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Up To Schedule - Forward To Let the Computer Do the Work

Introduction to The Shell

Material by Paul Wilson, Lauren Michael, Milad Fatenejad, Sasha Wood, and Radhika Khetani

What is the shell how do I access the shell?

The shell is a program that presents a command line interface which allows you to control your computer. Tasks are accomplished by entering commands with a keyboard instead of controlling graphical user interfaces (GUIs or application "windows") that use 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 our opinion, the most important reasons are that:

  1. It is very common to encounter the shell and command-line-interfaces in scientific computing, so you will probably have to learn it eventually

  2. The shell is a really powerful way of interacting with your computer. GUIs (clickable window interfaces) and the shell are complementary - by knowing both you will greatly expand the range of tasks you can accomplish with your computer. You will also be able to perform many tasks more efficiently.

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 unix-based systems (Mac or Linux operating systems), but Windows users can use something like Git Bash. Most commands, especially a lot of the basic ones, work across the various shells but some things may be different. We recommend sticking with bash and learning it well. (Here is a link for more information)

To open a terminal on a Mac or Linux computer, just single click on the "Terminal" icon on the Desktop (or in Applications). For Windows, open the Git Bash program you installed for the bootcamp.

The Example: Manipulating Data Files

We will spend most of our time learning about the basics of the shell by manipulating some survey data collected for a projct. To get the data, you will need internet access. Just enter the command:

git clone -b 2015-06-03 https://github.com/UW-Madison-ACI/boot-camps.git

This command will grab all of the data needed for this workshop from our central GitHub repository. (We will talk about the git command later in the workshop.)

Interacting with the Shell

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 as "standard output". The echo command is useful for printing from a shell script, for displaying variables, and for generating known values to pass to other programs.

1. Navigating the file system

Let's learn how to move around your file system using command line programs. This is really easy to do using a GUI (you 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 and other directories in the current directory. Directories are often called "folders" because of how they are represented in GUIs. Directories are just organizational groupings of files. They can contain files or other directories.

Whenever you start up a terminal, you will start in a special directory called the home directory. You can always find out your user name by entering the command whoami.

File Types

When you enter the ls command, you'll get back a list of contents of the current directory. There are several items in the home directory, notice that they are all colored blue (but not colored in Windows). These directories and files should be generally familiar to you.

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.

Some terminals will not color the directory entries (though yours might, already). In those terminals, use ls -F instead of ls. The -F argument modifies the results so that a slash is placed at the end of directories. If the file is executable meaning that it can be run like a program, then a star will be placed at the end of of the file name.

You can also use the command ls -l to see whether items in a directory are files or directories. ls -l gives a lot of other 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

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

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

cd shell

Now use the ls command to see what is inside this directory. Do you see files of different colors?

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.

Arguments

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, can take a variety of arguments. But how do we know what the options are to particular commands?

Most commonly-used shell programs have a manual. Unix-based (Mac and Linux) users can access the manual using the man program. Windows users may not have the man program, but can use Linux man pages online, using this link (http://man.he.net/) or just doing a google search.
On Mac or Linux, 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 quit.

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 frequently.

Short Exercise

Use the manual for ls to guess what you would expect from using the arguments -l, -t, -r at the same time.

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/shell

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

cd boot-camps/shell

and you will jump directly to shell 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. Navigate to your "home directory" with

cd ~

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 called <username>, and indicates the full path for that directory, starting with the top of the directory structure, which is indicated by /.

For example, you can enter a command to cd into boot-camps/shell, but using the full path based upon your output from pwd. How is the full path different for Windows versus unix-based computers?

Now go back to the home directory. We saw earlier that the command:

cd boot-camps/shell

had the same effect - it took us to the shell directory. But, instead of specifying the full path, 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 for you. If we are in the home directory, it is more convenient to just enter the relative path since it involves less typing.

Over time, it will become easier for you to keep a mental note of the structure of the directories that you are using and how to quickly navigate amongst them.

Short Exercise

List the contents of a directory of your own, by using the full path (and without using cd, so that you are running the command from your current location).

