Session 3: Shell and shell scripting

An extended version of this tutorial is available here:

Want to learn more? Come to one of the Software Carpentry bootcamps!

Material by Milad Fatenejad, Sasha Wood, Radhika Khetani and Tracy Teal

What is the shell and how do I access the shell?

The shell is a program that presents a command line interface which allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard combination.

A terminal is a program you run that gives you access to the shell. There are many different terminal programs that vary across operating systems.

Hello, World!

One very basic command is echo. This command just prints text to the terminal. Try the command:

echo Hello, World

Then press enter. You should see the text “Hello, World” printed back to you. The echo command is useful for printing from a shell script, for displaying variables, and for generating known values to pass to other programs.

Moving around the file system

Let’s learn how to move around the file system using command line programs. This is really easy to do using a GUI (just click on things). Once you learn the basic commands, you’ll see that it is easy to do in the shell too.

First we have to know where we are. The program pwd (print working directory) tells you where you are sitting in the directory tree. The command ls will list the files in the current directory. Directories are often called “folders” because of how they are represented in GUIs. Directories are just listings of files. They can contain other files or directories.

Whenever you start up a terminal, you will start in a special directory called the home directory. Every user has their own home directory where they have full access to do whatever they want. In this case, the pwd command tells us that the name of our home directory is. The last word in that listing should also be the name of your user. You can also find out your user name by entering the command whoami.

File Types

When you enter the ls command, it lists the contents of the current directory. There are several items in your home directory.

Let’s create an empty file using the touch command. Enter the command:

touch testfile

Then list the contents of the directory again. You should see that a new entry, called testfile, exists. The touch command just creates an empty file. ls -l gives a lot more information too, such as the size of the file and information about the owner. If the entry is a directory, then the first letter will be a “d”. The fifth column shows you the size of the entries in bytes. Notice that testfile has a size of zero.

Now, let’s get rid of testfile. To remove a file, just enter the command:

rm testfile

The rm command can be used to remove files. If you enter ls again, you will see that testfile is gone.

Changing Directories

For some parts of the tutorial we will be using sample data. In order to download them, type into the terminal the following command:

git clone TGAC-workshop

Now, let’s move to a different directory. The command cd (change directory) is used to move around. Let’s move into the TGAC-workshop directory. Enter the following command:

cd TGAC-workshop

Now use the ls command to see what is inside this directory. This directory contains all of the material for this workshop. Now move to the directory containing the data for the shell tutorial:

cd data

If you enter the cd command by itself, you will return to the home directory.

Arguments (flags)

Most programs take additional arguments that control their exact behavior. For example, -F and -l are arguments to ls. The ls program, like many programs, take a lot of arguments. But how do we know what the options are to particular commands?

Most commonly used shell programs have a manual. You can access the manual using the man program. Try entering:

man ls

This will open the manual page for ls. Use the space key to go forward and b to go backwards. When you are done reading, just hit q to exit.

Programs that are run from the shell can get extremely complicated. To see an example, open up the manual page for the find program, which we will use later this session. No one can possibly learn all of these arguments, of course. So you will probably find yourself referring back to the manual page frequently. Note: sometimes it can be pretty difficult to understand what it says in a man file. However, each time you read a man file you will understand more of it.

Examining the contents of other directories

By default, the ls commands lists the contents of the working directory (i.e. the directory you are in). However, you can also give ls the names of other directories to view. Let’s explore the directory where we downloaded the sample data:

ls TGAC-workshop

This will list the contents of the TGAC-workshop directory without you having to navigate there. Now enter:

ls TGAC-workshop/data

This prints the contents of data. The cd command works in a similar way. Try entering:

cd TGAC-workshop/data

and you will jump directly to data without having to go through the intermediate directory.

Full vs. Relative Paths

The cd command takes an argument which is the directory name. Directories can be specified using either a relative path or a full path. The directories on the computer are arranged into a hierarchy. The full path tells you where a directory is in that hierarchy, all the way from the root and downwards.

Navigate to the home directory. Now, enter the pwd command and you should see the full name of your home directory. This tells you that you are in a directory that is named the same as your user, which sits inside one or more other directories. The very top of the hierarchy is a directory called / which is usually referred to as the root directory.

