Basic Linux Tutoral

Original Material by Milad Fatenejad, Sasha Wood, and Radhika Khetani Modified by Jared Flater and Adina Howe

Remodified by Shane K. Dooley

Getting Started

In order to prepare for this tutorial please do the following before class:

If your laptop runs Windows:

1. Download the Putty excecutable

2. Download & Install WinSCP

3. Download & Install Notepad++

If your laptop runs MacOSX or Linux:

1. Download & Install Cyberduck
2. Download & Install a text editor (you can use the built in editor but we recommend either Sublime or TextWrangler)

Fundamentals

What is "shell"?

The shell is a program that allows users to talk to the operating system of a computer or group of cumputers (cluster) by typing in recognized commands (command line interface) to run programs instead of controlling what the computer does using a graphical user interface (GUI) 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. Today, if you are using Windows you will use the Putty terminal and if you are using a Mac or have Linux running on your laptop, you will be using the well named program Terminal as your terminal.

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 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). 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

Let's get started!

Please open your terminal program. For those using Putty please fill in the relevant information like you see in Picture 1, for those using terminal see Picture 2. We are using a program called ssh (secured shell) to connect to a training computer that was set up for us to use.

Once you are connected let's run your first program. Type the words as you see below and press enter.

echo hello world

You should see that the words hello world appeared on your screen. You just ran a program called echo.

Term	Definition	Example
program	the name (case sensitive) of the program	echo
arguement	additional information you give the program to get it to do what you want it to do.	echo hello world

Basic essential programs

To help us get started, we are going to download a bunch of files for the sake of this tutorial. We will talk more about this command later but for now copy and paste or type the command below exactly. This will download all of the files used in this tutorial from my public repository on github

git clone https://github.com/skDooley/shell_tutorial.git

Navigation

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.

Where am I?

First we have to know where we are. The program pwd (print working directory) tells you where you are sitting in the directory tree. 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.

What files and folders are available where I am at and how do I access them?

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.

To see files in a different directory, just add the directory you want to see as an arguement. To see what is in the shell_tutorial folder we downloaded with our git clone command type:

ls shell_tutorial

Now, there are a few things you need to know in order to be able to navigate. The first is that everything on a file system is under what we call the root directory. When we navigate every directory is separated by a / so the root is only 1 slash. Let's go to that directory now. To change directories we will use the program cd.

cd /
pwd

Now do an ls to see what is there. If you remember, when you first logged in you were in /home/. Your ls shows you that under the root directory is the folder home. Let's get back to our directory and our test data!

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Short Exercise

SE1. Navigate to the shell_tutorial folder in your home directory

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Relative vs. Absolute path

Where you are in the directory tree is called your path. Lots of programs require you to pass a file as an arguement. If you are in your home directory and the file you want to pass to the program is not in the same directory, you can either use what's called the absolute path eg. /home//shell_tutorial/TestFile.txt or you can use the relative path eg. shell_tutorial/TestFile.txt. These are equivalent because of where you are in the tree.

The writers of shell also included a few shortcut keys. Sometimes we are in a directory and we want to go to the directories parent. we can do that using ..

cd ..
pwd

This will put us 1 directory above where we were (ie back in our home directory). If we want to go 2 directories above where we are now:

cd ../../
pwd

Two periods is 1 directory above where you are at, 1 period is your current directory. So from your home directory this pattern ./../././.. is /home/username, /home, /home, /home, /. We were in the home directory, we navigated 2 directories up so now we are in the root directory. The next tip/trick I want to show you is how to go back to the directory you were just in without having to type in the relative or absolute path. To do that:

cd -
pwd

This will put you in the last directory you were in. You can run this command over and over to flip-flop what directory you are in, very usefull when you are working on a project were you have a few different folders you are working with.

Okay time to learn a new importan term:

Term	Definition	Example
flag	a special kind of arguement that is proceeded by either 1 or 2 -'s	ls -l

So now navigate to your shell_tutorial folder and try the ls -l.

ls -l

Picture 3

To see what flags are available use the program "man" with the arguement being the name of the 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 "shift" + "g" goes to the end. Finally, hit "q" to quit.

man ls

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.

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Short Exercise

SE2. Using what you have learned, use man to find out what flags to add as arguements to list files and folders in the root directory by date. What is the newest file/folder? What is the oldest?

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Creation/Destruction

We can now navigate pwd, ls, cd so now let's talk about how we create new files or folders/directories and how we delete them.

Command	Description
mkdir	makes a directory
rmdir	removes an empty directory
touch	creates an file
rm	removes a file
rm -r	removes an entire directory and all of its contents
cp	copy a file to a location
mv	moves a file to a location

mkdir testdir
cd testdir
touch testfile.txt
cd -
rm testdir

Turn to the person next to you, your battle-buddy, and explain why the last command in the list of commands didn't work. What are 2 ways that we have discussed to remove the directory and its contents?

** DANGER WILL ROBINSON!!!! The rm -r is EXTREMELY powerful!!!!

Saving time with shortcuts, wild cards, and tab completion

**Tilde ~**

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_tutorial directory, then enter the command:

ls ~

Wild card

Navigate to the ~/shell_tutorial/hearing_data/data/THOMAS directory. 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

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 words, the two commands:

ls *4*1
ls 0241 0341 0431 0481

are identical. The ls command cannot tell the difference between these two things.

