Amazon EC2 Cloud and Using circos for visualization

Ishwor Thapa

Using Putty to connect to EC2• Download your pem file from last session• If you don’t have it, meet me NOW.

• If Putty isn’t installed in your machine, search for putty in the internet and install it.

• If Putty is installed, Click on PuttyGen

Connecting to ec2 instance using putty (Windows)

Connecting to ec2 instance using putty (Windows)

Connecting to ec2 instance using putty (Windows)

Connecting to ec2 instance using putty (Windows)

Log in to: • https://uno-biocloud.signin.aws.amazon.com/console• username and password provided to you.

EC2Page

ec2-landing page

Selecting Instance (A)

Selecting Instance (B)

Selecting Instance (B)

Instance Details

Instance Details

Instance Details

Use Existing Key

Security Definitions

Review Page

EC2 console page (Start your instance!!)

Connecting to ec2 instance using putty (Windows)

Connecting to ec2 instance using putty (Windows)

Connecting to ec2 instance using putty (Windows)

Connecting to ec2 instance using putty (Windows)

command to change password:passwd

Login Name: root

Connecting to ec2 instance using putty (Windows)

adding user

root@domU-12-31-39-15-01-6A:~# adduser ithapaAdding user `ithapa' ...Adding new group `ithapa' (1001) ...Adding new user `ithapa' (1001) with group `ithapa' ...Creating home directory `/home/ithapa' ...Copying files from `/etc/skel' ...Enter new UNIX password: Retype new UNIX password: passwd: password updated successfullyChanging the user information for ithapaEnter the new value, or press ENTER for the default

Full Name []: Ishwor ThapaRoom Number []: Work Phone []: Home Phone []: Other []:

Is the information correct? [Y/n]

Enable Password

nano /etc/ssh/sshd_config

# Change to yes to enable challenge-response passwords (beware issues with# some PAM modules and threads)ChallengeResponseAuthentication no

# Change to no to disable tunnelled clear text passwords

PasswordAuthentication yes

# Kerberos options#KerberosAuthentication no

Hit Ctrl X and Y to save

Installing libraries in perlwget http://biobase2.ist.unomaha.edu/~ithapa/1_root_apt-update.sh

sh 1_root_apt-update.sh

perl –MCPAN –e shellhit Enter whenever it prompts you for any input

cpan[2]> o conf init urllist

Select your continent (or several nearby continents) [] 5Select your country (or several nearby countries) [] 3put them on one line, separated by blanks, hyphenated ranges allowede.g. '1 4 5' or '7 1-4 8' [] 12 13 14cpan[3]> o conf commit

Installing libraries in perl

wget http://biobase2.ist.unomaha.edu/~ithapa/2_root_perl_module.sh

sh 2_root_perl_module.sh

Using NXClient to use Desktop

Installing NX-client

Installing NX-client

Installing NX-client

Installing NX-client

Installing NX-client

Using NX-Client

Running Ubuntu Desktop

Open the terminal

Installing circos

wget http://biobase2.ist.unomaha.edu/~ithapa/3_user_circos_install.shsh 3_user_circos_install.sh

Using Circos to visualize genomes

• configuration files• circos.conf• ideogram.conf• ticks.conf

• data files• karyotype.txt

circos.conf<colors><<include etc/colors.conf>><<include etc/brewer.conf>></colors>

<fonts><<include etc/fonts.conf>></fonts>

<<include ideogram1.conf>><<include ticks.conf>>

<image> image parameters</image>

karyotype = NC_009080.NC_008836.karyotype.txtchromosome information

ideogram.conf• cytogenic bands in the circumference• size• color• label

• show_bands = no/yes

karyotype.txt• size, identity, label and color of each chromosome• position, identity and color of cytogenic bands• Has 7 columns

chr - NC_008836 NC_008836 0 3458208 greenchr - NC_009080 NC_009080 0 3495687 blue

band NC_009080 rband rband 8173 8340 transorangeband NC_009080 fband fband 42376 42513 transblue

chr/band

parent ID Label start end color