Updated Oct 2016 by Titus Brown.
Original author: Tracy Teal for Data Carpentry (http://datacarpentry.org).
Original contributors: Paul Wilson, Milad Fatenejad, Sasha Wood and Radhika Khetani for Software Carpentry (http://software-carpentry.org/)
Note: in-class quizlets will be answered here.
- What is the shell?
- How do you access it?
- How do you use it and what is it good for?
- Running commands
- Storing files in folders
- Manipulating files
- Automating actions
- Where are resources where I can learn more?
This workshop operates under the Software Carpentry Code of conduct: http://software-carpentry.org/conduct/
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.
There are many reasons to learn about the shell. A few specific ones:
- For most bioinformatics tools, you have to use the shell. There is no graphical interface. If you want to work in metagenomics or genomics you're going to need to use the shell.
- The shell gives you power. The command line gives you the power to do your work more efficiently and more quickly. When you need to do things tens to hundreds of times, knowing how to use the shell is transformative.
- To use remote computers or cloud computing, you need to use the shell.
You can also pretend to be a hacker from the moving pictures!
The most important reason to learn the shell is to learn about automation. Any time you find yourself doing roughly the same computational task more than few times, it may be worth automating it; the shell is often the best way to automate anything to do with files.
Part of our goal is to make you aware of this dynamic:
And here's a handy chart explaining when it pays to automate a task:
Today we're going to go through how to access Unix/Linux and some of the basic shell commands.
The challenge with UNIX is that it's not particularly simple - it's a power tool, with its own deep internal logic with lots of details. The joke is that Unix is user-friendly - it's just very selective about who its friends are!
shell cheat sheets:
- http://fosswire.com/post/2007/08/unixlinux-command-cheat-sheet/
- https://github.com/swcarpentry/boot-camps/blob/master/shell/shell_cheatsheet.md
Explain shell - a web site where you can see what the different components of a shell command are doing.
(We'll look at these at the bottom.)
The shell is already available on Mac and Linux. For Windows, you'll have to download a separate program.
On Mac the shell is available through Terminal Applications -> Utilities -> Terminal Go ahead and drag the Terminal application to your Dock for easy access.
For Windows, we're going to be using gitbash. Download and install gitbash; Open up the program.
You probably already know how to find the shell prompt.
We will spend most of our time learning about the basics of the shell by manipulating some experimental data.
Now we're going to download the data for the tutorial. For this you'll need internet access, because you're going to get it off the web.
Open up the shell and type the command:
pwd
and then hit ENTER - this will give you a directory name. Remember it!
We next want to use our Web browser to download the file:
https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/shell-data.zip
to our computer, and then use the file browser to copy it to the directory shown by pwd above.
Now, then unpack it in that directory (probably by double clicking on it).
Once that's done, type:
ls
and hit ENTER. You should see a listing of files, with 'shell-data.zip' and 'data' among them.
Once you see that, put up your green stickies. If you don't know where to start, put up your pink sticky.
'pwd' and 'ls' are examples of commands - programs you run at the shell prompt that do stuff. pwd stands for 'print working directory', while 'ls' stands for 'list files'.
Another command you'll find yourself using a lot is 'cd', which stands for 'change directory'. Try typing:
cd data
and then:
pwd
You should see that you're now in the data/ subdirectory (or folder) underneath the original directory. Type 'ls' to see what files are in here.
What's going on?
The shell has a concept of "working directory", which is basically the default location for commands to look when you run them. When you run 'ls', by default it looks in your current working directory; when you run 'cd', it changes your current working directory.
What's the difference between 'cd' and 'data'? Here, 'cd' is the command, and 'data' is an argument to that command - think of the command as the verb, and the argument as the noun upon which the verb acts.
Now type:
cd ..
and type 'ls'. You should see at least two entries,
shell-data.zip and data. Here you're using shorthand notation
to go back up a directory.
Type:
ls data
to tell ls to look in a different directory than your current working directory. This is equivalent to:
cd data ls cd ..
