Introducing the Shell

What is the shell?

The Shell is one of the ways we can interact with a computer. It is a program that allows users to tell the computer what to do, to give the computer a “command”, and is commonly used through a command line interface (CLI).

Another, perhaps more common way we tell the computer what to do is through the use of a graphical user interface (GUI). This usually involves a “point and click” approach.

(a) Command Line Interface (CLI)

(b) Graphical User Interface (GUI)

Figure 1: Different ways to interact with a computer

Why use the shell?

Isn’t pointing and clicking easier?

Thought experiment

For example, let’s say that we need to take the third line of a file and put it into a single new file. This is easy to do with a GUI and requires just 4 steps:

  1. Open the original file.
  2. Copy from original file
  3. Paste to the new file.
  4. Close each file.

What if we make it more complicated?

  • Do this with 1000 files?
  • Each file is in it’s own directory?

Take a look below to see the process for GUI and CLI.

1. Open the original file.
2. Copy from original file
3. Paste to the new file.
4. Close each file.
5. Navigate to another file.
6. Repeat steps 2 through 5 999 times until you are done.
for i in */*.txt;
do;
    sed -n3 '3p' $i > new.txt;
done

For this task, the GUI was tedious, time-consuming, and error-prone while the CLI was a single-command, quick, and relatively error proof.

Using the shell

Let’s start using the shell. Open the shell (terminal) on your computer.

Running our first command

Once we open our terminal, the $ shows us that shell is ready for input.

ls commmand
  • ls stands for list
  • lists objects (files, directories, etc.) in a location

In terminal, type ls and press enter/return.

(base) czimacos3304:~ csifuentes$ ls
Applications            Downloads               Movies                  VirtualBox VMs          miniconda               setup.sh
CytoscapeConfiguration  Dropbox-Uploader        Music                   bin                     miniconda3              single-cell-curation
Desktop                 EnsDb.Xtropicalis.v101  Pictures                course                  notebooks
Documents               Library                 Public                  igv                     notes
(base) czimacos3304:~ csifuentes$

Everything that is in your home directory is listed, alphabetically.

Tip

Upon successful completion of the ls command, the $ prompt is displayed, signalling that the shell is ready again.

Our first error

This is great, but what if we make a mistake? What happens then?

The shell provides (usually) helpful and informative error messages. Let’s test this by typing ks into the terminal instead of ls.

(base) czimacos3304:~ csifuentes$ ks
bash: ks: command not found
(base) czimacos3304:~ csifuentes$

The shell returned an error bash: ks: command not found. In this instance, it tells you that ks is not a command, or at the very least that it cannot find that command.

We’ll learn more about commands and command structure soon, but first let’s learn about the filesystem.

Command syntax

Shell commands follow a general syntax.

command option argument

  • command is the main command
  • option modifies the behavior of the command
  • argument the source and/or target of the command

Let’s take a look at a few examples:

Command Option Argument
ls -F /
mv -i /Users/path/file /other/directory
Note
  • Options use either - or -- to signal their usage.
  • Options are sometimes called flags.
  • Arguments are sometimes called parameters.
  • Depending on the command, arguments can be either a target (as in the ls command) or both a source and target (as in the mv command)

Case matters

What happens if we run the same command, but change the case? Let’s try with an example. We’ll use the ls command and the size option, s, which lists the directories and files, but add their block sizes alongside.

First, let’s run the command ls -s.

(base) czimacos3304:~ csifuentes$ ls -s
total 8
0 Applications                  0 Dropbox-Uploader              0 Pictures                      0 igv                           8 setup.sh
0 CytoscapeConfiguration        0 EnsDb.Xtropicalis.v101        0 Public                        0 miniconda                     0 single-cell-curation
0 Desktop                       0 Library                       0 VirtualBox VMs                0 miniconda3
0 Documents                     0 Movies                        0 bin                           0 notebooks
0 Downloads                     0 Music                         0 course                        0 notes
(base) czimacos3304:~ csifuentes$

Now let’s do the same, but with a capital s, ls -S.

(base) czimacos3304:~ csifuentes$ ls -S
Downloads               CytoscapeConfiguration  Dropbox-Uploader        igv                     Music                   miniconda
Library                 course                  EnsDb.Xtropicalis.v101  Applications            Public                  notes
Documents               miniconda3              Movies                  notebooks               VirtualBox VMs
setup.sh                single-cell-curation    Pictures                Desktop                 bin

We get a very different output. In the output above, we have the files/directories sorted by size (largest) file first.

Getting help

Command usage is not always intuitive. Additionally, we’re often not aware of all the options/flags that can be used with a particular command. If you need help with how to use a command, you can try the following (depending on the command).

Method of getting help Description Example
--help or -h option/flag Displays help menu for the command/program ls --help
man command Displays the manual for the command/program in-depth man ls

(a) Using the --help flag

(b) Using the man command

Figure 2: Different ways to interact with a computer

Useful ls flags

There are A LOT of ls options/flags. A few quite useful ones are shows below.

Flag Description
-l

Returns the results in a long format, which provides information about

  • the item type (- for file, d for directory, l for link)
  • item permissions
  • thenumber of links or files inside that item
  • the item owner
  • the item group
  • the time the item was created
  • item size
  • item name
-h Returns the results with a human-readible size value

Figure 3: Using the -lh options/flags.

Above the results are now listed, one item per line, in alphabetical order, and the additional information provided when using the -l flag/option. Using the -h flag/option, the sizes are much easier to read (in bytes or kilobytes, megabytes, and gigabytes) as well.

Note

Multiple options or flags can be used at the same time by simply putting them one after the other, as above.