Introduction to Bio-Linux

Introduction to Bio-Linux
Logging in and exploring the desktop
You can log into your Bio-Linux machine locally or remotely. Today you are logging onto a machine locally,
which means that the monitor you are looking at is attached directly to the machine running the system. You may
also hear this referred to as logging in at the console.
Log in using the username and password you have been given.
The view you now see is referred to as the desktop.
Exercise
Take some time to explore the desktop. Look at what options are available under the menus, what clicking the
icons on the desktop does, etc. Also try using the right and middle mouse buttons when the mouse pointer is over
a blank area of the desktop and explore the menus presented to you.
At the right hand side of the toolbar on the bottom of the screen are 4 “virtual desktops”. These effectively give
you 4 times the working space of your monitor. Try going to a different virtual desktop and starting up some
windows/applications there.
Click on the icon for your “home” at the top left of the screen. The file manager that appears is a graphical
representation of your files, similar to what you might see on a Mac or PC. Leave this window open for the next
part of the practical.
How Linux and Unix files are organized
Your Bio-Linux machine can be thought of as a huge file folder, inside of which are many other file folders, and
inside these are more nested file folders, and so on. As in the real world, file folders can hold other file folders, or
documents/files.
Terminology alert: In Linux /Unix systems, documents are usually referred to as files, and file folders are referred
to as directories.
The graphical representation of your account can be a good initial way to visualise what folders and documents
you have, and to move around in your account. However, as you grow more comfortable with Linux, you may
begin to find it slow and unnecessary. It is a good way to learn about the overall filesystem of the machine
though!
Your account is one directory (file folder) within your Bio-Linux system. In it you can create other directories,
store data, run programs, etc.
Just like with a regular filing cabinet, if you threw all your documents in without any ordering or organisation, it
would rapidly become difficult to find things. The same thing will happen to your account if you choose to keep
all your documents in your home directory instead of creating subdirectories and storing associated data together
within them.
If you look at the graphical representation of your home directory – you should see the following next to the word
location:
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home/user1
The name of the base file folder, the one within which everything else is, is “/”, usually referred to as the “root
directory”.
/home
/home/user
home is a file folder located within the root directory
user is a file folder within the directory home which is within the root directory
All the directory names are separated with a forward slash – so the directory user1 is located within the directory
home, which is within /.
The real power on Linux/Unix systems is the command line. You usually access the command line from within
terminals.
You can open a terminal by:
• clicking on the icon on the top tool bar
• right-clicking on the desktop and choosing the menu option “New terminal”
• or by going to the Utilities option under the Programs drop down menu, and choosing Terminal
You can also start new terminals by typing their name on the command line. There are in fact a number of
different types of terminals – each type has its own idiosyncrasies. The terminals brought up by clicking on the
terminal icon are called “gnome-terminals”. You can start one from the command line by typing:
gnome-terminal &
The & allows you to keep working in the original window by starting up the process, (in this case, a gnometerminal),
and putting that process in the “background”. If you want to know more about this, please ask a
demonstrator.
Listing files in a directory
Use the ls command to list files in a directory
By default, the command will list the filenames of the files in your current working directory. At the moment, this
is your home directory.
If you add a –l after the ls command, it alters the behaviour of the command – it will now list the files in your
current directory, but with details about them including who owns them, what the size is, what kind of file it is,
etc.
There are many options that modify what information is returned by ls. To find out about them, you can refer to
the manual pages for this command by typing:
man ls
By giving the name (or full path) of a directory you wish to list the contents of, you can find out what is in
directories other than the one you are running your command from.
ls /usr/local/bin
ls –lR /usr/software
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You can also use regular expressions to limit the files you wish to list.
* means any character
? means a single character
[ ] can be used to designate a group of characters
Exercise
List the files in your current directory. Compare this to what you see in the file manager.
List the files in your current directory with full details.