First, figure out again what the full path to your home directory was. Now enter the following command (replace the stuff in <> with the results from pwd).

cd <pwd-results>/TGAC-workshop/data

This jumps to data. Now go back to the home directory. We saw earlier that the command

cd TGAC-workshop/data

had the same effect - it took us to the data directory. But, instead of specifying the full path which started with a /, we specified a relative path. In other words, we specified the path relative to our current directory. A full path always starts with a /. A relative path does not. You can usually use either a full path or a relative path depending on what is most convenient. If we are in the home directory, it is more convenient to just enter the relative path since it involves less typing.

Now, list the contents of the /bin directory. Do you see anything familiar in there?

Saving time with shortcuts, wild cards, and tab completion


There are some shortcuts which you should know about. Dealing with the home directory is very common. So, in the shell the tilde character, ~, is a shortcut for your home directory. Navigate to the shell directory, then enter the command:

ls ~

This prints the contents of your home directory, without you having to type the full path. The shortcut .. always refers to the directory above your current directory. Thus:

ls ..

prints the contents of the ~/TGAC-workshop directory. You can chain these together, so:

ls ../../

prints the contents of what should be your home directory. Finally, the special directory . always refers to your current directory. So, ls, ls ., and ls ././././. all do the same thing, they print the contents of the current directory. This may seem like a useless shortcut right now, but we’ll see when it is needed in a little while.

To summarize, the commands ls ~, ls ~/., ls ../../, and ls <absolute path to home directory> all do exactly the same thing. These shortcuts are not necessary, they are provided for your convenience.

Wild cards

Navigate to the ~/TGAC-workshop/data/THOMAS directory. This directory contains our hearing test data for THOMAS. If we type ls, we will see that there are a bunch of files which are just four digit numbers. By default, ls lists all of the files in a given directory. The * character is a shortcut for “everything”. Thus, if you enter ls *, you will again see all of the contents of a given directory. This * can be combined with other characters. Now try this command:

ls *1

This lists every file that ends with a 1. This command:

ls /usr/bin/*.sh

Lists every file in /usr/bin that ends in the characters .sh. And this command:

ls *4*1

lists every file in the current directory which contains the number 4, and ends with the number 1. There are four such files: 0241, 0341, 0431, and 0481.

So how does this actually work? Well...when the shell (bash) sees a word that contains the * character, it automatically looks for files that match the given pattern. In this case, it identified four such files. Then, it replaced the *4*1 with the list of files, separated by spaces. In other words, the two commands:

ls *4*1
ls 0241 0341 0431 0481

are exactly identical. The ls command cannot tell the difference between these two things.

Tab Completion

Navigate to the home directory. Typing out directory names can waste a lot of time. When you start typing out the name of a directory, then hit the tab key, the shell will try to fill in the rest of the directory name. For example, enter:

cd T<tab>

The shell will fill in the rest of the directory name for TGAC-workshop. Press enter to enter the workshop directory. Next, go into the data directory and do:

ls 3<tab><tab>

When you hit the first tab, nothing happens. The reason is that there are multiple file in this directory which start with 3. Thus, the shell does not know which one to fill in. When you hit tab again, the shell will list the possible choices.

Tab completion can also fill in the names of programs. For example, enter e<tab><tab>. You will see the name of every program that starts with an e. One of those is echo. If you enter ec<tab> you will see that tab completion works.

Command History

You can easily access previous commands. Hit the up arrow. Hit it again. You can step backwards through your command history. The down arrow takes your forwards in the command history.

^-C will cancel the command you are writing, and give you a fresh prompt.

You can display all your command history (since the last login) using command:


Which program?

Commands like ls, rm, echo, and cd are just ordinary programs on the computer. A program is just a file that you can execute. The program which tells you the location of a particular program. For example:

which ls

Will return “/bin/ls”. Thus, we can see that ls is a program that sits inside of the /bin directory. Now enter:

which find

You will see that find is a program that sits inside of the /usr/bin directory.

So ... when we enter a program name, like ls, and hit enter, how does the shell know where to look for that program? How does it know to run /bin/ls when we enter ls. The answer is that when we enter a program name and hit enter, there are a few standard places that the shell automatically looks. If it can’t find the program in any of those places, it will print an error saying “command not found”. Enter the command:

echo $PATH

This will print out the value of the PATH environment variable. Notice that a list of directories, separated by colon characters, is listed. These are the places the shell looks for programs to run. If your program is not in this list, then an error is printed. The shell ONLY checks in the places listed in the PATH environment variable.

