Amazon EC2 Cloud and Using circos for visualization Ishwor Thapa.
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Transcript of Amazon EC2 Cloud and Using circos for visualization Ishwor Thapa.
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Amazon EC2 Cloud and Using circos for visualization
Ishwor Thapa
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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
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Log in to: • https://uno-biocloud.signin.aws.amazon.com/console• username and password provided to you.
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EC2Page
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ec2-landing page
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Selecting Instance (A)
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Selecting Instance (B)
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Selecting Instance (B)
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Instance Details
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Instance Details
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Instance Details
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Use Existing Key
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Security Definitions
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Review Page
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EC2 console page (Start your instance!!)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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command to change password:passwd
Login Name: root
Connecting to ec2 instance using putty (Windows)
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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]
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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
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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
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Installing libraries in perl
wget http://biobase2.ist.unomaha.edu/~ithapa/2_root_perl_module.sh
sh 2_root_perl_module.sh
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Using NXClient to use Desktop
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Installing NX-client
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Installing NX-client
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Installing NX-client
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Installing NX-client
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Installing NX-client
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Using NX-Client
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Running Ubuntu Desktop
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Open the terminal
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Installing circos
wget http://biobase2.ist.unomaha.edu/~ithapa/3_user_circos_install.shsh 3_user_circos_install.sh
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Using Circos to visualize genomes
• configuration files• circos.conf• ideogram.conf• ticks.conf
• data files• karyotype.txt
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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
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ideogram.conf• cytogenic bands in the circumference• size• color• label
• show_bands = no/yes
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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