List all the files in the directory intro_pract. Click on the icon for the intro_pract directory in the file
manager and compare the output of the ls command to what you see.
List all the files in the directory intro_pract. that start with the letters tes
ls intro_pract/tes*
List all the files in your directory that start with tes, and end in 1.embl, 2.embl or 3.embl
ls intro_pract/tes*[1-3].embl
Changing the look of the terminal
If you don’t like the colour scheme of the terminal you are working in, you can change it using the Preferences
option under the Settings menu on the terminal.
Exercise
Go to the Preferences option under the Settings menu on the terminal. Choose the panel Colours, and then
choose the colour scheme you want. Please note that the option “black on white” actually produces black on grey.
To get black print on a white background, choose Custom Colours and choose the colours you want.
After this, any new terminal you open will inherit your new colour scheme.
Pressing the right hand mouse button can bring up menus of options for the terminal you are working in.
You can close terminals by typing exit on the command line or choosing Exit under the File menu.
There is also a menu under the tiny icon to the left of the word Terminal at the top of your terminal window. Try
out some of the options. Try choosing the option Sticky under Toggle. This makes that terminal appear in every
virtual desktop, instead of just one desktop. Note: please use the exit options mentioned above to close your
terminal, rather than the Close option in this menu.
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File naming conventions
a.) Certain characters should not be used in filenames in Linux/Unix.
If you stick with letters, numbers, hyphens, underscores and full stops, you will be fine.
b.) Linux/Unix cannot deal with spaces in filenames!
Make sure your filenames do not contain them.
Filenames with spaces in them are a common problem when transferring files to Linux/Unix from a computer
running Windows, or Mac operating systems.
If you end up with filenames with spaces in them, you will need to enclose the entire filename in quotation marks
so that Linux/Unix understands that the space is part of the name.
Alternatively, you can “escape” the space using a backslash. For example, if I have a file called
my document
Linux/Unix will see this as two filenames, “my” and “document”.
But you could write either of the following to make it understand you mean a single file:
“my document”
my\ document
We advise that you change the name of such files to remove the space. A common practice is to replace the space
with an underscore. E.g.
mv “my document” my_document
Keeping points a and b in mind, the files in your account can be named whatever you like.
If you have a lot of files with names including spaces in your account on your Bio-Linux machine (or which you
will be moving into your account), then please get in touch with us – we may be able to help you automate the
renaming of these files.
Having said this, please note that there are common naming conventions in place that you should try to follow.
More is said on this in the bioinformatics practical.
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Basic commands
It is possible for users to achieve a great deal with only a small number of commands.
Anatomy of a Command
Linux/Unix commands usually take the form:
command
parameters arguments
what I want to do how I want to do it on what do I want to do it
You have already seen a command with this structure when you used ls with the parameter l and the argument of
a file or directory name.
ls -l intro_pract
Some commands may not need parameters or arguments, or will use defaults if nothing is specified, but most will
have options available to you if you choose to use them.
For example, just typing ls will list the contents of the current directory.
If a command is executed without any problems, it will usually not report anything back to you, (unless reporting
to you was the purpose of the command!). If the command does not execute properly, you will often see an error
message returned. Whether or not the error is meaningful to you depends on what your level of experience with
Linux/Unix is and how user-friendly the errors generated by that command were designed to be.
Linux/Unix shorthand and shortcuts
At first understanding example Linux/Unix commands can seem daunting. This is often due to shorthand that can
be employed when using commands. However, the common shorthand characters are very useful.
The following incomplete list covers the symbols you will see most often today and describes their meanings as
you will most likely encounter them in this course.
Warning: some symbols have different meanings depending where they are used,
A short incomplete list includes:
* matches any character appearing 0 or more times, also known as a wildcard
ls mydir/* list all the files under the directory mydir
ls cat* list all files starting with the letters cat
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ls cat*hat
list all files starting with the letters cat and ending in hat
? matches a single character
ls cat??hat list all files starting with the letters cat followed by any 2 letters, and then hat
. “the directory I am currently in”
.. the directory one level above
~ my home directory
~username
the home directory of the user username
Changing directories
The command used to change directories is cd
If you think of your directory structure, (i.e. this set of nested file folders you are in), as tree structure, then the
simplest directory change you can do is move into a directory directly above or below the one your are in.
To change to a directory one below you are in, just use the cd command followed by the subdirectory name:
cd subdir_name
To change directory to the one above the one your are in, use the Unix shorthand for “the directory above” ..
cd ..
If you need to change directories to one far away on the system, you could explicitly state the full path:
cd /usr/local/bin
If you wish to return to your home directory at any time, just type cd by itself.
cd
To switch between directories, you can use the cd – command. This returns you to the last directory you were
working in before this one.
If you get lost and want to confirm where in the directory structure you are, use the pwd command (push working
directory). This will return the full path of the directory you are currently in.
Note also that by default in Bio-Linux, you see the name of the current directory you are working in as part of
your prompt. This is to help you remember where you are in your account.
Exercise
Change directory from your home directory to the directory intro_pract.
cd intro_pract
Type pwd to see the full path to where you are.
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Making a directory
To make a new file folder, you use the command mkdir (make directory). E.g.
mkdir newdir
would create a new directory called newdir.
Exercise
Move to your home directory (recall the cd command).
Make a new directory called testdir.
mkdir testdir
Hit the refresh button of the file manager of your account to update it.
Move into the new directory testdir (using the command line)
Move back into the intro_pract directory – try to do this with a single command.
Using text editors
There are a number of different text editors available on Bio-Linux. Note that what we are referring to here is not
a word processor, (e.g. MS Word); text editors only deal in text.
The text editors available range in ease of use from simple to complex, and each has its pros and cons. In this
practical we will briefly look at two editors, pico and nedit.
Pico
Pros:
• very easy – e.g. command options are visible at the bottom of the window
• can be used when logged in without graphical support
• fast to start up and use
Cons:
• by default it is set to put returns into lines too long for the screen (i.e. using pico for system administration
is dangerous!)
• is not completely intuitive for people who are used to word processors
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Nedit
Pros:
very easy
quite intuitive
colouring schemes are available for programming syntax
Cons: it is an X program (i.e. graphical), and can’t be run from a text-only environment
it is (slightly) slower to start up than non-graphical editors
Exercise
Editing a file with pico
In a terminal, type pico.
Write some information into this file. Try the options listed at the bottom of the screen. the ^ means the Control
key (Ctrl). So, for example, to check the spelling, use Ctrl-t. The command Ctrl-o saves the file and allows you to
continue working on it, and Ctrl-x saves the file and exits pico.
When you are done, save your file and exit.
Editing a file with nedit
Type nedit &
Type some text into the window.
Look under the menus for the kinds of options available to you.
Under the Shell menu, try the options wc (word count) and number lines.
Save your file under a different name than the one you used for the file you created with pico and exit nedit.
Reading text files
There are many commands available for reading text files on Linux/Unix. Among the most common are cat,
more, and less.
cat streams the entire contents of a file to your terminal. It is not generally a good command to use to read files
except ones with very little text. cat is a very useful command for concatenating files though! (More on this
function later.)
more and less are commands that show the contents of a file one page at a time. less has more functionality than
more.
With both more and less, you can use the space bar to scroll down the page, and typing the letter q causes the
program to quit – returning you to your command line prompt.
In addition, once you are reading a document with more or less, typing a forward slash / will start a prompt at the
bottom of the page, and you can then type in text that is searched for below the point in the document you were at.
Typing in a ? also searches for a text string you enter, but it searches in the document above the point you were at.
Hitting the n key during a search looks for the next instance of that text in the file.
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With less (but not more), you can use the arrow keys to scroll up and down the page, and the b key to move back
up the document if you wish to.
