Lesson 5: Introduction to Shell Scripting - joslynnlee/CHEM-454 GitHub Wiki

Introduction to Shell Scripting

We are finally ready to see what makes the shell such a powerful programming environment. We are going to take the commands we repeat frequently and save them in files so that we can re-run all those operations again later by typing a single command. For historical reasons, a bunch of commands saved in a file is usually called a shell script, but make no mistake: these are actually small programs.

Not only will writing shell scripts make your work faster — you won’t have to retype the same commands over and over again — it will also make it more accurate (fewer chances for typos) and more reproducible. If you come back to your work later (or if someone else finds your work and wants to build on it) you will be able to reproduce the same results simply by running your script, rather than having to remember or retype a long list of commands.

  • How can I save and re-use commands?

  • Write a shell script that runs a command or series of commands for a fixed set of files.

  • Run a shell script from the command line.

  • Write a shell script that operates on a set of files defined by the user on the command line.

  • Create pipelines that include shell scripts you, and others, have written.

Let’s start by going back to molecules/ and creating a new file, middle.sh which will become our shell script:

cd molecules

nano middle.sh

The command nano middle.sh opens the file middle.sh within the text editor nano (which runs within the shell). If the file does not exist, it will be created. We can use the text editor to directly edit the file – we’ll simply insert the following line:

head -n 15 octane.pdb | tail -n 5

This is a variation on the pipe we constructed earlier: it selects lines 11-15 of the file octane.pdb. Remember, we are not running it as a command just yet: we are putting the commands in a file.

Then we save the file (Ctrl-O in nano), and exit the text editor (Ctrl-X in nano). Check that the directory molecules now contains a file called middle.sh.

Once we have saved the file, we can ask the shell to execute the commands it contains. Our shell is called bash, so we run the following command:

bash middle.sh

More examples to follow!