Using Amazon Web Services

Cloud computing. Using the sRNA Workbench on Amazon Web Services (AWS)

We have created a preconfigured virtual machine (known as an Amazon Machine Instance or AMI) for using the workbench on AWS. The following page details instructions for creating an AWS account (if you do not already have one) and obtaining and running the workbench via the EC2 (Elastic Compute Cloud) web service.

Install a Virtual Network Client (VNC)

Windows, Linux/Unix(MACOS): A free VNC viewer or alternative will be required if you are planning on accessing the workbench’s graphical features. An example can be found at the following link:

http://tigervnc.org

Alternatively if planning CLI usage only, the VNC client will not be needed.

Create an AWS account

Follow the following link to sign up to AWS if you haven’t already created an account:

Sign up for an AWS account

Create a key pair to use for login

Amazon EC2 Key Pairs. Amazon EC2 uses public–key cryptography to encrypt and decrypt login information. Public–key cryptography uses a public key to encrypt a piece of data, such as a password, then the recipient uses the private key to decrypt the data. The public and private keys are known as a key pair.

A key pair will be required to More information on creation of a key pair and all relevant information can be found here

Upload Sequence data

There are a variety of options available for storage on AWS. The most common is the S3 storage system but this requires extra setup when attempting to access files stored in an S3 bucket from within a preconfigured AMI.

Elastic Block Storage

The Workbench AMI’s EBS volume can also be directly accessed via an FTP client such as FileZilla.  The FTP client should be configured with the key pair Data is placed directly into the EBS volume that underpins the AMI. Alternatively, mount a storage bucket from your S3 storage. Note: EBS volumes underpinning your instance cannot be accessed until the instance is running.

S3 (Simple Storage Solutions)

S3 is the standard place for high volume storage on the Amazon Cloud. More information on pulling data from S3 into an EC2 instance can be found here. Alternatively S3 storage buckets can be directly mounted into an AMI. More information on this can be found here.

Launch the Workbench Amazon Machine Instance (AMI)

Use our preconfigured AMI

Follow the steps required to configure an AMI from the EC2 management console. Usage options are up to you and depend on your budget. If using from the free tier (see this page for more info) then ensure you select the free tier eligible options.

The preconfigured AMI containing libraries for displaying a GUI over the linux install and the workbench binaries (plus tutorial data) can be found at the following bookmark:

https://console.aws.amazon.com/ec2/v2/home?region=eu-west-1#LaunchInstanceWizard:ami=ami-14b88c72

Alternatively, the search through the community AMIs for the ID: ami-14b88c72 will yield the workbench AMI.

Potentially add new security groups during instance review

During setup of the AMI, select the launch-wizard-2 security group. In the event that this group is not available in the AMI you must have the following rule in place to allow the VNC protocol to access the instance:

Type
Protocol
Port Range
Source
SSH
TCP
22
Custom TCP Rule
TCP
5901 – 5903

Note the source IPs are left blank. AWS help specifies that this field determines the traffic that can reach your instance. Specify a single IP address, or an IP address range in CIDR notation (for example, 203.0.113.5/32). If connecting from behind a firewall, you’ll need the IP address range used by the client computers. If left as all 0s (default) the instance becomes available to the world (not recommended)

Boot the workbench

The workbench can now be accessed as it would by any linux user. Open the terminal and navigate to the Desktop/srna-workbenchV$ (where $ is the current installed build). Then follow the instructions given hereNote: As this AMI is likely to be used exclusively for running the workbench, use the second option to configure Workbench.jar by hand and give the software close to as much RAM as you have assigned to the AMI (leaving some aside for the OS to function)

Run your analysis

Analysis can now be run as normal either via the GUI or CLI. All instruction pages and tutorial files now apply as they would in the stand alone downloaded client.

A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices