At this point you’re pretty familiar with using the command line; you should be able to do a variety of things:

• Navigate and create folder structures.
• Edit text files.
• Convert files between various formats.
• Filter lines from text files.
• Read and change permissions on files.
• Use version control software.
• Find files by name or properties.
• Redirect standard input, output, and error.
• Construct pipelines of commands.

While there’s a whole world of things you can still learn about using the command line, and more command line tools than you can imagine to learn about (which sometimes themselves contain entire programming languages!), you’ve learned and demonstrated a lot! 🎉

As you’re getting more used to using the command line, you may find yourself repeating similar, complex commands over and over again. Or maybe you find yourself doing the same kinds of things over and over again, maybe running multiple commands repeatedly. Or maybe you’ve built a complex pipeline that you want to keep for use later because you’ll need to use it again.

In their very simplest form, shell scripts are plain text files that contain a sequence of commands or statements, separated by newlines or semi-colons. As you grow shell scripts, they can contain things like conditional statements, loops, functions, and… uh, hey, wait a minute. That, uh, that sounds an awful lot like programming.

Most of the time we spend interacting with shells is interactive: the shell is waiting for us to enter a command, and when we press Enter, the shell runs the command, waits for it to finish (it actually wait(2)s, it’s a C function), then patiently waits for us to enter another command.

Most shells can also run non-interactively: you give the shell the name of a file that contains a sequence of commands and the shell will just interpret, then run the sequence of commands like it’s a program.

Shells and languages

Similar to different programming languages, different shells use different syntax to express similar ideas. Deciding which shell program to use defines what syntax you’re going to use and the kinds of keywords you should be using when you’re looking for help (in the manual page for the shell, on the shell’s website, or generally online).

While your default shell on Aviary is tcsh, we’re going to be using bash as a shell interpreter for scripting. This is an opinionated choice, just as using vim instead of emacs is an opinionated choice. As you get more comfortable using the command line, you may want to choose a different shell (like fish) and thus a different shell language, but bash and its syntax are common enough that we’ll treat it like a “lingua franca”.

Basic scripting

Let’s start with the basics: the general structure of a shell script and some very simple shell scripts.

General structure

Shell scripts all start with a “shebang” line — a line that starts with the symbols #!. The first line indicates which program is going to be run to interpret the rest of the file.

#!/usr/bin/env bash # this is a bash script

Everything after the first line is the actual contents of the script, the sequence of commands to be executed.

Simple scripts

Here’s an example of a very simple script:

#!/usr/bin/env bash

ls -la

Copy and paste this into a new plain text file on Aviary; give it a file name that represents what this does (I recommend la, “list all”).

cat > la

Once you’ve written the file, exit your editor. Before we can run a shell script, we need to mark it as executable using chmod:

chmod a+x la

Then we can run the script:

./la

🎉, your first shell script!

Shell scripts consist of one or more lines of commands to run. Add another line to your script:

find . -name "*.md"

Then run it again (you don’t need to chmod again). Now two commands worth of output appear.

One command that you might find helpful when you’re scripting is the echo command, this is a “print” command for shells:

echo "Hello, world!"

You can also write comments using the # symbol, anything following is a comment:

echo "Hello, world" # a friendly message
find . -name "*.docx" -delete # clean up Word files

#!/usr/bin/env bash

echo "Here's what's in the current directory:"
# list all with long listings
ls -al

echo "Here are all the Markdown files:"
# find all files with the `.md` extension
find . -name "*.md"

Environment variables and the $PATH

Shell languages, like other programming languages, support variables.

Almost all shells follow the same convention for naming variables:

• Variable names start with a $,
• Variable names are all UPPERCASE,
• Variable names are SNAKE_CASE (they use underscores to separate words).

All shells have special variables, and those special variables help your shell make decisions, or help define the behaviour that your shell has. These special variables are called “environment variables”.

echo $SHELL

When you enter the names of programs on the command line, your shell has to figure out where that program actually is in a folder structure.

man hier 

### OR

man 7 hier # hier is in section 7 for miscellaneous

Your shell uses a special environment variable called $PATH (often called the $PATH) to find where the command you just entered exists as a file. The $PATH contains a list of directories that your shell will look in to find the file representing the command you asked it to run. Different shells use different separators for directory entries in the path. Both tcsh and bash use a colon : to separate directories.

echo $PATH

Your $PATH will contain many folders on Aviary, but it importantly includes two directories:

1. .: the current directory, and this is why you don’t have to type ./ in front of programs you’ve written and compiled yourself.
2. ~/bin: a directory named bin relative to your home directory. When you echo $PATH, the ~ will be listed as an absolute path (e.g., /home/student/you/bin).

What this means is that we can put scripts we write into the directory ~/bin, then we can run them anywhere.

rehash

cd ~

### Or just `cd` with no arguments

cd

You can find out which environment variables are currently set and what their values are using the env command.