Go back into the 'data' directory and list the files:
cd data ls
In here, all mixed up together are files and directories/folders. If we want to know which is which, we can type:
ls -F
Anything with a "/" after it is a directory. Things with a "*" after them are programs. It there's nothing there it's an otherwise unremarkable file (e.g. a data 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.
Most programs take additional options (or "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, 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. No
one can possibly learn all of these arguments, of course. So you will
probably find yourself referring back to the manual page frequently.
As you've already just seen, you can move around in different directories or folders at the command line. Why would you want to do this, rather than just navigating around the normal way.
When you're working with bioinformatics programs, you're working with your data and it's key to be able to have that data in the right place and make sure the program has access to the data. Many of the problems people run in to with command line bioinformatics programs is not having the data in the place the program expects it to be.
Let's practice moving around a bit.
We're going to work in that data directory we just downloaded.
First let's navigate there using the regular way by clicking on the different folders.
First we did something like go to the folder of our username. Then we opened 'data'
This is called a hierarchical file system structure, like an upside down tree with root (/) at the base that looks like this.
That (/) at the base is often also called the 'top' level.
When you are working at your computer or log in to a remote computer, you are on one of the branches of that tree, your home directory (/home/username)
Now let's go do that same navigation at the command line.
Type:
cd
This puts you in your home directory. This folder here.
Now using cd and ls, go in to the 'data' directory and list its
contents.
Let's also check to see where we are. Sometimes when we're wandering around in the file system, it's easy to lose track of where we are and get lost.
Again, if you want to know what directory you're currently in, type:
pwd
What if we want to move back up and out of the 'data' directory? Can we just
type cd home? Try it and see what happens.
To go 'back up a level' we need to use ...
Type:
cd ..
Now do ls and pwd. See now that we went back up in to the home
directory. .. means go back up to the enclosing folder level.
Try entering:
cd data/hidden
and you will jump directly to hidden without having to go through
the intermediate directory. Here, we're telling cd to go into 'data'
first, and then 'hidden'.
Then do:
cd ../..
to go back up two levels. (Try typing pwd to see where you are!)
You could put more directories and a file on the end, too; for example,
ls data/hidden/tmp1/notit.txt
You can do the same thing with any UNIX command that takes a file or directory name.
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, type cd to get back to your home directy, then enter:
cd da<tab>
The shell will fill in the rest of the directory name for 'data'. Now cd to data/MiSeq and try:
ls F3D<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
F3D. 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.
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 the home directory. Now, enter the pwd
command and you should see:
/home/username
which is the full name of your home directory. This tells you that you
are in a directory called username, 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: username is a
directory in home which is a directory in /.
Now enter the following command:
cd /home/username/data/hidden
This jumps to hidden. Now go back to the home directory (cd). We saw
earlier that the command:
cd data/hidden
had the same effect - it took us to the hidden directory. But,
instead of specifying the full path
(/home/username/data), 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.
A relative path is like getting directions from someone on the street. They tell you to "go right at the Stop sign, and then turn left on Main Street". That works great if you're standing there together, but not so well if you're trying to tell someone how to get there from another country. A full path is like GPS coordinates. It tells you exactly where something is no matter where you are right now.
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.
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.
(Time for a quizlet!)
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 data
directory:
cd cd data
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/username directory. You can chain these together, so:
ls ../../
prints the contents of /home' which is above 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, while you are in the shell directory, the commands
ls ~, ls ~/., ls ../../, and ls /home/username all do
exactly the same thing. These shortcuts are not necessary, they are
provided for your convenience.
We did an experiment and want to look at the bacterial communities of mice in two treatments using 16S sequencing. We have 10 mice in one treatment and 9 in another.each treatment. We also sequenced a Mock community, so we can check the quality of our data. So, we have 20 samples all together and we've done paired-end MiSeq sequencing.
