Updated and presented by : Ian Langmore
Modified by : Sasha Wood, Radhika Khetani
This presentation originally developed by: Milad Fatenejad
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.
There are many reasons to learn about the shell. In my opinion, the most important reasons are that:
The shell is just a program and there are many different shell programs that have been developed. The most common shell (and the one we will use) is called the Bourne-Again SHell (bash). Even if bash is not the default shell, it is usually installed on most systems and can be started by typing bash in the terminal. Many commands, especially a lot of the basic ones, work across the various shells but many things are different. I recommend sticking with bash and learning it well. (Here is a link for more information
To open a terminal, just single click on the “Terminal” icon on the Desktop.
We will spend most of our time learning about the basics of the shell by manipulating some experimental data from a hearing test. To get the data for this test, you will need internet access. Just enter the command:
git clone https://github.com/adina/boot-camps.git
Followed by:
cd boot-camps
These 2 commands will grab all of the data needed for this workshop from the internet.
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.
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 really 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 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 me that I am in the /home/langmore/ directory. This is the home directory for the langmore user. That is my user name. You can always find out your user name by entering the command whoami.
File Types
When you enter the ls command lists the contents of the current directory. On most terminals, there are several items in the home directory that are colored blue. This tells us they are directories rather than files.
Lets 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. It is colored white meaning that it is a file, as opposed to a directory. The touch command just creates an empty file.
You can also use the command ls -l to see whether items in a directory are files or directories. 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.
Try entering
ls -a
ls -al
What do you think this did?
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
Now, let’s move to a different directory. The command cd (change directory) is used to move around. Let’s move into the boot-camps directory. Enter the following command:
cd boot-camps
Now use the ls command to see what is inside this directory. You will see that there is an entry which is green. This means that this is an executable.
This directory contains all of the material for this boot camp. Now move to the directory containing the data for the shell tutorial:
cd 1-Shell
If you enter the cd command by itself, you will return to the home directory. Try this, and then navigate back to the shell directory.
Most programs take additional arguments that control their exact behavior. For example, -a 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 up/down arrow keys to go forward/backwards. When you are done reading, just hit q to exit. The manual is written as a reference for experienced users. Beginners are also encouraged to search for examples on the internet.
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.
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). You can always find the directory you are in using the pwd command. However, you can also give ls the names of other directories to view. Navigate to the home directory if you are not already there. Then enter the command:
ls boot-camps
This will list the contents of the boot-camps directory without you having to navigate there. Now enter:
ls boot-camps/1-Shell
This prints the contents of 1-Shell. The cd command works in a similar way. Try entering:
cd boot-camps/1-Shell
and you will jump directly to 1-Shell without having to go through the intermediate directory.
The cd command takes an argument which is the directory name. Directories can be specified using either a relative path 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. Navigate to the home directory. Now, enter the pwd command and I see:
/home/langmore
which is the full name of my home directory. This tells me that I am in a directory called langmore, which sits inside a directory called home which sits inside the very top directory in the hierarchy. The very top of the hierarchy is a directory called / which is usually referred to as the root directory. So, to summarize: langmore is a directory in home which is a directory in /.
Now enter the following command:
cd /home/your-username/boot-camps/1-Shell
This jumps to 1-Shell. Now go back to the home directory. We saw earlier that the command:
cd boot-camps/1-Shell
had the same effect - it took us to the 1-Shell directory. But, instead of specifying the full path (/home/your-username/boot-camps/1-Shell), 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?
Shortcuts
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 1-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 /home/your-username/boot-camps. You can chain these together, so:
ls ../../
prints the contents of /home/your-username which is 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 /home/swc all do exactly the same thing. These shortcuts are not necessary, they are provided for your convenience.
Our data set: Cochlear Implants
A cochlear implant is a small electronic device that is surgically implanted in the inner ear to give deaf people a sense of hearing. More than a quarter of a million people have them, but there is still no widely-accepted benchmark to measure their effectiveness. In order to establish a baseline for such a benchmark, our supervisor got teenagers with CIs to listen to audio files on their computer and report:
To participate, subjects attended our laboratory and one of our lab techs played an audio sample, and recorded their data - when they first heard the sound, or first heard a difference in the sound. Each set of test results were written out to a text file, one set per file. Each participant has a unique subject ID, and a made-up subject name. Each experiment has a unique experiment ID. The experiment has collected 351 files so far.
The data is a bit of a mess! There are inconsistent file names, there are extraneous “NOTES” files that we’d like to get rid of, and the data is spread across many directories. We are going to use shell commands to get this data into shape. By the end we would like to:
If we can get through this example in the available time, we will move onto more advanced shell topics...
Wild cards
Navigate to the ~/boot-camps/1-Shell/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 see all of the contents of a given directory. 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 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.
Short Exercise
Do each of the following using a single ls command without navigating to a different directory.
Tab Completion
Navigate to the boot-camps/ 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 s<tab>
The shell will fill in the rest of the directory name for 1-Shell. Using tab-completion, navigate to data/alexander. Now enter:
ls d<tab><tab>
When you hit the first tab, d becomes data_ but does not complete to a full filename. The reason is that there are multiple directories in this directory which start with data_. 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*
down arrow takes your forwards in the command history.
^-C will cancel the command you are writing, and give you a fresh prompt.
^-R will do a reverse-search through your command history. This is very useful.