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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 the data directory ~/shell_tutorial/data/hearing_data/gerdal that contain the number 2
2. List all of the files in that contain the number 2, followed by the number (in any position) 9

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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, enter:

cd s<tab>

The shell will fill in the rest of the directory name for shell_tutorial. Now enter:

ls ~/shell_tutorial/data/ex<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 e. Thus, the shell does not know which one to fill in. When you hit tab again, the shell will list the possible choices.

Tab completion can also fill in the names of programs. For example, enter e<tab><tab>. You will see the name of every program that starts with an e. One of those is echo. If you enter ec<tab> you will see that tab completion works.

Command History

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.

^-C will cancel the command you are writing, and give you a fresh prompt.

history

Which program?

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_tutorial/data 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 ~/shell_tutorial/data 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/username/shell_tutorial/data/hello

Or by entering:

data/hello

When there are no / characters, the shell assumes you want to look in one of the default places for the program.

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Take a short 5 minute break, you earned it!

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Examining Files on the command line

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

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

cat ex_data.txt

This prints out the contents of the ex_data.txt file. If you enter:

cat ex_data.txt ex_data.txt

It will print out the contents of ex_data.txt twice. cat just takes a list of file names and writes them out one after another (this is where the name comes from, cat is short for concatenate).

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Short Exercises

1. Print out the contents of the dictionary.txt file. What does this file contain?

2. Without changing directories, (you should still be in /home/<username>/shell_tutorial/data), use one short command to print the contents of all of the files in the hearing_data/THOMAS/ directory.

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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 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!

Redirection

Let's turn to the experimental data from the hearing tests that we began with. This data is located in the ~/shell_turorial/data/hearing_data directory. Each subdirectory corresponds to a particular participant in our fake 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.txt

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.

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Short Exercise

Use >>, to append the contents of all of the files which contain the number 4 in the directory:

~/shell_turorial/data/hearing_data/gerdal

to the existing all_data.txt file. Thus, when you are done all_data.txt should contain all of the experiment data from Bert and any experimental data file from gerdal that contains the number 4.

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Practice Creating, moving, copying, and removing

We've created a file called all_data.txt 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.txt all_data_backup.txt

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

mv all_data_backup.txt /tmp/

This moves all_data_backup.txt 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.txt all_data_IMPORTANT.txt

Now the file name has been changed to all_data_IMPORTANT.txt. Let's delete the backup file now:

rm /tmp/all_data_backup.txt

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Short Exercise

Do the following:

1. Rename the all_data_IMPORTANT.txt file to all_data.txt.
2. Create a directory in the data directory called foo
3. Then, copy the all_data.txt file into foo
4. Delete foo and all of its contents

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Count the words

The wc program (word count) counts the number of lines, words, and characters in one or more files. Make sure you are in the data directory, then enter the following command:

wc Bert/* gerdal/*4*

For each of the files indicated, wc has printed a line with three numbers. The first is the number of lines in that file. The second is the number of words. Finally, the total number of characters is indicated. The final line contains this information summed over all of the files. Thus, there were 10445 characters in total.

Remember that the Bert/* and gerdal/*4* files were merged into the all_data file. So, we should see that all_data.txt contains the same number of characters:

wc all_data.txt

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.txt

Remember that ls -l prints out detailed information about a file and that the fifth column is the size of the file in bytes.

The awesome power of the Pipe

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.txt

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.txt
tail all_data.txt

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.txt
tail -n 1 all_data.txt

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 CONTROL+d. You should is the lines:

are
good

printed back at you. The CONTROL+d keyboard shortcut inserts an end-of-file character. It is sort of the standard way of telling the program "I'm done entering data". The | character 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: |, >, >>.

Searching files

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 *

Finding files

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).

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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):

1. Find any file whose name is "NOTES" within data and delete it

2. Create a new directory called cleaneddata

3. Move all of the files within data to the cleaneddata directory

4. 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:

1. Navigate to the data directory

2. Delete the hearing_data directory

3. Enter the command: git checkout -- hearing_data You should see that the hearing_data directory has reappeared in its original state

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REAL DATA

Now let's play with some real data and get the hang of Linux.

cd ~/shell_tutorial/fastas

** Short Excercise **

This Directory contains a fasta file called DiverseCas9s.faa. Talk to your battle buddy and answer the following questions:

1. How many sequences are in the fasta file?
2. Why might it be usefull to know how many sequences were in a fasta file?
3. Discuss how you would create a file with all of the ids in the fasta file. Create that file and call it Cas9IDs.txt

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Now let's do some bioinformatics. In the file query.faa is a protein we suspect is a Cas9. We will use BLAST on the command line to explore and see which of the DiverseCas9s this is closest to. To do this make sure you have blast installed.

conda install -c bioconda blast

To start out we have to make a blast database.

makeblastdb -in DiverseCas9s.faa -dbtype prot -out DiverseCas9s.faa
ls

Now BLAST is ready to do it's job. Let's run the BLAST!

blasp -h
blastp -db DiverseCas9s.faa -query query.faa -out MysteryCas9.blastresults -outfmt 6
less -S MysteryCas9.blastresults

GUIs - YAY!!

All this command line stuff is great, but sometimes I just want to use Excel or Jump or some other program. Time for WinSCP and Cyberduck.

Now that you're connected let's change the defualts to add our editor of choice.

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Cheat sheet

Exercise solutions have been posted as an ipython notebook.

You can view solutions here

Bonus

alias -> rm -i

variables -> use a path example

.bashrc

du

ssh and scp

Regular Expressions

Permissions

ln

Thanks for joining us! For other P3 bootcamp tutorials please see