Amazon EC2 Cloud and Using circos for visualization Ishwor Thapa
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