2. Saving time with shortcuts, wild cards, and tab completion

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, as we used it with cd before. 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 boot-camps folder when you are in shell. You can chain these together, so:

ls ../../

prints the contents of your home directory from shell.

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, while you are in the shell directory, the commands ls ~, ls ~/., and ls ../../ all do exactly the same thing. Or you could use the full path, too.

Introducing our sample data set: Event Survey Data

At a recent event, a group of university students collected demographic information from attendees in order to draw conclusions about the make-up of the crowd. For example, the students recorded the following information after interviewing each individual:

  1. Age
  2. Gender
  3. State of residence
  4. Income
  5. Education Level (on a standardized scale)
  6. Hours worked per week

Unfortunately, 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 different directories corresponding to each student that collected it. We are going to use shell commands to get this data into shape. By the end we would like to:

  1. Get rid of the extraneous "NOTES" files.

  2. Put all of the data into one directory called "cleaneddata"

  3. Have all of the data files in there, and ensure that every file has a ".txt" extension

After we get through this example, we will move on to more advanced shell topics...

Wild cards

Navigate to the ~/boot-camps/shell/data/THOMAS directory. This directory contains our data collected by 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 02**

lists every file that begins with 02. This command

ls *1*7

lists every file in the current directory whose name contains the number 1 and ends with the number 7 (so it has also established that 1 must be before 7 in the filename). There are four such files: 0147, 0157, 0187 and 0317.

So how does this actually work? Well...when the shell (bash) sees a word that contains the * character, it automatically looks for filenames that match the given pattern. Using the wildcard does NOT exclude cases where there are no characters between 1 and 7, as the wildcard includes cases where there are any number of characters in place of the * character, even if there are zero characters.

In this case, it identified four such files. Then, it replaced the *1*7 with the list of files, separated by spaces. In other words, the two commands:

ls *1*7
ls 0147 0157 0187 0317

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.

  1. List all of the files in /bin that contain the letter a or the letter b (including files that may contain both).
  2. List all of the files in /bin that contain the letter a AND the letter b.

Tab Completion

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

cd b<tab>

The shell will fill in the rest of the directory name for boot-camps. Now enter:

ls s<tab><tab>

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

3. 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 you forward in the command history.

CONTROL+c will cancel the command you are writing, and give you a fresh prompt.

CONTROL+r will do a reverse-search through your command history. You can also use the up and down arrows to navigate through your command history, which can be usefule for easily repeating a recent command. Useful, right?

You can also review all of your recent commands at once with the history command. Just enter:

history

to see a numbered list of recent commands, including this just-issued history command.

If your history looked like this:

259  ls ../../
260  cd ~/boot-camps/shell/data/THOMAS
261  ls *1

then you could repeat command #260 by simply entering:

!260

(that's an exclamation mark).

Short Exercise

  1. Find the line number in your history for the last exercise (listing directories in /bin) and reissue that command.

4. Which program?

Commands like ls, rm, echo, and cd are just ordinary programs that exist on the computer (or that come along with Git Bash, for Windows users). A program is just a file that you can execute, otherwise known as an executable. If you want to find the location of a program, you can use which. For example:

which rm

will return /bin/rm. Thus, we can see that rm 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, if you're on a unix-based computer.

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".

These standard places are stored in your path. To see your path, enter the following 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 is displayed, separated by colon characters. These are the places the shell looks for programs to run.

If your program is not in this list, then an error is printed. For example, 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:

hello

You should get an error saying that hello cannot be found. That is because the directory ~/boot-camps/shell is not in the PATH. Instead, 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 that is located in your current location. So, you can run any program by entering the path to that program. You can run hello equally well by specifying:

~/boot-camps/shell/hello

5. Working with 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. For example, enter the following command:

cat ex_data.txt

This prints out the contents of the ex_data.txt file to the terminal as standard output. 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 out their contents one after another (this is where the name comes from, cat is short for "concatenate").

Want to see what our hello program contains?

Short Exercises

  1. Print out the contents of the ~/boot-camps/shell/dictionary.txt file. What does this file contain?

  2. Without changing directories (you should still be in shell), use one short command to print the contents of all of the files in the ~/boot-camps/shell/data/THOMAS directory.

Viewing file contents with less

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/shell/dictionary.txt

less opens the file, and lets you navigate through it. The commands are identical to the man program.

Some commands in less

key action
"space" to go forward
"b" to go backward
"g" to go to the beginning
"G" to go to the end
"q" to quit

less also gives you a way of searching through files. Just hit the "/" key to begin a search, type the name of 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 only searches forward from the current location. Note: 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 (by typing g) and then search. Now quit the less program.

Pro-tip: The man program actually uses less to show you the contents of the manual file for each program, so you can search program manuals using "/" and use all other less commands as well!

Redirection

Let's turn to the survey data that we began with. This data is located in the ~/boot-camps/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 data files which contain Bert's collected survey results. Lets print them all:

cat su*

Now enter the following command:

cat su* > ../all_data

This tells the shell to take the output from the cat su* command and redirect 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 have overwritten it because the > character tells the shell to take the output from the command on the left and turn that into the contents of 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 whose names contain the number 4 in the directory ~/boot-camps/shell/data/THOMAS to the existing all_data file. Thus, when you are done, all_data should contain all of the survey data from Bert AND any survey data file from THOMAS with filenames that contain the number 4.

Creating, moving, copying, and removing

We first created a file called all_data using the redirection operator >. Let's say that this file is critical - it's our analysis results - so we want to make copies so that the data is backed up. Let's 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

Let's make a temporary directory to store that file. The mkdir command is used to make a directory. Just enter mkdir followed by a space, then the directory name:

mkdir backup

This makes a directory called backup in the current directory, data.

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

mv all_data_backup backup/

This moves all_data_backup into your directory within backup.

The mv command is also how you can rename files and directories. 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 backup/all_data_backup

Short Exercise

Do the following:

  1. Rename the all_data_IMPORTANT file back to all_data.
  2. Create a directory in the data directory called foo.
  3. Then, copy the all_data file into foo.

By default, rm, will NOT delete directories. You can tell rm to delete a directory and all of its contents using the -r option. Enter the following command:

rm -r foo

Finding files

The find program can be used to find files based on arbitrary criteria. Navigate to the shell 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 these commands:

find . -type f -name "*1*"
find . -maxdepth 1 -type f -print
find . -mindepth 2 -type f -print
find . -type f -name "*1*" -print -o -name "*2*" -print
find . -type f -name "*1*" -and -name "*2*" -print

The find command can acquire a list of files and perform some operation on each file. Try this command out:

find . -type f -exec grep Income {} \;

This command finds every file within and below the current directory, and then searches each file for a line which contains the word "Income". How does it do this? The -exec argument allow find to run to the program grep, multiple times, such that each file name is inserted whenever the {} occurs (as an argument to grep. The trailing \; is used to terminate the command, in order to end the task run by -exec.

We'll talk a bit more about grep after the break, but you'll use the {} trick in the exercises below.

Also: Using xargs to pass information to another program

The above command is slow, because it is calling a new instance of grep for each item the find returns. A faster way to repeat the same task is to use the xargs command:

find . -type f -print | xargs grep Income

find generates a list of all the files we are interested in, then we pipe (|) them to xargs. xargs takes the items given to it and passes them as arguments to grep. xargs generally only creates a single instance of grep (or whatever program it is running). We'll also use the pipe (|) more after the break.

Exercises

Let's clean up this data! Navigate to the data directory. Use a single find command to perform each of the below exercises (aside from exercise 1, which does not require find):

  1. Create a new directory called cleaneddata.

  2. Copy all of the files within the subdirectories of data into cleaneddata, not including the directories, themselves.

  3. Find any files in cleaneddata containing "NOTES" in the name, and then delete them.

  4. Rename all of the files to ensure that they end in .txt (note: it is okay for certain files to end in .txt.txt, as some already end with .txt.)

BONUS

Redo exercise 4, except rename only the files which do not already end in .txt. You will have to use the man command to figure out how to search for files which do not match a certain name.

Jump to look at the solutions to all the exercises.

Up To Schedule - Forward To Let the Computer Do the Work