We get our data back from the sequencing center as FASTQ files, and we stick them all in a folder called MiSeq. This data is actually data generated by Pat Schloss and used in mothur tutorials.
We want to be able to look at these files and do some things with them.
Navigate to the data/MiSeq directory (hint: use cd). This
directory contains our FASTQ files and some other ones we'll need for
analyses. If we type ls, we will see that there are a bunch of
files with long file names. Some of them end with .fastq.
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 *fastq
This lists every file that ends with a fastq. This command:
ls /usr/bin/*.sh
Lists every file in /usr/bin that ends in the characters .sh.
We have paired end sequencing, so for every sample we have two files. If we want to just see the list of the files for the forward direction sequencing we can use:
ls *R1*fastq
lists every file in the current directory whose name contains the
number R1, and ends with fastq. There are twenty such files which
we would expect because we have 20 samples.
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. In this case, it identified
four such files. Then, it replaced the *R1*fastq with the list of
files, separated by spaces.
What happens if you do ls R1*fastq?
(Time for another quizlet!)
TODO: explain how to deal with filenames that being with '-' (use '--'), have spaces (use quotes/backslashes/tab completion), and/or quotes (use the other kind of quotes/backslashes/tab completion).
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 F3D0_S188_L001_R1_001.fastq
This prints out the contents of the F3D0_S188_L001_R1_001.fastq file.
- Print out the contents of the
~/data/MiSeq/stability.filesfile. What does this file contain? - Without changing directories, (you should still be in
data), use one short command to print the contents of all of the files in the/home/username/data/MiSeqdirectory.
Make sure we're in the right place for the next set of the lessons. We
want to be in the MiSeq directory. Check if you're there with pwd
and if not navigate there. One way to do that would be
cd ~/data/MiSeq
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 F3D0_S188_L001_R1_001.fastq
less opens the file, and lets you navigate through it. The commands
are identical to the man program.
Some commands in ``less``
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.
For instance, let's search for the sequence 1101:14341 in our file.
You can see that we go right to that sequence and can see
what it looks like.
Remember, the man program actually uses less internally and
therefore uses the same commands, so you can search documentation
using "/" as well!
There's another way that we can look at files, and in this case, just look at part of them. This can be particularly useful if we just want to see the beginning or end of the file, or see how it's formatted.
The commands are head and tail and they just let you look at
the beginning and end of a file respectively.
head F3D0_S188_L001_R1_001.fastq tail F3D0_S188_L001_R1_001.fastq
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 F3D0_S188_L001_R1_001.fastq tail -n 1 F3D0_S188_L001_R1_001.fastq
We showed a little how to search within a file using less. We can also
search within files without even opening them, using grep. Grep is a command-line
utility for searching plain-text data sets for lines matching a string or regular expression.
Let's give it a try!
Let's search for that sequence 1101:14341 in the F3D0_S188_L001_R1_001.fastq file.
grep 1101:14341 F3D0_S188_L001_R1_001.fastq
We get back the whole line that had '1101:14341' in it. What if we wanted all four lines, the whole part of that FASTQ sequence, back instead.
grep -A 3 1101:14341 F3D0_S188_L001_R1_001.fastq
The -A flag stands for "after match" so it's returning the line that
matches plus the three after it. The -B flag returns that number of lines
before the match.
Now we can move around in the file structure and look at files. But what if we want to do normal things like copy files or move them around or get rid of them. Sure we could do most of these things without the command line, but what fun would that be?! Besides it's often faster to do it at the command line, or you'll be on a remote server like Amazon where you won't have another option.
The stability.files file is one that tells us what sample name goes with what sequences. This is a really important file, so we want to make a copy so we don't lose it.
Lets copy the file using the cp command. The cp
command backs up the file. Navigate to the MiSeq directory and enter:
cp stability.files stability.files_backup
Now stability.files_backup has been created as a copy of stability.files.
Let's make a backup directory where we can put this file.
