Linux intro 2 basic terminal

Programming for Evolutionary Biology
April 3rd – 19th 2013
Leipzig, Germany

Introduction to Unix systems
Part 2: Introducing the terminal
Giovanni Marco Dall'Olio
Universitat Pompeu Fabra
Barcelona (Spain)

Schedule
 9.30 – 11.00: “What is Unix?” and hands on a
Fedora system
 11.30 – 12.30: Introducing the terminal
 14:30 – 16:30: Grep & Unix philosophy
 17:00 – 18:00: awk, make, and question time

What is the terminal?
 The terminal is a software that allows to execute
commands by typing
 Instead of clicking an icon in a menu, we call a
software by writing its name

How does a terminal looks
like?

The terminal: history and
why
 Back in the '70s, when Unix was developed,
computers did not have graphical interfaces
 Also, computer were mostly used for data
analysis.

The terminal: history and
why
 Back in the '70s, when Unix was developed,
computers did not have graphical interfaces
 Also, computer were mostly used for data
analysis.
● The most common operations were analysis of
datasets and manipulation of text files

Why use the terminal
today?
 A common problem in bioinformatics is to deal
with big collections of text files
 The terminal is a good instrument to manage big
collections of text files. More than 30 years of
experience.

some Terminology
 Terminal emulator: the software that shows the
window where you type the commands, and
prints the output of the commands
 Interpreter: the software that translate
commands to the computer
 Bash: name of the most commonly used
interpreter

Terminal emulator, interpreter and
bash

Bash, a terminal interpreter,will translate
all the commands submitted from
this terminal

Terminal
Emulator

Your first command: ls
 ls is the command to show all the files in a folder
 It stands for “List Short” (list files in a short way)
 Try it!

Output of “ls”
 ls will list the files in the
current directory
 By default, when you
open the terminal, you
are in your “home”
folder

“ls” is showing the contents of the
“home” folder
 If you want to see which files are being shown by ls, you can type
nautilus as we did in the previous session

Anatomy of a command
 Each command call is usually composed by three
parts:
● The command itself
● Parameters (optionals)
● Arguments

ls: some parameters
 Parameters are optional items that can be used to
customize the behaviour of a command
 For example:
● ls l shows the list of files in a long format
● ls a shows hidden files
● ls t list files by modification time

“ls -l”
 ls l shows the same files as ls, but on a more
detailed format

“ls -a”
 ls a shows all the
files, including the
hidden ones
 Hidden files have a
name that begin with
a “.”
 Most of them are
configuration files,
you can ignore them.

“ls -t”
 ls t lists the files by modification date

“ls -lt”
 You can combine parameters together
 ls lt shows the files in a long format, sorted by
date

Arguments
 Arguments define the target of the command
 On which files/folders/targets do I want to run my
command?
 Example:
● ls unix_intro > shows the files in the unix_intro
directory

Quick exercise
 In the following call, which are the commands,
the parameters and the arguments?
● ls la /homes/evopadmin

How to get the
documentation of a
command?
 Three methods:
● help
● man
● info

“ls --help”
 The simplest way to get the documentation of a
command is by using the help parameter
 For example:
ls help
 Most unix command accept a help or h
parameter

Consulting the
documentation of a
command: man
 The command man is used to see the
documentation of a command
 Understanding how to read the documentation is
the key to learn how to use the shell

Your second command: man
 The command “man” is used to see the
 Usage: man <name of the command>
 Try it:
● man ls

Understanding a man page
 Each manual page is composed by at least three
sections:
● NAME (the name of the command)
● SYNOPSIS (how to launch the command)
● DESCRIPTION/OPTIONS (description of what
the command does, and its options)

“man ls”
Name of the command

Synopsis (how to use it)
Options in square
brackets are optional

Parameters & arguments

Using a man page
 Use arrows or PageUp/PageDown keys to scroll
the man page
 Press “/” followed by a word to search text
● Example: /sort
 Press “q” to exit

Searching for a man page
 You can search all the manuals using the k
option
● Example: man k “list dir”
 Another similar command is “apropos”
● Example: apropos “list dir”

