Table of Contents

First Steps on the Linux Command Line 1.1

Directories and files 1.2
Edit text files 1.3
Copy and remove files 1.4
Process text data 1.5
Unzip files 1.6
Run useful programs 1.7
Acknowledgements 1.8

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First Steps on the Linux Command Line

First steps on the Linux Command Line

What this tutorial is about?

This tutorial lets you learn the basics of the Linux command line. You can learn commands
to navigate directories, manipulate files and start other programs. If you have no previous
experience with Unix-like systems or know a few commands but would like to know more,
this tutorial is for you.

Prerequisites
This tutorial was prepared for Ubuntu Linux, but it works on MacOS, Cygwin and the Git
bash as well, given that Python 3 is installed on your system.

Preparations
Copy the file Exercises.zip from
https://github.com/krother/Linux_Commandline_Tutorial/raw/master/Exercises.zip) to a
computer with Ubuntu (or some other Linux) installed.
Unzip the file.
Type:

chmod -R a+x unix_tutorial/ chmod -R a-x unix_tutorial/exercise6/check_permissions

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First Steps on the Linux Command Line

Explain trainees how to open a Unix shell

Make this tutorial and a ‘Unix/Linux Command Reference’ document available (see
PDFs in exercise material).

Your Task
In this tutorial, you will be looking for a word with 22 characters. All characters are hidden in
the exercises below. All exercises can be solved using the Unix command line.

License
(c) 2010 Dr. Kristian Rother

This tutorial is published under the Creative Commons Attribution Share-alike License 4.0

You can find the full sources on https://github.com/krother/Linux_Commandline_Tutorial.

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Directories and files

1. Directories and files

1.1. Navigating directories

The first character is hidden in a file somewhere in the exercise1 directory tree. Use the
commands

cd <directory_name>

(do not type the pointy brackets, just insert the directory name) and

ls

to move from one directory to the next. Look through subdirectories until you find one with
the name solution_1.1 and list its contents. If you went to a wrong directory, you can go back
one level by typing:

cd ..

or to go back to the beginning:

cd

1.2. Show a hidden file

Some files are not visible immediately. To see them, you need the command

ls -a

The second character, is in the same directory as the first one, but in a hidden file.

1.3. Execute a program

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Directories and files

Use cd .. to go back to the directory exercise_1/directoryB/. When listing its contents, you
should see a program file. To find the third character, you need to execute the program. In
Unix, this is done by typing

./program_name

1.4. Find out how big a file is

Go to the exercise_1/directoryC/ catalog. To find the fourth character, you need to find out
how big the text file in the directory is. This is done with the command

ls –l

In the table the command produces, you will find the file size in bytes, the file’s owner,
permissions to read and modify it, and the date/time of the last modification. When you want
to obtain the fourth character, type

./file_size_check

The program will ask you for a file size.

Hint
When typing names of directories or files, try typing the first three characters, and press
<TAB>. Unix tries to guess what you are typing.

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Edit text files

2. Edit text files

Please use cd .. to go back to the top directory of the tutorial material. Then, change to the
directory exercise_2.

2.1. See what is in a text file

In the directory exercise_2/, you will find a text file solution_2.1.txt. The fifth character is
inside that file. To see its contents, use the command

more <filename>

2.2. Edit text files

To get character number six, you will need to create a text file in the exercise_2 directory.
On Ubuntu, you can do this using the editor gedit. You can start it typing the name of the
program, or

gedit <filename>

Create a text file with a name of your choice in the exercise_2 directory that contains the
phrase

Please give me solution 2.2

Afterwards, run the program

./text_file_check

Hint
If you want to know more about a particular command, type

man <command>

You get shown a help page that you can leave by pressing 'q'.

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Edit text files

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Copy and remove files

3. Copy and remove files

Please go to the directory exercise_3.

3.1. Create a directory and copy a file to it.

To find characters seven and eight, you need to create a subdirectory named solution in
exercise_3/ and copy the file code.txt to it. For creating directories, you can use the
command

mkdir <directory name>

For copying, you can use the command

cp <filename from> <filename to>

Use ls solution/ afterwards to see whether the file is there. The program

./check_code

will give you the solution.

3.2. Removing files

In the same directory, there is a file junk.txt that does not contain anything useful, and should
be deleted. To do so, use the command

rm <filename>

Also, there are more files to be deleted in the data directory. To remove more than one file at
once, you can use '*' as a wildcard, i.e. 'rm pro*' will delete all of profile, 'protein.txt and
prototype.doc. To get characters nine and ten, please run the program

./check_junk

after removing the files.

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Copy and remove files

WARNING
On Unix, it is not possible to undelete files!

Hint
To remove an empty directory, you can use

rmdir <directory name>

To delete a directory and everything in it, the command rm -r exists. In combination with the
'*' symbol, this is dangerous, because it gives you the possibility to wipe out all your data
with a single command (e.g. if you type the wrong directory by accident). Thus, first make a
backup and then play with this command.

