Introductory Unix Shell¶

Updated June 2018 by Ulas Karaoz

Credits¶

Original author: Tracy Teal for Data Carpentry

Original contributors: Paul Wilson, Milad Fatenejad, Sasha Wood and Radhika Khetani for Software Carpentry

Additional contributors: Titus Brown, Karen Word (https://github.com/ngs-docs/2015-shell-genomics/)

Notes¶

This workshop operates under the Software Carpentry Code of conduct

Learning Objectives¶

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?

Important

Before starting:

Download the test data. Launch your shell terminal, type or copy/paste the following:

wget https://s3-us-west-1.amazonaws.com/mtb-bioinformatics-workshop/shell-data.zip

Unpack the .zip archive:

unzip shell-data.zip

We’ll be posting code snippets to: https://public.etherpad-mozilla.org/p/mtb_bioinformatics_shell

What is the shell?¶

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

Some specific reasons to learn about the shell:

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.

Information on the shell¶

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:

Explain shell - a web site where you can see what the different components of a shell command are doing.

Starting with the shell¶

We will spend most of our time learning about the basics of the shell by manipulating some experimental data we downloaded (see above)

Open up the shell and type the command

pwd

and then hit ENTER - this will give you a directory name.

Once that’s done, type:

ls

and hit ENTER. You should see a listing of files, with ‘shell-data.zip’ and data among them.

Running commands¶

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.

In this tutorial, commands are shown as I am a command: you can type me in your shell terminal.

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 ..

Files and directories¶

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.

Command line options¶

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.

The Unix directory file structure¶

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.

Moving around the file system¶

Let’s practice moving around the file system 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/mtb_upm)

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.

Looking folder within folder within folder within…¶

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.

Shortcut: Tab Completion¶

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

ls S1<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 S1. 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.

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 the home directory. Now, enter the pwd command and you should see:

/home/mtb_upm

which is the full name of your home directory. This tells you that you are in a directory called mtb_upm, 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: mtb_upm is a directory in home which is a directory in /.

Now enter the following command:

cd /home/mtb_upm/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/mtb_upm/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.

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. 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/mtb_upm 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 data directory, the commands ls ~, ls ~/., ls ../../, and ls /home/mtb_upm all do exactly the same thing. These shortcuts are not necessary, they are provided for your convenience.

Our dataset: FASTQ files¶

Assume that we whole-genome sequenced 9 bacterial genomes and generated paired-end Illumina reads. We get our data back from the sequencing center as FASTQ files, and we stick them all in a folder called IlluminaReads. We want to be able to look at these files and do some things with them.

Wild cards¶

Navigate to the data/IlluminaReads 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 18 such files which we would expect because we have 9 samples.

So how does this actually work? Well…when the shell (we are using a particular flavor called bash shell for this tutorial) 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?

When wildcards go bad¶

To discuss: 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).

Examining Files¶

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

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

cat S190_L001_R1_001.fastq

This prints out the contents of the S190_L001_R1_001.fastq file.

Print out the contents of the ~/data/IlluminaReads/upm.files file. 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/mtb_upm/data/IlluminaReads directory.

Make sure we’re in the right place for the next set of the lessons. We want to be in the IlluminaReads directory. Check if you’re there with pwd and if not navigate there. One way to do that would be

cd ~/data/IlluminaReads

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 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``

key	action

“space”	to go forward
“b”	to go backwards
“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. 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 S188_L001_R1_001.fastq file for “TACGGAGGATGC”. 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 1101:9376:4054 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 S188_L001_R1_001.fastq
tail 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 S188_L001_R1_001.fastq
tail -n 1 S188_L001_R1_001.fastq

Searching files¶

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 1101:9376:4054 in the S188_L001_R1_001.fastq file.

grep 1101:9376:4054 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 1101:9376:4054 S188_L001_R1_001.fastq

Command flags are options that we use to change the behaviour of a program. 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.

Creating, moving, copying, and removing¶

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 where you won’t have another option.

The upm.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 IlluminaReads directory and enter:

cp upm.files upm.files_backup

Now upm.files_backup has been created as a copy of upm.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 upm.files_backup backup/

This moves upm.files_backup into the directory backup/; the full path would be ~/data/IlluminaReads/backup.

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

mv upm.files upm.files_IMPORTANT

Now the file name has been changed to upm.files_IMPORTANT. Let’s delete the backup file now:

rm backup/upm.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 ARE REALLY GONE.

By default, rm, will NOT delete directories. You can tell rm to delete a directory using the -r option (flag); we could test it out on backup, but let’s not… ;)

Writing files¶

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 FASTQ 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.

Running programs, revisited¶

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/mtb_upm/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/mtb_upm/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?)

Writing scripts¶

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 IlluminaReads 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.

Congratulations, you just created your first shell script!

Challenge:¶

write a script that:

resides in the data directory;
changes to the IlluminaReads/ 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;

WE ARE DONE!

More resources¶

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. Open pdfs from the command line, automate something you don’t really need to automate….

Some books you should look into –