls

notes.txt

$ cd ..

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

$ rm complex_features_experiment

rm: cannot remove `complex_features_experiment': 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 complex_features_experiment

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 complex_features_experiment/notes.txt

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

$ rmdir complex_features_experiment

Let’s create that directory and file one more time. (Note that this time we’re running nano with the path complex_features_experiment/notes.txt, rather than going into the complex_features_experiment directory and running nano on notes.txt there.)

$ pwd

/mnt/home/nelle

$ mkdir complex_features_experiment

$ nano complex_features_experiment/notees.txt
$ ls complex_features_experiment

notes.txt

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

$ mv complex_features_experiment/notes.txt complex_features_experiment/experiments.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 complex_features_experiment/notes.txt to complex_features_experiment/experiments.txt which has the same effect as renaming the file. Sure enough, ls shows us that complex_features_experiment now contains one file called experiments.txt:

$ ls complex_features_experiments

experiments.txt

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

Let’s move experiments.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 complex_features_experiment/experiments.txt .

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

$ ls complex_features_experiment

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 experiments.txt

experiments.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 experiments.txt complex_features_experiment/planned_experiments.txt
$ ls 

experiments.txt complex_features_experiment/planned_experiments.txt

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

$ rm experiments.txt
$ ls experiments.txt complex_features_experiment/planned_experiments.txt

ls: cannot access experiments.txt: No such file or directory
complex_features_experiment/planned_experiments.txt

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

To get ready for the next step, let’s make a few more directories:

$ cd complex_features_experiment
$ mkdir configs
$ mkdir results
$ mkdir results/all_rewarded
$ mkdir results/equ_rewarded

Now let’s copy the Avida config files into our configs directory, so that we always know what configs we used to run this experiment:

$ cp ~/avida/cbuild/work/*.cfg configs
$ cp ~/avida/cbuild/work/*.org configus
$ cp ~/avida/cbuild/work/avida configus

$ 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