Navigate to the shell directory and list the contents. You will notice that there is a program (executable file) called hello in this directory. Now, try to run the program by entering:


You should get an error saying that hello cannot be found. That is because the directory <your home directory>/TGAC-workshop is not in the PATH. You can run the hello program by entering:


Remember that . is a shortcut for the current working directory. This tells the shell to run the hello program which is located right here. So, you can run any program by entering the path to that program. You can run hello equally well by specifying:

<path to home directory>/TGAC-workshop/hello

Or by entering:


When there are no / characters, the shell assumes you want to look in one of the default places for the program.

Examining Files

We now know how to switch directories, run programs, and look at the contents of directories, but how do we look at the contents of files?

The easiest way to examine a file is to just print out all of the contents using the program cat. Enter the following command:

cat ex_data.txt

This prints out the contents of the ex_data.txt file. This file contains an example of how our data looks like. If you enter:

cat ex_data.txt ex_data.txt

It will print out the contents of ex_data.txt twice. cat just takes a list of file names and writes them out one after another (this is where the name comes from, cat is short for concatenate).

cat is a terrific program, but when the file is really big, it can be annoying to use. The program, less, is useful for this case. Enter the following command:

less ~/TGAC-workshop/data/dictionary.txt

less opens the file, and lets you navigate through it. The commands are identical to the man program. Use “space” to go forward and hit the “b” key to go backwards. The “g” key goes to the beginning of the file and “G” goes to the end. When you are done, hit “q” to quit.

less also gives you a way of searching through files. Just hit the “/” key to begin a search. Enter the word you would like to search for and hit enter. It will jump to the next location where that word is found. Try searching the dictionary.txt file for the word “cat”. If you hit “/” then “enter”, less will just repeat the previous search. less searches from the current location and works its way forward. If you are at the end of the file and search for the word “cat”, less will not find it. You need to go to the beginning of the file and search.

Remember, the man program uses the same commands, so you can search documentation using “/” as well!


Let’s turn to the experimental data from the hearing tests. This data is located in the data directory. Each subdirectory corresponds to a particular participant in the study. Navigate to the Lawrence subdirectory in data. First, press ls to look at the files. There are a bunch of text files which contain experimental data results. Lets print them all:

cat *

Now enter the following command:

cat * > ../all_data

This tells the shell to take the output from the cat * command and dump it into a new file called ../all_data. To verify that this worked, examine the all_data file. If all_data had already existed, we would overwritten it. So the > character tells the shell to take the output from whatever is on the left and dump it into the file on the right. The >> characters do almost the same thing, except that they will append the output to the file if it already exists.

Creating, moving, copying, and removing

We’ve created a file called all_data using the redirection operator >. This file is critical - it’s our analysis results - so we want to make copies so that the data is backed up. Lets copy the file using the cp command. The cp command backs up the file. Navigate to the data directory and enter:

cp all_data all_data_backup

Now all_data_backup has been created as a copy of all_data. We can move files around using the command mv. Enter this command:

mv all_data_backup /tmp/

This moves all_data_backup into the directory /tmp. The directory /tmp is a special directory that all users can write to. It is a temporary place for storing files. Data stored in /tmp is automatically deleted when the computer shuts down.

The mv command is also how you rename files. Since this file is so important, let’s rename it:

mv all_data all_data_IMPORTANT

Type in ls, and you will see that file name has been changed to all_data_IMPORTANT. Let’s delete the backup file now:

rm /tmp/all_data_backup

The mkdir command is used to create a directory. Just enter mkdir followed by a space, then the directory name.

Count the words

The wc program (word count) counts the number of lines, words, and characters in one or more files. Make sure you are in the data directory, then enter the following command:

wc Lawrence/*

For each of the files indicated, wc has printed a line with three numbers and also the relative file name. The first is the number of lines in that file. The second is the number of words. Third, the total number of characters is indicated. The bottom line contains this information summed over all of the files.

Remember that the Lawrence/* files were merged into the all_data file. So, we should see that all_data contains the same number of characters:

wc all_data

Every character in the file takes up one byte of disk space. Let’s confirm this:

ls -l all_data

Remember that ls -l prints out detailed information about a file and that the fifth column is the size of the file in bytes.

