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Amazon EC2 Cloud and Using circos for visualization

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.

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Amazon EC2 Cloud and Using circos for visualization

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  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)

  4. Connecting to ec2 instance using putty (Windows)

  5. Connectingto ec2 instance using putty (Windows)

  6. 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)

  12. Selecting Instance (B)

  13. Instance Details

  14. Instance Details

  15. 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)

  21. Connecting to ec2 instance using putty (Windows)

  22. Connecting to ec2 instance using putty (Windows)

  23. Connecting to ec2 instance using putty (Windows)

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

  25. adding user root@domU-12-31-39-15-01-6A:~# adduserithapa 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 wgethttp://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 confiniturllist 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 sh2_root_perl_module.sh

  29. Using NXClient to use Desktop

  30. Installing NX-client

  31. Installing NX-client

  32. Installing NX-client

  33. Installing NX-client

  34. Installing NX-client

  35. Using NX-Client

  36. Running Ubuntu Desktop

  37. Open the terminal

  38. Installing circos wgethttp://biobase2.ist.unomaha.edu/~ithapa/3_user_circos_install.sh sh 3_user_circos_install.sh

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

  40. 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.txt chromosome information

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

  42. 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 rbandrband 8173 8340 transorange band NC_009080 fbandfband 42376 42513 transblue

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