Access SRA sequence data using Amazon Web Services (AWS)

Introduction for First Time Users

Amazon Elastic Compute Cloud (EC2) is the Amazon Web Service you use to create and run virtual machines in the cloud. AWS calls these virtual machines 'instances'. Please follow this Amazon step-by-step guideoffsite image that will help you launch a Linux virtual machine on Amazon EC2 within Amazon AWS Free Tier.

Access SRA data

Exclamation point Users will need to address accounts on their own.
Please work with your organization for credential and billing questions. If using a personal account, this guide attempts to stay within AWS Free Tier for users who are still eligible.

Exclamation point Users of this guide are expected to have experience using a Unix command-line interface.

Sign-in and Enter the Amazon EC2 Console

Sign-in using your AWS account: Amazon AWS Consoleoffsite image.

Launch an Amazon EC2 Instance

1. Choose an Amazon Machine Image (AMI)

  • Search for the SRA AMI ami-0d57e13fe62227b2e
  • Select the 1 result from the Community AMIs "SDDP workbench"

2. Choose an Instance Type

  • Select the t.2micro instance

3. Configure Instance Details

  • Many users will not need to change anything on this page.

4. Add Storage

  • Use General Purpose SSD with an 8 GiB volume size.

5. Add Tags

  • Add a tag Key = "Project" and Value = "SRA Cloud Demo"

6. Configure Security Group

  • For this demo an open security group can be used. For subsequent work we recommend to follow Amazons' advice and limit access to known appropriate IP addresses.
  • Click Review and Launch.

7. Review Instance Launch

  • Make sure the details of the instance are correct and click Launch.
  • Use an existing key pair if possible. If not you will need to generate a new key pair.
  • Click Launch Instance.

Connect to the Instance

Use either a Unix/OSX terminal or your preferred ssh application to connect the same as the Amazon tutorial linked above.

  • This AMI user name is ec2-user.

Follow the README.txt in the home directory

  • The README.txt has example commands to mount and unmount a fusera directory and several SRA sequence data files stored in the cloud.
  • The samtools and BWA-MEM programs are installed on this AMI for testing access.
  • Make sure not to store any results from testing in the SRR directories.

Terminate the Instance

  • Remember to terminate the EC2 instance from the AWS console when you have finished using it. If you do not terminate the instance, charges can be generated on your account even when no users are connected.
  • Data stored on the EC2 instance will be deleted when the instance is terminated. Users will likely want to have stable s3 storage to store results from their work.

Contact SRA

Contact SRA staff for assistance at sra@ncbi.nlm.nih.gov

Support Center

Last updated: 2019-09-20T18:59:15Z