The Shell
Adapted from Software Carpentry http://software-carpentry.org
What and Why
At a high level, computers do four things:
- run programs
- store data
- communicate with each other
- interact with us
Most of us use windows, icons, mice, and pointers to interact with computers. These technologies didn't become widespread until the 1980s. Going back even further, the only way to interact with early computers was to rewire them. But in between, from the 1950s to the 1980s, most people used line printers. These devices only allowed input and output of the letters, numbers, and punctuation found on a standard keyboard, so programming languages and interfaces had to be designed around that constraint.
This kind of interface is called a command-line interface, or CLI, to distinguish it from the graphical user interface, or GUI, that most people now use. The heart of a CLI is a read-evaluate-print loop, or REPL: when the user types a command and then presses the enter (or return) key, the computer reads it, executes it, and prints its output. The user then types another command, and so on until the user logs off.
This description makes it sound as though the user sends commands directly to the computer, and the computer sends output directly to the user. In fact, there is usually a program in between called a command shell. What the user types goes into the shell; it figures out what commands to run and orders the computer to execute them.
A shell is a program like any other. What's special about it is that its job is to run other programs rather than to do calculations itself. The most popular Unix shell is Bash, the Bourne Again SHell (so-called because it's derived from a shell written by Stephen Bourne—this is what passes for wit among programmers). Bash is the default shell on most modern implementations of Unix, and in most packages that provide Unix-like tools for Windows.
Using Bash or any other shell sometimes feels more like programming than like using a mouse. Commands are terse (often only a couple of characters long), their names are frequently cryptic, and their output is lines of text rather than something visual like a graph. On the other hand, the shell allows us to combine existing tools in powerful ways with only a few keystrokes and to set up pipelines to handle large volumes of data automatically. In addition, the command line is often the easiest way to interact with remote machines. As clusters and cloud computing become more popular for scientific data crunching, being able to drive them is becoming a necessary skill.
Key Points
- A shell is a program whose primary purpose is to read commands and run other programs.
- The shell's main advantages are its high action-to-keystroke ratio, its support for automating repetitive tasks, and that it can be used to access networked machines.
Navigating Files & Directories
The part of the operating system responsible for managing files and directories is called the file system. It organizes our data into files, which hold information, and directories (also called “folders”), which hold files or other directories.
Several commands are frequently used to create, inspect, rename, and delete files and directories. To start exploring them, let's open a shell window:
$
The dollar sign is a prompt, which shows us that the shell is waiting for input; your shell may show something more elaborate.
Type the command whoami, then press the Enter key (sometimes marked Return) to send the command to the shell. The command's output is the ID of the current user, i.e., it shows us who the shell thinks we are:
$ whoami
jens
More specifically, when we type whoami the shell:
- finds a program called whoami,
- runs that program,
- displays that program's output, then
- displays a new prompt to tell us that it's ready for more commands.
Next, let's find out where we are by running a command called pwd (which stands for “print working directory”). At any moment, our current working directory is our current default directory, i.e., the directory that the computer assumes we want to run commands in unless we explicitly specify something else.
$ pwd
/home/users/jens/
To understand what a “home directory” is, let's have a look at how the file system as a whole is organized. At the top is the root directory that holds everything else. We refer to it using a slash character / on its own; this is the leading slash in /home/users/jens.
Inside that directory are several other directories: bin (which is where some built-in programs are stored), data (for miscellaneous data files), users (where users' personal directories are located), tmp (for temporary files that don't need to be stored long-term), and so on:
