Based on material by Milad Fatenejad, Sasha Wood, and Radhika Khetani
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. The most important reasons are that:
It is very common to encounter the shell and command-line-interfaces in scientific computing, so you will probably have to learn it eventually
The shell is a really powerful way of interacting with your computer. GUIs 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 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 or search for another terminal program in your OS.
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/scopatz/aims-scicomp.git scicomp
Followed by:
cd scicomp
These 2 commands will grab all of the data needed we'll need.
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. For
example, if our user ID is me, the pwd command tells us that we
are in the /home/me directory. This is the home directory for the
me user. That is our 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. There are several items in the home directory, notice that
they are all colored blue. This tells us that all of these items are
directories as opposed to 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.
Some terminals will not color the directory entries in this very
convenient way. 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 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
Now, let's move to a different directory. The command cd (change
directory) is used to move around. Let's move into the
thw-shell directory. Enter the following command:
cd thw-shell
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. If you use ls -F you will see that this file ends
with a star.
This directory contains all of the material for this bootcamp. 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. Try this, and then navigate back to the data
directory.
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.
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 scicomp
This will list the contents of the scicomp directory without
you having to navigate there. Now enter:
ls scicomp/thw-shell
This prints the contents of thw-shell. The cd command works in a
similar way. Try entering:
cd scicomp/shell
and you will jump directly to thw-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 absolute path tells you where a directory is in that
hierarchy. Navigate to the home directory. Now, enter the pwd
command and you should see something like:
/home/me
which is the full name of your home directory. This tells you that you
are in a directory called me, 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: me is a
directory in home which is a directory in /.
Now enter the following command:
cd /home/me/scicomp/thw-shell
This jumps to thw-shell. Now go back to the home directory. We saw
earlier that the command:
cd scicomp/thw-shell
had the same effect - it took us to the thw-shell directory. But,
instead of specifying the absolute path
(/home/me/scicomp/shell), we specified a relative
path. In other words, we specified the path relative to our current
directory. A absolute path always starts with a /. A relative path does
not. You can usually use either a absolute 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 shell
directory, then enter the command:
ls ~
This prints the contents of your home directory, without you having to
type the absolute path. The shortcut .. always refers to the directory
above your current directory. Thus:
ls ..
prints the contents of the /home/swc/scicomp. You can chain
these together, so:
ls ../../
prints the contents of /home/me 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/me 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:
Put all of the data into one directory called "alldata"
Have all of the data files in there, and ensure that every file has a ".txt" extension
Get rid of the extraneous "NOTES" files
If we can get through this example in the available time, we will move onto more advanced shell topics...
Wild cards
Navigate to the 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.
/bin that contain the letter a/bin that contain the letter a or the letter b/bin that contain the letter a AND the letter bTab 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 s<tab>
The shell will fill in the rest of the directory name for
scicomp. Now enter:
ls 3<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
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.
^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 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 this directory 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/me/scicomp/thw-shell/hello
Or by entering:
../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 appaloosa.txt
This prints out the contents of the appaloosa.txt file. If you enter:
cat appaloosa.txt appaloosa.txt
It will print out the contents of appaloosa.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:
Print out the contents of the shell/dictionary.txt
file. What does this file contain?
Without changing directories, (you should still be in shell),
use one short command to print the contents of all of the files in
the /home/swc/{{page.bootcamp_slug}}/shell/data/thomas directory.
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 shell/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. Finally, hit "q" to quit.
less also gives you a way of searching through files. Just hit the
"/" key to begin a search. Enter 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 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!
Short Exercise
Use the commands we've learned so far to figure out how to search
in reverse while using less.
Let's turn to the experimental data from the hearing tests that we
began with. This data is located in the 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:
/home/me/scicomp/thw-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 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
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:
all_data_IMPORTANT file to all_data.data directory called fooall_data file into fooBy default, rm, will NOT delete directories. You can tell rm to
delete a directory using the -r option. Enter the following command:
rm -r fooThe 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. Thus, I
have wasted a precious 7062 bytes of hard disk space. 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 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/Data0559 | 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 ^d. You should see the lines:
are
good
printed back at you. The ^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 is 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:
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 to-be-sorted
Now enter the four names as shown above. When you are done, press
^O to write out the file. Press enter to use the file name
to-be-sorted. Then press ^x to exit nano.
When you are back to the command line, enter the command:
sort to-be-sorted
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 thw-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:
-k 3: Sort based on the third column-n: Sort in numerical order as opposed to alphabetical orderNotice 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 tail to do this.
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 these commands:
find . -type f -name "*1*"
find . -type f -name "*1*" -or -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 Volume {} \;
This command finds every file starting from .. Then it searches each
file for a line which contains the word "Volume". The {} refers to
the name of each file. The trailing \; is used to terminate the
command. This command is slow, because it is calling a new instance
of grep for each item the find returns.
A faster way to do this is to use the xargs command:
find . -type f -print | xargs grep Volume
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).
Short Exercise:
Navigate to the data directory. Use one find command to perform each
of the operations listed below (except number 2, which does not
require a find command):
Find any file whose name is "NOTES" within data and delete it
Create a new directory called cleaneddata
Move all of the files within data to the cleaneddata directory
Rename all of the files to ensure that they end in .txt (note:
it is ok for the file name to end in .txt.txt
Hint: If you make a mistake and need to start over just do the following:
Navigate to the shell directory
Delete the data directory
Enter the command: git checkout -- data You should see that the
data directory has reappeared in its original state
BONUS
Redo this exercise, 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.
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