1. Amazon EC2 Cloud and Using circos for visualization Ishwor Thapa

2. 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

3. Connecting to ec2 instance using putty (Windows)

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

8. EC2Page

9. ec2-landing page

10. Selecting Instance (A)

11. Selecting Instance (B)

13. Instance Details

16. Use Existing Key

17. Security Definitions

18. Review Page

19. EC2 console page (Start your instance!!)

20. Connecting to ec2 instance using putty (Windows)

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

25. adding user root@domU-12-31-39-15-01-6A:~# 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]

26. 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

27. Installing libraries in perl wget http://biobase2.ist.unomaha.edu/~ithapa/1_root_apt-update.shhttp://biobase2.ist.unomaha.edu/~ithapa/1_root_apt-update.sh 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 '7 1-4 8' [] 12 13 14 cpan[3]> o conf commit

28. Installing libraries in perl wget http://biobase2.ist.unomaha.edu/~ithapa/2_root_perl_module.sh sh 2_root_perl_module.sh

29. Using NXClient to use Desktop

30. Installing NX-client

35. Using NX-Client

38. Running Ubuntu Desktop

39. Open the terminal

40. Installing circos wget http://biobase2.ist.unomaha.edu/~ithapa/3_user_circos_install.sh sh 3_user_circos_install.sh

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

42. circos.conf > > > image parameters karyotype = NC_009080.NC_008836.karyotype.txt chromosome information

43. ideogram.conf cytogenic bands in the circumference size color label show_bands = no/yes

44. 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 green chr - NC_009080 NC_009080 0 3495687 blue band NC_009080 rband rband 8173 8340 transorange band NC_009080 fband fband 42376 42513 transblue chr/ba nd parentIDLabelstartendcolor