The awesome power of the Pipe

Suppose I wanted to only see the total number of character, words, and lines across the files Lawrence/*. I don’t want to see the individual counts, just the total. Of course, I could just do:

wc all_data

Since this file is a concatenation of the smaller files. Sure, this works, but I had to create the all_data file to do this. We can do this without creating a temporary file, but first I have to show you two more commands: head and tail. These commands print the first few, or last few, lines of a file, respectively. Try them out on all_data:

head all_data
tail all_data

The -n option to either of these commands can be used to print the first or last n lines of a file. To print the first/last line of the file use:

head -n 1 all_data
tail -n 1 all_data

Let’s turn back to the problem of printing only the total number of lines in a set of files without creating any temporary files. To do this, we want to tell the shell to take the output of the wc Lawrence/* and send it into the tail -n 1 command. The | character (called pipe) is used for this purpose. Enter the following command:

wc Lawrence/* | tail -n 1

This will print only the total number of lines, characters, and words across all of these files. What is happening here? Well, tail, like many command line programs will read from the standard input when it is not given any files to operate on. In this case, it will just sit there waiting for input. That input can come from the user’s keyboard or from another program. Try this:

tail -n 2

Notice that your cursor just sits there blinking. Tail is waiting for data to come in. Now type:


then CONTROL+d. You should get the lines:


printed back at you due to you asking tail to return the last two by doing -n 2.The CONTROL+d keyboard shortcut inserts an end-of-file character. It is sort of the standard way of telling the program “I’m done entering data”. The | character replaces the data from the keyboard with data from another command. You can string all sorts of commands together using the pipe.

The philosophy behind these command line programs is that none of them really do anything all that impressive. BUT when you start chaining them together, you can do some really powerful things really efficiently. If you want to be proficient at using the shell, you must learn to become proficient with the pipe and redirection operators: |, >, >>.

A sorting example

Let’s create a file with some words to sort for the next example. We want to create a file which contains the following names:


To do this, we need a program which allows us to create text files. We will use gedit. Navigate to /tmp and enter the following command:

gedit toBeSorted

Now enter the four names as shown above.

When you are back to the command line, enter the command:

sort toBeSorted

Notice that the names are now printed in alphabetical order.

Try looking at this file with less - note that the file itself has not changed.

Let’s navigate back to data. Enter the following command:

wc Lawrence/* | sort -k 3 -n

We are already familiar with what the first of these two commands does: it creates a list containing the number of characters, words, and lines in each file in the Lawrence directory. This list is then piped into the sort command, so that it can be sorted. Notice there are two options given to sort:

  1. -k 3: Sort based on the third column
  2. -n: Sort in numerical order as opposed to alphabetical order

Notice that the files are sorted by the number of characters.

Printing the smallest file seems pretty useful. We don’t want to type out that long command often. Let’s create a simple script, a simple program, to run this command. The program will look at all of the files in the current directory and print the information about the smallest one. Let’s call the script smallest. Navigate to the data directory, then:

gedit smallest

Then enter the following text:

wc * | sort -k 3 -n | head -n 1

Now, cd into the Lawrence directory and enter the command ../smallest. Notice that it says permission denied. This happens because we haven’t told the shell that this is an executable file. If you do ls -l ../smallest, it will show you the permissions on the left of the listing.

Enter the following commands:

chmod a+x ../smallest

The chmod command is used to modify the permissions of a file. This particular command modifies the file ../smallest by giving all users (notice the a) permission to execute (notice the x) the file. If you enter:

ls -l ../smallest

You will see that the file permissions have changed. Congratulations, you just created your first shell script!

Let’s see if we can create a more useful script based on what we learnt from the mRNAseq normalization and assembly module. The module is actually in the teaching materials Copy it over to your home directory.

Searching files

You can search the contents of a file using the command grep. The grep program is very powerful and useful especially when combined with other commands by using the pipe. Navigate to the Lawrence directory. Many data files in this directory have a line which says “Volume”. Let’s see how many times Volume occurs

grep Volume *

Finding files

The find program can be used to find files based on arbitrary criteria. Navigate to the data directory and enter the following command:

find . -print

This prints the name of every file or directory, recursively, starting from the current directory. Let’s exclude all of the directories:

find . -type f -print

This tells find to locate only files. Now try this command:

find . -type f -name "*1*"