Exercise
Read the file hsy14678.embl using the commands cat, more and less.
cat hsy14768.embl
more hsy14768.embl
less hsy14768.embl
Use the spacebar to scroll down
Press q to quit.
Use the spacebar to scroll down, b to go up a page, and the up and
down arrow keys to move up and down the file line by line.
Press the / key and search for the letters sequen in the file.
Press the ? key and search for the letters gene in the file.
Press the n key to search for other instances of gene in the file.
There are many command line options available for each of the above commands, as well as functionality we do
not cover here. To read more about them, consult the manual pages:
man cat
man more
man less
Copying and pasting text
To select text for copying, press the left mouse button to highlight the text.
To paste, you have the window you wish to paste to selected, (usually meaning it is the top window on view), and
press the middle mouse button once – if you have a two button mouse, press both buttons simultaneously to
emulate the middle mouse button.
Exercise
Open two terminals. In one, use the command less to open one of the files you created in the previous exercise.
Open up another terminal and start pico.
Copy and paste text from the first terminal into the window running pico.
Save your file (if you want to), and exit pico.
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Command history and filename completion
(aka. how to cut down on typing!)
Using your history
A history of the commands you have used is stored as you work. You can access this list and use it to see previous
commands, and to re-run previous commands.
If you use the up arrow key when you are at the prompt in your terminal, you can see previous commands you
have run. This is particularly useful if you have mistyped something and want to edit the command without
writing the whole command out again.
You can view past commands using the command history.
To re-run a command listed by the history command, you can just type the command number, preceded by an
exclamation mark. E.g.
!268
By default, if you type the command history, you will see the last 15 commands. To see more, just put the
number of previous commands you wish to see after a hyphen. For example, to see the last 30 commands, type:
history -30
Using filename completion
If you type in a command with a filename, and instead of completing the filename, you press the tab key part way
through, the system will try to complete the filename for you. If the part of the filename you have written is
unambiguous, i.e. there is only one filename that would fit that pattern, the rest of the filename will be filled in for
you. If the pattern is ambiguous, all the filenames that match it will be presented to you. You can then choose to
type out the full name of the file, continue typing until the pattern is not ambiguous and press tab again, or,
instead, if you press tab twice, you will see that the system will cycle through all the filenames that fit your
pattern – you can just keep hitting tab until you get to the correct filename.
Exercise
Type
ls hsy
and hit the tab key.
Type
ls test
and hit the tab key. Hit the tab key again. Cycle through the filename options given to you.
Type
history
Run one of your previous commands using ! followed by the number of the command.
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Piping commands – how to make the output of one command be the input
for the next
There are many instances when you will want to use the output of one command as the input for the next
command. For example: what if you wanted to see the last 200 commands you ran? This would scroll of
the screen before you could read it. However, if you could take the output from the history command
and run it through a command like less, you could view the list page by page.
To do this, you need to use the pipe symbol |
This is usually found in the bottom left of your keyboard, although on some keyboards, it may be
elsewhere. The picture on the keyboard may be a straight line up and down, or it may look like two
lines, one on top of the other.
To call up the last 200 commands run, and run them through the less command, you would type:
history -200 | less
Finding patterns with grep
An important function in Linux/Unix is grep. If you provide grep with a bit of text, it will search for that
text in a file and return any lines that contain that text. By default, grep is case sensitive.
Exercise
Search the file hsy14768.embl for the term DE.
grep DE hsy14768.embl
If you give grep the –i parameter, what happens?
grep –i DE hsy14768.embl
If you want to specify that you only want to see lines that begin with the letters DE, then you can preface
them with ^:
grep ^DE hsy14768.embl
If you only want to see lines that end in UK, you can specify this by using the $ symbol at the end of the
text:
grep UK$ hsy14768.embl
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Note: While grep is a very useful utility, if you want to search biological sequences for patterns, there
are sophisticated programs designed especially for this, and we advise against using grep in all but the
most trivial cases.
