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)

Log in to: username and password provided to you.

EC2Page

ec2-landing page

Selecting Instance (A)

Selecting Instance (B)

Instance Details

Use Existing Key

Security Definitions

Review Page

EC2 console page (Start your instance!!)

Connecting to ec2 instance using putty (Windows)

command to change password: passwd Login Name: root Connecting to ec2 instance using putty (Windows)

adding user adduser ithapa Adding 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 successfully Changing the user information for ithapa Enter the new value, or press ENTER for the default Full Name []: Ishwor Thapa Room 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 perl wget sh 1_root_apt-update.sh perl –MCPAN –e shell hit Enter whenever it prompts you for any input cpan[2]> o conf init urllist Select your continent (or several nearby continents) [] 5 Select your country (or several nearby countries) [] 3 put them on one line, separated by blanks, hyphenated ranges allowed e.g. '1 4 5' or ' ' [] cpan[3]> o conf commit

Installing libraries in perl wget sh 2_root_perl_module.sh

Using NXClient to use Desktop

Installing NX-client

Using NX-Client

Running Ubuntu Desktop

Open the terminal

Installing circos wget sh 3_user_circos_install.sh

Using Circos to visualize genomes configuration files circos.conf ideogram.conf ticks.conf data files karyotype.txt

circos.conf > > > image parameters karyotype = NC_ NC_ karyotype.txt chromosome 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_ NC_ green chr - NC_ NC_ blue band NC_ rband rband transorange band NC_ fband fband transblue chr/ba nd parentIDLabelstartendcolor