Creating a Biolinux AMI at Amazon’s EC2. Joe Steele firstname.lastname@example.org. Amazon E2. aws.amazon.com Computing cluster – create an account and provide a credit card. Let Amazon take care of the hardware. Cloud BioLinux.
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Creating a BiolinuxAMIat Amazon’s EC2 Joe Steele email@example.com
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.
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.
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.
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.
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.
First connection to Biolinux A window opens, telling you how to connect to your new VM, eg,: “ssh -i key_pair_name.pem firstname.lastname@example.org” However, for biolinux, or any unbuntu VM, do: ssh –i key_pair_name.pem email@example.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>
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.
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
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)
Mount the Volume From your VM: >sudomkfs –t ext3 /dev/sdf >sudomkdir /mnt/datasets >sudo mount –t ext3 /dev/sdf /mnt/datasets 200GB of genbank data are now in /mnt/datasets