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. More on environment variables later. 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 1-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:
hello
You should get an error saying that hello cannot be found. That is because the directory /home/your-username/boot-camps/1-Shell is not in the PATH. You can run the hello program by entering:
./hello
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:
/home/your-username/boot-camps/1-Shell/hello
Or by entering:
../1-Shell/hello
When there are no / characters, the shell assumes you want to look in one of the default places for the program.
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. 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).
Short Exercises
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 ~/boot-camps/1-Shell/dictionary.txt
less opens the file, and lets you navigate through it. The commands are identical to the man program. Here’s some commands you can use:
Short Exercise
Use less to search for all the words in 1-Shell/dictionary.txt that contain the string hi.
Let’s turn to the experimental data from the hearing tests that we began with. This data is located in the boot-camps/1-Shell/data directory. Each subdirectory corresponds to a particular participant in the study. Navigate to the Bert subdirectory in data. There are a bunch of text files which contain experimental data results. Lets print them all:
cat au*
Now enter the following command:
cat au* > ../all_data
This tells the shell to take the output from the cat au* 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 what ever 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.
Short Exercise
Use >>, to append the contents of all of the files which contain the number 4 in the directory:
boot-camps/1-Shell/data/gerdal
to the existing all_data file. Thus, when you are done all_data should contain all of the experiment data from Bert and any experimental data file from gerdal that contains the number 4.
We’ve created a file called all_data using the redirection operator >. This is critical file so we have 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
Now the 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.
Short Exercise
Do the following:
By default, rm, will NOT delete directories. You can tell rm to delete a directory using the -r option. Enter the following command:
rm -r foo
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 Bert/* gerdal/*4*
For each of the files indicated, wc has printed a line with three numbers. The first is the number of lines in that file. The second is the number of words. Finally, the total number of characters is indicated. The final line contains this information summed over all of the files. Thus, there were 10445 characters in total.
Remember that the Bert/* and gerdal/*4* 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. Thus, the size of the file in bytes should also be 10445. 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.
Short Exercise
Figure out how to get wc to print the length of the longest line in all_data.
Suppose I wanted to only see the total number of character, words, and lines across the files Bert/* and gerdal/*4*. 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. Doing this often leads to lots of little files that clutter up your directory. We can however 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 Bert/* gerdal/*4* and send it into the tail -n 1 command. The | character (called pipe) is used for this purpose. Enter the following command:
wc Bert/* gerdal/*4* | 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:
French
fries
are
good
then CONTROL+d. You should see the lines:
are
good
printed back at you. 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.
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:
Bob
Alice
Diane
Charles
To do this, we need a program which allows us to create text files. There are many such programs, the easiest one which is installed on almost all systems is called nano. Navigate to /tmp and enter the following command:
nano toBeSorted
Now enter the four names as shown above. When you are done, press CONTROL+O to write out the file. Press enter to use the file name toBeSorted. Then press CONTROL+x to exit nano.
When you are back to the command line, enter the command:
sort toBeSorted
Notice that the names are now printed in alphabetical order.
Short Exercise
Use the echo command and the append operator, >>, to append your name to the file, then sort it and make a new file called Sorted.
Let’s navigate back to ~/boot-camps/1-Shell/data. Enter the following command:
wc Bert/* | 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 Bert directory. This list is then piped into the sort command, so that it can be sorted. Notice there are two options given to sort:
Notice that the files are sorted by the number of characters.
Short Exercise
Use the man command to find out how to sort the output from wc in reverse order.
Short Exercise
Combine the wc, sort, head and tail commands so that only the wc information for the largest file is listed
Hint: To print the smallest file, use:
wc Bert/* | sort -k 3 -n | head -n 1
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. We’ll use nano to create this file. Navigate to the data directory, then:
nano smallest
Then enter the following text:
#!/bin/bash
wc * | sort -k 3 -n | head -n 1
Now, cd into the Bert 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
../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 name is green and the permissions have changed. Congratulations, you just created your first shell script!
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 Bert directory. Every data file in this directory has a line which says “Range”. The range represents the smallest frequency range that can be discriminated. Lets list all of the ranges from the tests that Bert conducted:
grep Range *
Short Exercise
Create an executable script called smallestrange in the data directory, that is similar to the smallest script, but prints the file containing the file with the smallest Range. Use the commands grep, sort, and head to do this.
Navigate to the shell/babynames directory and unzip names.zip using the utility unzip. This will extract the babynames files. FYI, this file can be found online here.
Short Exercises
One pipeline that accomplishes number 4 is:
$ grep ,F, yob1982.txt | sort -t, -k3 -n | tail -n1
it produces the output
Jennifer,F,57099
Suppose we only want Jennifer, and not F,57099. We can use the cut utility. You will want to use the delimiter and field options. The command is: cut -d, -f1. Put this together with the above pipeline.
Suppose we want to print out the most popular name in every year. Let’s make a shell script for it. Note that if you’re generating useful data, using a shell script has the advantage that you can add the shell script to your repository, thus keeping a record of how your data was generated.
Create a file called getpopular.sh that contains the following:
#!/bin/bash
for file in $(ls *txt); do
echo $file
done
Run this shell script. It should print out all the names of the text files in the current directory. Now, add a pipeline (rather than just echo $file to print out the most popular names year by year.
Start your inner commands using:
cat $file \
| next-command... \
| and so on
The allows you to continue the command on the next line. This lets you clearly see that the first line is the file, then each other command is on a new line.
Now replace cat with head -n20. This will, instead of reading in the whole file, give you just the top. This will make the program run much faster. This is useful when debugging longer programs.
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For an introduction to the documentation format please see the reST primer.