Introduction to Unix

Elana J. Fertig
Johns Hopkins University
Department of Oncology, Division of Biostatistics and
Bioinformatics

Computational Genomics Workshop

18 November 2011
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Lesson Overview

1 Unix filesystem

2 File processing

3 Redirecting commands and scripts

4 Additional information

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ssh

The “ssh” command enables secure login to a machine to which

you have access.

$ ssh [user]@[host]

You will then be prompted for your password.

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The most useful command: man

For help with the structure of a command, use the following:

$ man command

Type the enter key to get a the next line, spacebar to get the
next page, and q to exit.
For example,:

$ man ssh
$ man man
The “-k” option lets you search within the help pages:

$ man -k bash

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Less typing through tab, copy, and paste

If you start typing a command, the tab key will autocomplete

it. E.g., $ ma tab
In the Terminal program on Mac, copy and paste from the
edit menu and shortcuts command-c and command-v will
work.
In putty program on Windows and most unix machines, copy
and paste work by simply highlighting the text that you want
to copy and then clicking the middle mouse button.

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Re-using past commands

The history command will display a list of the most recent

commands that were executed.
The up and down arrows will allow you to scroll through
commands that were previously executed.
The !! command will repeat the previous command.
!command will repeat the last command that contains the text
command. E.g., $ !his will repeat the previous history
command. The ! can also be used to repeat a command from
the history when referenced by number.
^text1^text2 will repeat the last command, replacing the
first instance of “text1” with “text2”.

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Other special characters

* a wildcard for searching

$ the start of a variable name
# starts a comment (a line that will be ignored)

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Where am I?

The “pwd” (print working directory) command will get the current
directory in which you are located.

$ pwd

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The home directory ($HOME, ∼)

The “pwd” (print working directory) command will get the current
directory in which you are located.

$ pwd

By default, will be your home directory

$ echo $HOME

(where “echo” prints the command to the screen and $ represents

the start of a variable name).
The ∼ symbol is also used to represent the home directory

$ echo ∼

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Finding contents of directories (ls)

To see the contents your current path:

$ ls

To see the contents of another directory (e.g., the Data directory):

$ ls Data

The * command serves as a placeholder for any characters. E.g.,

$ ls myFile*

The -l option will display details of all the files listed and -a
option will also display hidden files.

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Changing directories (cd)

The following command will move you into the directory Data

$ cd Data
$ pwd
$ cd ∼ # moves you back to your home directory

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Direct vs relative referencing

Relative referencing gives the Direct referencing gives the full

path relative to your current name of the path (always will
working directory. start with /).
e.g., Data e.g., /home/user/Data

What would be reasons for using relative referencing? Direct

referencing?

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Structure of the filesystem

Folders are separated by the “/” symbol (e.g., )

./ represents the current directory and ∼/ the home
directory. Usually /home/user.
../ represents the “parent” directory (up one in the tree
structure).
The “/” symbol alone represents the base directory of the file
system like the Machintosh HD on Mac or the C:\\ folder on
Windows.
The “executable” program files are usually in folders labeled
with bin (e.g., /usr/bin; /usr/local/bin). The system
will look in the directories in $PATH for any program.

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Exercises

1 List the folders contained in the base directory “/”.

2 Move from the home directory to the Data directory. What
files are contained in this directory?
3 Move from the base directory to the Data directory.
4 Determine all possible programs that this system can run.
5 List the files in another user’s home directory.

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Exercises solutions

1 List the folders contained in the base directory “/”.

$ ls /
2 Move from the home directory to the Data directory. What
files are contained in this directory?
$ cd Data/
$ ls
3 Move from the base directory to the Data directory.
$ cd /
$ cd ∼/Data
$ pwd

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Exercises solutions, cont.

4 Determine all possible programs that this system can run.

$ echo $PATH
$ ls /usr/local/sbin
$ ˆsbinˆbin # a lazy way of typing ls /usr/local/bin
$ ls /usr/sbin
$ ls /usr/bin
etc
5 List the files in another user’s home directory.
$ ls /home
$ ls /home/secret0

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Viewing text files

head: View the first 10 lines of a file.

tail: View the last 10 lines of a file.
cat: Display the contents of the entire file.
more or less: Display contents of the entire file in a
controlled format.

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Examples of viewing files

Text files

$ cd ∼/Data
$ head HG-U133 Plus 2.na32.annot.csv
$ tail HG-U133 Plus 2.na32.annot.csv
$ cat HG-U133 Plus 2.na32.annot.csv
$ more HG-U133 Plus 2.na32.annot.csv
Non-text files

$ more /bin/more

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Editing files

Standard unix file editors:

vi: Gives users a lot of control over file editing and searching
abilities, but has a steep learning curve.
emacs: Easier to use, but presence of mouse-clickable menus
depends on graphical link and version of emacs on the server.
pico: One of the easiest editors to use.
Use can also use your favorite text editor on Windows (e.g.,
Notepad) or Mac (e.g., TextEdit) and copy files over to the server.
Be careful that the text editor saves everything as a true
text file. NEVER USE MICROSOFT WORD FOR THIS!!!!

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Demo of file editing with pico

$ pico

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Copying files onto server

The “scp” (secure copy) is the most standard command to

copying files from one location to another.
Some servers also allow ftp or sftp access.
The easiest way to copy files between a local Windows
machine and a server is using a program like FileZilla
http://filezilla-project.org/.

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Copying files onto server (scp)

Generic command:

$ scp [user1]@[host1]:file1 [user2]@[host2]:file2

To copy to the server:

$ scp file [user]@[host]:∼/

What directory will file be copied into on the server?

To copy from the server:

$ scp [user]@[host]:∼/file .
What directory will file be moved to on your machine?

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Copying files to server: exercises

1 Create a text file on your machine using your favorite text file.
Save it in a directory that you can find on your machine.
2 Copy that file into your home directory.
3 Copy that file into your Data directory.
4 Copy that file from your home directory back into the
directory on your machine with a new filename.
5 Try to copy that file into the path /home/secret0.
6 Copy the file /home/secret0/mySecretFile into a directory
on your machine.

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Copying files locally (cp)

Generic command:

$ cp file1 file2

To create a new copy of a file in the home directory:

$ cp myCopyFile.txt myCopyFile2.txt

To create a copy of a file in the Data directory:

$ cp myCopyFile.txt ∼/Data

BE CAREFUL: the cp command will overwrite file2 with the

contents of file1 if already file2 exists.

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Copying files locally (cp)

Generic command:

$ cp file1 file2

BE CAREFUL: the cp command will overwrite file2 with the

contents of file1 if already file2 exists.
Safer to use the “interactive” command:

$ cp -i file1 file2

Try the following two commands.

$ cp myCopyFile.txt myCopyFile2.txt
$ cp -i myCopyFile.txt myCopyFile2.txt

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Moving files (mv)

Generic command:

$ mv file1 file2

BE CAREFUL: the mv command will overwrite file2 with the

contents of file1 if already file2 exists.
Safer to use the “interactive” command:

$ mv -i file1 file2

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Deleting files (rm)

Generic command:

$ rm file

BE CAREFUL: rm will not move files to a trash can, so there is

often no recovering files after using the rm command.
Safer to use the “interactive” command:

$ rm -i file

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Creating directories

Creating a new folder:

$ mkdir folder

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Managing directories

Creating a new folder:

$ mkdir folder

Copying contents of one folder to another:

$ cp -r folder1 folder2

Moving contents of one folder to another:

$ mv folder1 folder2

Be careful to check when folder2 already exists. Often will create a

copy of folder1 within folder2.

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Deleting directories

The following command will irretrievably remove a folder and all of

its contents:

$ rm -r folder

Some versions of unix will not allow you to remove a folder

containing any files. In these cases, use the following command
with great care:

$ rm -rf folder

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Exercises

1 Create a new directory within the Data directory from within

that directory.
2 Create another new directory within the Data directory from
within the home directory.
3 Copy a file into each of the subdirectories that you created in
the Data directory.
4 Copy a file from the home directory of the user secret0 into
your home directory.
5 Try to move a file from the home directory of the user
secret0 into your home directory.
6 Try to move a file from your directory into the home directory
of the user secret0.

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Hidden files vs private files

Hidden files begin with a . and

will not be displayed using the
default ls command. Seeing
them requires the following
command:

$ ls -a

Hidden files are usually used by

programs to determine default
settings, e.g., .bashrc.

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Hidden files vs private files

Hidden files begin with a . and Files have different levels of

will not be displayed using the permission to different users,
default ls command. Seeing which you can see in the first
them requires the following column from the following
command: command:

$ ls -a $ ls -l

Hidden files are usually used by Unless your unix system is

programs to determine default specially encrypted, there is
settings, e.g., .bashrc. no such thing as a truly
private file. Your system
administrator will always have
access to all of your files.
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User, group, world

The first column of the ls -l command will return a string of the

type drwxrwxrwx.

d: directory
r: read access
w: write access
x: execute
access
-: no access

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User, group, world

The first column of the ls -l command will return a string of the

type drwxrwxrwx.

d: directory User: accessible to yourself (and the

r: read access system administrator).
w: write access Group: accessible to others in your group
(check ls -l /home).
x: execute
access World: accessible to everyone with an
account on this machine.
-: no access

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Changing file permissions (chmod)

The chmod can add permissions with the + symbol or remove

permissions with the - symbol.

$ chmod u,g,o,a±r,w,x file

E.g., to the following command will give everyone execute

permissions to file

$ chmod a+x file

The following command will remove read permissions from

non-group members to file

$ chmod o-r file

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Changing file permissions (chmod)

The chmod can add permissions with the + symbol or remove

permissions with the - symbol.

$ chmod u,g,o,a±r,w,x file

u: user r: read
g: group w: write
o: other x: execute
a: all

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Other chmod options

Even if you remove user read option of a file, if you are the
owner of that file you can always run the chmod command to
restore your write access.
Multiple chmod options can also be specified with a numeric
key. For example, $ chmod 755 file is commonly used to
give the user read, write, execute permissions and both group
and world only read and execute permissions. (see
$ man chmod ).
The chmod command can set all the files in a folder to have
the same permission using the -R option.

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Exercises

1 Use the ls -l command to determine which files you can

access and which files you cannot for the user secret0. What
command should that user have to make their files
inaccessible to outsiders?
2 Create a new file with read and write access to other members
in your unixclass group, but no other users. Work with your
neighbor to check that you can both read and write this file
from their account. Log in as one of the users hopkins0-7
(password matches user name) and verify that you cannot
read or write this file from those accounts.
3 Discussion: Why are there different levels of security on unix
machines? Why is it so dangerous for a hacker to obtain the
login information for any user on a machine?

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Writing command output to files

command > file will output the

results of the command to file.

$ ls /usr/bin > binFiles

$ head binFiles
$ tail binFiles

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Writing and appending output to files

command > file will output the command >> file appends the
results of the command to file. output to file.

$ ls /usr/bin > binFiles $ ls /bin >> binFiles

$ head binFiles $ head binFiles
$ tail binFiles $ tail binFiles

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Redirecting output and the cut command

The cut command selects portions of the line of a file (see

$ man cut ).
For example, the following code will select columns 1 and 11 from
the annotation file and output it to a new file.

$ cut -f 1,11 ∼/HG-U133 Plus 2.na32.annot.txt > ∼/HG-U133 Plus 2.Unigene.txt

$ more ∼/HG-U133 Plus 2.Unigene.txt

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Combining commands through the pipe command (|)

command1 | command2 first runs command1 and then runs its

output through command2.

$ ls /usr/bin | head
$ ls /usr/bin | more
$ cut -f11 ∼/HG-U133 Plus 2.na32.annot.txt | grep Hs | sort | head
$ cut -f11 ∼/HG-U133 Plus 2.na32.annot.txt | grep Hs | sort | uniq | head

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Piping and grep

grep string will find “string” within the specified list. In files,
this can be used with piping as follows.

$ ls /usr/bin | grep vi
$ history | grep head
$ cat ∼/Data/HG-U133 Plus 2.na32.annot.csv | grep Notch

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Exercises

1 Create a file that contains all of the commands we applied to

files in the Data directory.
2 Create a file containing an alphabetical list of all the unique
programs in $PATH.

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Why use shell scripts instead of piping commands?

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Why use shell scripts instead of piping commands?

Reproducibility
Facilitates generalization and reuse of commands.

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Creating first shell script

Use pico to create a new script file
$ cd ∼/Scripts
$ pico HelloWorld.sh

Type in the following code

#!/bin/bash # the starting line of every script

# show “hello world” on the screen

echo hello world

To run the script

$ chmod a+x HelloWorld.sh
$ ./HelloWorld.sh

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Creating a script with a command

This script will print the first 10 lines of

HG-U133 Plus 2.na32.annot.txt.
#!/bin/bash # the starting line of every script

outputFile=∼/Data/HG-U133 Plus 2.na32.annot.txt

# show the first ten lines

head $outputFile

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Creating a script with a command and input arguments

This script will print the first 10 lines of the file specified as
./myScript.sh file.
#!/bin/bash # the starting line of every script

outputFile=$1

# remind the user of the file they selected

echo $outputFile

# show the first ten lines

head $outputFile

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Command line arguments

#!/bin/bash
$0 name of the script
$# number of arguments echo Running script $0
$@ vector of all the echo $# command line arguments
arguments echo $1 argument one
$1 first argument echo $2 argument two
$2 second argument
...

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Command line arguments

#!/bin/bash #!/bin/bash

echo Running script $0 echo Running script $0

echo $# command line arguments echo $# command line arguments
echo $1 argument one for argVar in “$@”
echo $2 argument two do
echo $argVar
done

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Looping

Loops facilitate repeating a task for some pre-specified criterion

(e.g., a set number of times, over a list of files, etc.)

For loop repeats task over a #!/bin/bash

specified list
for i in list echo Running script $0
do echo $# command line arguments
task(s) for argVar in “$@”
done do
echo $argVar
done

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Another example with loops

This script will output the number of lines of each file in the
specified directory.
#!/bin/bash

inputDirectory=$1

# looks at every element in a listing of inputDirectory

# and puts it into a variable called $afile
for afile in $(ls $inputDirectory)
do
echo The line count for $afile in the directory $inputDirectory is:
# use the full path for wc
wc -l $inputDirectory/$afile
done
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Conditionals (if, then)

But what if the user forgets to specify an input directory or that

directory doesn’t exist?

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Conditionals (if, then)

This script will check the input directory

#!/bin/bash

inputDirectory=$1

if [ ”$inputDirectory” == ”” ]
then
echo You must give a directory as the first argument
exit
fi

if [ ! -d $inputDirectory ]
then
echo $inputDirectory is not a valid directory
exit
fi

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Structure of conditionals (if,then)

if [ condition ]
then
task(s)
elif [ condition ]
then
task(s)
else
task(s)
fi

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Structure of conditionals (if,then, while)

if [ condition ] While loops will run as long as

then the condition is true.
task(s)
elif [ condition ]
then while [ condition ]
task(s) do
else task(s)
task(s) done
fi Be careful of infinite loops!!!

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Conditionals

String conditionals (True File conditionals (True when. . .)

when. . .) [ -d file ] file is a directory
[ -z s ] s is of length zero [ -e file ] file exists
[ s1 == s2 ] s1 and s2 match [ -r file ] file is readable
[ s1 != s2 ] s1 and s2 do not match
[ s1 < s2 ] s1 is less than [ -w file ] file is writable
s2 alphabetically [ -x file ] file is executable
[ s1 > s2 ] s1 is greater than
s2 alphabetically
Combining expressions
Can also use -eq, -ne, -lt, -le, -gt, [ !EXPR1 ] not
or -ge to compare two binary [ EXPR1 -a EXPR2 ] and
arguments. [ EXPR1 -o EXPR2 ] or

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Exercises

1 Write a script that goes into all of the folders in your home
directory and copies any executable files into a new directory
on your machine.
2 Write a script to go into a specified user’s home directory and
copies over all their readable files to a specified directory in
your folder.
3 Write a script that will go into as many directories as specified
in command line arguments and copy over all their readable
files. Extend the program to go through these folders
recursively if any of the command line arguments is
“recursive”.

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diff

diff file1 file2 compares the contents of file1 to the contents of

file2. The command can also be used to compare the contents
of folders.

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Converting characters

tr string1 string2 string3 replaces all instances of string1 with

string2 inside of string3. For example, we can regenerate the
tab delimited data file by

$ cat ∼/Data/HG-U133 Plus 2.na32.annot.csv | tr ’,’ ’\t’ >

∼/Data/HG-U133 Plus 2.na32.annot.new.txt
$ diff ∼/Data/HG-U133 Plus 2.na32.annot.new.txt ∼/Data/HG-
U133 Plus 2.na32.annot.txt
More controlled modifications to text can be made using the sed
or awk commands (see the additional resources).

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which

Indicates directory within those listed in $PATH that contains a

program of interest.

$ which pico

Will also indicate if the program cannot be found.

$ which fakeProgram

E. J. Fertig Intro Unix

 Unix filesystem
File processing Useful commands
Redirecting commands and scripts Resources
Additional information

clear

Will erase all commands from your current workspace. But, your
history will not be lost.

E. J. Fertig Intro Unix

 Unix filesystem
File processing Useful commands
Redirecting commands and scripts Resources
Additional information

passwd

Will change your password.

Requires knowledge of your current password.
If you forget your current password, your system administrator
can help you to reset it.

E. J. Fertig Intro Unix

Additional resources

Google is your friend!

http:
//loris.som.jhmi.edu/linux_course/resources.html