Clearing your terminal of text
Your terminal windows can fill up with lots of text, and it can become difficult to see the information
you want because of all the clutter.
You can clear the terminal window of all previous text by typing
clear
The result is a prompt in a nice clean window.
Copying files
To copy files, the basic command is cp. At minimum, you must also specify the name of the file(s) to be copied,
and the destination location.
cp firstfile dest_location
cp file1 file2 file3 location
cp directory/* location
copies all files in the directory to location
To move whole directories, with all the subfiles and subdirectories, use the –R option, (meaning recursive).
cp –R mydir location
The Linux/Unix shorthand for “this directory right here” (a dot . )comes in very handy when copying:
cp –R mydir .
Copy all files/directories under mydir to this directory here
Make sure you leave a space between the directory name and the shorthand dot.
Also useful is the shorthand for someone’s home account. e.g. instead of having to know and type the location of
their account, you can use ~username In the case of your own account, you need only use ~
cp ~user2/somefile . copy the file somefile from user2’s home directory here. Note that user2 would have
to have given you permission to do this!
cp ~/somedir/somefile .
copy the file somefile from within my account/somedir to here.
Exercise
Copy all the files that start with the letters tes and end in .embl into the directory testdir that you made earlier.
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There are many different ways to accomplish the above. If you have problems, or would like to know if you have
done it in the most efficient way, then please ask a demonstrator.
Removing files and directories
To remove a file or files, use the rm command followed by the name of the file(s) you wish to delete.
rm file1
rm file2 file3 file4
rm cat*
remove all files starting with the letters cat
Note
On Bio-Linux the command rm has been aliased to rm –i.
This means the system will ask you if you really mean to delete the file you have just asked to delete, and you
must answer yes if you do. Other Linux/Unix systems may not be so polite, and unlike Windows systems, the files
you delete are not stored in a trash can for you to retrieve – they’re gone! (Unless the file has been there for some
time and you are making proper backups….which you should be!)
If you have a lot of files to delete, confirming each one can be tedious. You can escape this safety feature by using
a backslash in front of the rm command.
\rm files
To remove an empty directory, you can use the rmdir command:
rmdir thisdir
If that directory contains any files, you will not able to delete the directory using rmdir until you have deleted all
the files within it.
To delete a directory and all the files in it, use the rm command with the options -rf
rm –rf fulldir
You may be prompted to confirm that you wish to delete each file.
If this is too tedious, and you are certain that you want to delete all the files in that directory as well as the
directory itself, remember that you can “escape” this safety feature using the backslash:
Exercise
\rm –rf fulldir
Delete one of the files you created earlier with pico or nedit.
Delete the entire testdir directory.
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Changing permissions on files and directories
The command to change permissions is chmod. You have to specify who you are modifying the permissions of,
what the new permissions are, and what file or directory to act on.
The format of the chmod command is:
who can take the value(s):
chmod who ± permissions filename
u
g
o
a
means user and refers to the owner of the file
means group, and refers to the group the file belongs to
means others, everyone on your systems apart from those above
means all three, i.e. user, group and others
Permissions can be:
r
w
x
means read permission
means write permission
means execute permission
So, for example, to give read permission to someone in the same group for a file called
“filename” in ~/intro_pract.
chmod g+r ~
gives permission to people in my group to read my home directory
chmod g+rx ~/intro_pract give permission to people in the group to list files in the intro_pract directory
chmod g+r ~/intro_pract/myfile give permission to people in the group to read the file
myfile (assuming they already have permission to “see” into the intro_pract directory).
A very basic way to stop a process
Sometimes a command or program goes on too long, or is obviously doing something you did not plan. If it is not
a situation where there is an obvious way (e.g. a menu option) to stop the program running, try using Control-c.
i.e. the Control key and c-key at the same time.
Logging out of a session
To logout, you can choose the option logout under the System menu.
Please do this at the end of the day – but not now.
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