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Process text data

4. Process text data

Please go to the directory exercise_4.

4.1. comparing two files

There are two different versions of a text, foo_long.txt, and foo_short.txt. To find out, how
they differ, Unix provides the command

diff <filename1> <filename2>

Of course, you can look at the text first using more or a text editor. The 11th character of
the solution is the first character of the third last word in the output of diff.

4.2. Sorting a text file

Unix has a small program to sort text files alphabetically. It is called by

more <filename> | sort

The symbol '|' is called a pipe and is often used to connect Unix programs to each other. The
12th character of the solution is the first character of the last word of the first line from the
alphabetically sorted file 10000_lines.txt.

Hint
To store the sorted lines in a new file, you can add an output file, like

more <filename> | sort > result.txt

4.3. Finding words in a text file

To look for specific words in a text file, the

grep <word> <filename>

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Process text data

command should be used. It produces all lines from the given file that contain the given
word. The grep command is very powerful and can handle fuzzy search patterns called
Regular Expressions (not covered here). The 13th character of the solution is the first
character of the second word in a line containing 'fool'.

Hint:
You can search through many files at once by including a '*' in the filename.

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Unzip files

5. Unzip files
Please go to the directory exercise_5.

5.1. unzipping archives

Unzipping compressed files is a very basic and important task. On Unix, you often encounter
WinZip archives, .tar archives, and .gz compressed files. For unpacking Win zip files, use

unzip <filename>

for .tar and .tar.gz files

tar -xf <filename>

and for .gz files,

gunzip <filename>

The 14th and 15th character of the solution are in a multiply wrapped archive in the
exercise_5 directory.

Hint
To pack a directory and everything within, you can use the command

tar -cf backup.tar <directory>

To subsequently compress it, use

gzip backup.tar

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Run useful programs

6. Run useful programs

Please go to the directory exercise_6.

6.1. Changing file access rights

Each file on Unix has separate permissions for reading 'r', writing 'w', and executing 'x'.
When displaying them with

ls -l

there is one triplet of these permissions for the files owner, one for a group of users, and one
for all others. The chmod command allows to change these permissions, e.g.

chmod a+x <filename>

grants all users the permission to execute a file, while u-w forbids the current user (oneself)
to write to the file (thereby protecting it from being deleted accidentally). The next two
characters of the solution will be shown when you execute the program

./check_permissions

Hint:
You can grant permissions for a whole directory tree using

chmod -R a+x <directory>'.

6.2. How much disk space have I left?

To find out, how much disk space you have left, you can use the command

df

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Run useful programs

It lists all hard disk partitions, CD-ROMs, pendrives etc. Your data is stored in /home/, if it
does not exist, in /. All numbers are given in kilobyte (1000 byte or one 1000000th GB). To
obtain the 18th character, run the program

./check_disk

6.3. Set an environment variable

To install some programs, it is necessary to set so-called environment variables. These can
be set using the command

export <variable-name>=<value>

But then the variable will only be present in the same console window where you typed the
command. You can see all variables by the command

env

To obtain the 19th character, you need to set the variable SOLUTION to the value 6.3, and
run the program

./check_variable

Hint:
If you want to have an environment variable to be automatically set for eachconsole window,
write the export command to the file .bashrc in your home directory (it is a hidden file).

Hint:
The env command can be combined nicely with grep, e.g. to check your PATH variable, you
can type:

env | grep PATH

6.4. Check whether you have internet

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Run useful programs

The easiest way to check from the Unix command line whether the internet connection
works, is to send a request to a known server (e.g. www.academis.eu) using the command

ping <web address>

The command reports, how long a message takes back and forth to the given server. To
interrupt the messages, press Ctrl+C. You can use the program

./check_ping

to get the 20th character.

6.5. Managing processes

To see what programs are running on your machine, type

top

It displays you a list of all currently active programs. Shift+P sorts them by the CPU time
they are using, Shift+M by the amount of memory they are using (if you don't see any
program consuming lots of memory, start a web browser).

The last two characters of the solution are the first two characters of the second word in
the highlighted bar containing the column labels.

Hint:
If you want to get rid of one of the programs you started (e.g. because it crashed), you can
do so by typing

kill <pid>

You find the pid number in the first column of the top output. Of course, you may only
interrupt your own programs, not those owned by root, the system administrator.

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Acknowledgements

Acknowledgements
This tutorial was created for participants in a bioinformatics workshop organized by Janusz
M. Bujnicki for the EURASNET consortium in 2010. I would like to thank the organizers and
all course participants, as well as Joachim Jacob for reviewing the material. Further thanks
go to the German Academic Exchange Service (DAAD) for financial support.

Special thanks go to Allegra Via for using this tutorial in our course over the years, and to
Pedro Fernandes for suggesting publication via Gitbook.

Contact
Dr. Kristian Rother

krother@academis.eu

www.academis.eu

License
This tutorial is published under the Creative Commons Attribution Share-alike License 3.0

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