Creating a Biolinux AMI at Amazon’s EC2 Joe Steele jrsteele@unomaha.edu

Amazon E2 aws.amazon.com Computing cluster – create an account and provide a credit card. Let Amazon take care of the hardware.

Cloud BioLinux JCVI (J. Craig Venter Institute) created cloud version of NERC BioLinux VM. An Ubuntu machine with over 100 NEBC software packages. Image stored at EC2, is available to be copied at no charge, by EC2 users.

http://aws.amazon.com

Create a new account

Enter your information

Sign up for an EC2 account

Click on “Sign up for Amazon EC2”

EC2 Account Signing up for EC2 automatically signs you up for Amazon Simple Storage Service, and Amazon Virtual Private Cloud. Requires credit card information. No charges until you start using the services. Amazon will email with Access Identifiers, and instructions for your first log in.

Click on “AWS Management Console”

Click the EC2 Tab

Launch an Instance

I recommend biolinux

Click “Select”

Pricing Amazon has a variety of VM sizes available – pricing is at: http://aws.amazon.com/ec2/pricing/ You are charged for CPU usage, for data storage, and for data transferred to or from Amazon. Charges continue until a VM is “Terminated”. You can set up a small test VM for free – select “Micro” for the size.

Kernel defaults are fine

Key files For biolinux, you don’t need to add “User Data”. For some machines, the Amazon key IS needed to connect. When you create a Key Pair (next slide), save the *.pem file to a safe place.

Create a Key Pair

PEM file Save the *.pem file to a safe place. Linux: the *.pem file has to be protected: >chmod 400 <key_file>.pem Windows: Download PuTTYgen, and use it to change the *.pem file to a *.ppk file.

Create security group

Launch

Machine info

“Terminate” to end charges

First connection to Biolinux A window opens, telling you how to connect to your new VM, eg,: “ssh -i key_pair_name.pem root@ec2-76-202-01-919.compute-1.amazonaws.com” However, for biolinux, or any unbuntu VM, do: ssh –i key_pair_name.pem ubuntu@ec2-76-202-01-919.compute-1.amazonaws.com from a Linux machine, make sure the key_pair_name.pem is set to read only for the user only.

First Connection From Windows: Use PuTTYgen to change key_pair_name.pem to key_pair_name.ppk. Use PuTTY to connect, and put key_pair_name.ppk under “SSH” -> “Auth”. When connected to biolinux, you will be asked to set a password for ubuntu. If not, you need to start NX client: >./configure_freenx.sh

NX Use NX for the graphical display (built in to biolinux already). Open source, can be found at http://www.nomachine.com/ Must ssh into VM FIRST, using the key pair. You can stick with the ubuntu user, or add new users: >adduser <username> >groups >usermod -G <grp1>,<grp2>,ssh <username>

Start NX

“Configure”

Configure NX Note the use of “GNOME” and “LAN”. The Host should be “ec2-72-…amazonaws.com”. Also, the “Key…” works with the default key.

BioLinux over NX

BioLinux over NX

BioLinux over NX

BioLinux over NX

Data Stored at Amazon There are large datasets stored at Amazon, available for use – free of charge (mostly). You are charged for any data you copy. http://aws.amazon.com/datasets to search through them. Datasets that might be of interest in bioinformatics are listed at: http://biodoc.ist.unomaha.edu/wiki/Inventory_of_amazon_data

http://aws.amazon.com/datasets

Datasets Human DNA sequences: 1000 Genomes Project (7,300 GB) Ensembl Annotated Human Genome - FASTA (115 GB) Ensembl Annotated Human Genome - MySQL (200 GB) GenBank (200 GB) Human Liver Cohort (Sage Bionetworks) (0.6 GB) Illumina - Jay Flatley's Human Genome Data Set. (350 GB) YRI Trio Data - complete genome sequence for three individuals (700 GB) Other (might include some human data): Ensembl - FASTA DB (100 GB) Influenza Virus (including Swine Flu) - from NCBI (1 GB) UniGene - from NCBI (10 GB) PubChem Library - from NCBI (230 GB)

Public Snapshots

Select “Volumes”

Create a Volume

Instance Information

Attach it to your Instance

Mount the Volume From your VM: >sudo mkfs –t ext3 /dev/sdf >sudo mkdir /mnt/datasets >sudo mount –t ext3 /dev/sdf /mnt/datasets 200GB of genbank data are now in /mnt/datasets

Test Usage for the First Year

CPU charges

Data Transfer charges

Data storage charges