The mkdir command is used to make a directory. Just enter mkdir
followed by a space, then the directory name.
mkdir backup
We can now move our backed up file in to this directory. We can
move files around using the command mv. Enter this command:
mv stability.files_backup backup/
This moves stability.files_backup into the directory backup/;
the full path would be ~/data/MiSeq/backup.
The mv command is also how you rename files. Since this file is so
important, let's rename it:
mv stability.files stability.files_IMPORTANT
Now the file name has been changed to stability.files_IMPORTANT. Let's delete the backup file now:
rm backup/stability.files_backup
The rm file removes the file. Be careful with this command. It doesn't
just nicely put the files in the Trash. They're really gone.
By default, rm, will NOT delete directories. You can tell rm to
delete a directory using the -r option; we could test it out on
backup, but let's not... ;)
(Time for a quizlet again!)
We've been able to do a lot of work with files that already exist, but what if we want to write our own files. Obviously, we're not going to type in a FASTA file, but you'll see as we go through other tutorials, there are a lot of reasons we'll want to write a file, or edit an existing file.
To write in files, we're going to use the program nano. We're
going to create a file that contains the favorite grep command so you
can remember it for later. We'll name this file 'awesome.sh':
nano awesome.sh
Now you have something that looks like
Type in your command, so it looks like
Now we want to save the file and exit. At the bottom of nano, you see
the "^X Exit". That means that we use Ctrl-X to exit. Type
Ctrl-X. It will ask if you want to save it. Type y for yes. Then
it asks if you want that file name. Hit 'Enter'.
Now you've written a file. You can take a look at it with less or cat, or open it up again and edit it.
Exercise
Open 'awesome.sh' and add "echo AWESOME!" after the grep command and save the file.
We're going to come back and use this file in just a bit.
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 data directory and list the contents. You will
notice that there is a program (executable file) called hello.sh in
this directory. Now, try to run the program by entering:
hello.sh
You should get an error saying that hello.sh cannot be found. That is
because the directory /home/username/data is not in the
PATH. You can run the hello.sh program by entering:
./hello.sh
Remember that . is a shortcut for the current working
directory. This tells the shell to run the hello.sh program which is
located right here. So, you can run any program by entering the path
to that program. You can run hello.sh equally well by specifying:
/home/username/data/hello.sh
Or by entering:
~/data/hello.sh
When there are no / characters, the shell assumes you want to look
in one of the default places for the program.
(Why doesn't it look at your current directory by default? Any ideas?)
We know how to write files and run scripts, so I bet you can guess where this is headed. We're going to run our own script!
Go in to the 'MiSeq' directory where we created 'awesome.sh' before. Remember we wrote our favorite grep command in there. Since we like it so much, we might want to run it again, or even all the time. Instead of writing it out every time, we can just run it as a script.
It's a command, so we should just be able to run it. Give it try.:
./awesome.sh
Alas, we get -bash: ./awesome.sh: Permission denied. This is because
we haven't told the computer that it's a program. To do that we have
to make it 'executable'. We do this by changing its mode. The command
for that is chmod - change mode. We're going to change the mode of
this file, so that it's executable and the computer knows it's OK to
run it as a program.:
chmod +x awesome.sh
Now let's try running it again:
./awesome.sh
Now you should have seen some output, and of course, it's AWESOME!
Congratulations, you just created your first shell script! You're set to rule the world!
write a script that:
- resides in the data directory;
- changes to the MiSeq/ subdirectory of the current working directory;
- makes two subdirectories, "left" and "right";
- moves all of the R1 sequencing files into the left directory;
- moves all of the R2 sequencing files into the right directory;
And we're done!
- Software Carpentry tutorial - The Unix shell
- The shell handout - Command Reference
- explainshell.com
- http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO.html
- man bash
- Google - if you don't know how to do something, try Googling it. Other people have probably had the same question.
Most importantly - learn by doing. There's no real other way to learn this than by trying it out. Write your next paper in nano (really emacs or vi), open pdfs from the command line, automate something you don't really need to automate....
Some books you should look into --