Other sections in a man
page
 SEE ALSO: some man pages contain references
to similar commands
 EXAMPLES: some man pages contain an
“examples” section

“SEE ALSO” and
“EXAMPLES” sections

“man -k 'list dir'” and
apropos

Another way to access
documentation: “info”
 The command “info” shows a more descriptive
 Example:
● info ls

The “info” command

Use arrows to scroll
Press Enter on a keyword to
open a page
Press “n” and “p” to change pages

Short exercise
 Which parameter can be passed to “ls” to sort
files by size?
 How to show the contents of directory recursively
 Which command can be used to show the
contents of a folder as a tree? (hint: use apropos)

How to get help: Internet
 Apart from “help”, man and info, the best place
to look for help on a command is.. Internet!

How to get help: Internet
 Apart from “help”, man and info, the best place
to look for help on a command is.. Internet!
 Tips to get better results when searching the
documentation of a Unix command on Internet:
● Add keywords such as “Unix”, “bash”, “fedora”
● Use the “” operator on google to remove junk
results
● If you have problem with a software or with your
installation, copy and paste the error on google.

Adding keywords such as “Unix”,
“bash”, “fedora”, “terminal”

The “-” operator on google

Navigating the file system
from the terminal
 We will now see how to navigate folders and files
from the terminal

Change directory: cd
 Let's start navigating the file system!
 The command cd allows you to move to another
folder
 Let's enter the folder of the course:
● cd unix_intro
● ls

The “cd” man page
 Note: the cd command is documented inside the
“bash” man page
● Type man bash and then look for ls
 You can also look at:
● man dir (dir is a similar command to ls)
● info coreutils ls

Which folder am I?
 If you don't know which folder are you in, you
can use the command pwd
 Also, if you run cd without arguments, it will
return to the home folder

If you get lost: type “cd”
without arguments
 Typing cd without arguments will bring you to
your home directory

“cd ..”
 “cd ..” lets you return to the parent folder
 Example:
● cd unix_intro → goes to the unix_intro folder
● cd .. → returns to the home folder

A tip: bash completion
 You can use the “tab” key on the keyboard to
complete commands and arguments
 Example:
● cd Docu<tab> will complete to cd Documents
 Thanks to tab completion, you can save a lot of
typing

Let's look at the files in the
course folder
 Type, in the following order:
cd (to go back to the home folder)
cd /homes/evopserver/evopadmin/unix_intro (use the tab key for autocompletion)
ls
cd exercises
ls

Check with your teaching assistant that you are in the correct folder.

Let's see some “fasta” files
 Go to the folder
leipzig_course/unix_intro/exercises/fasta
● fasta, not fastq!
 You should see some fasta files there:
● MGAT1.fasta, MGAT2.fasta, MGAT3.fasta,
MGAT4A.fasta, MGAT5.fasta

head & tail
 The head and tail print the first or the last lines in
a file
 Let's try it:
● head MGAT1.fasta → the first lines of
MGAT1.fasta
● tail MGAT3.fasta → the last lines of the file
 head and tail are useful to inspect big text files

The symbol “*”
 The symbol * (wildcard) can be used to represent
all the files in the current folder
 Try it:
● head * → will show the first lines of all the files in
the folder

The man page for “head”
 Exercise:
● open the man page for head
● determine which parameter is used for printing a
custom number of lines

“cat” & “less”
 The cat command prints the content of a file to
the screen
 The less command allows to read the content of a
file, with the same interface as for the man pages

Launching gedit from the
command line
 Note that you can use the command line to launch
any software installed in the computer
● gedit → text editor
● googlechrome → web browser
● gnometerminal → other terminal

Other useful commands (1)
 clean → clear the terminal
 rm → delete files
 mkdir → create directory
 more → like less, good for piping

Other useful commands (2)
 echo → print a message
 history → show the history of the commands
typed
 dos2unix → clean files edited in MS Windows
notepad for unix

Resume of the session:
 man and info → documentation
 cd, ls, pwd → navigate folders
 head, less → show contents of files

Time for lunch!

See you here at 14:30!

Linux intro 2 basic terminal

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