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Step1-SetupDeploymentInstance.md

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Deployment Instance

Ensure all steps below are executed in AWS region: London (eu-west-2).

Step 1. Create Deployment Instance

Time to deploy: Approximately 10 minutes

Step 1A. Create the EC2 instance

Log in to the AWS Management Console using your TRE Project 1 Prod account and Admin privileges.

  • Go to Service: AWS CloudFormation
  • Select the Stacks menu option on the left side
  • Press button: Create Stack with new resources
  • Select option Upload a template file to upload CloudFormation template file: deployment instance and press on button Next
  • Provide Stack name: "TREDeploymentInstance". Adjust default parameter values if needed. Press on button Next twice and then on button Create stack
  • Confirm the stack status is "CREATE_COMPLETE"

Step 1B. Log in to the EC2 instance

  • Follow these instructions to learn how to connect via SSM to the EC2 instance created in Step 1A.
  • Run the following command to initialise your environment:
sudo -iu ec2-user

Step 1C. Download TREEHOOSE TRE

  • Run the following commands to get a copy of the TREEHOOSE TRE open-source repository:
cd /home/ec2-user/tmp
VERSION=v1.0.0-beta1
mkdir TREEHOOSE
wget https://github.com/HicResearch/TREEHOOSE/archive/$VERSION.tar.gz
tar --strip-components=1 -xzf $VERSION.tar.gz -C TREEHOOSE

Change VERSION if you want to install a different release of TREEHOOSE. If you are familiar with git you can clone the repository instead.

Note: The installation process requires 3rd party open-source libraries to be installed on the EC2 instance that does not come bundled by default with the Operating System.
The list is as below \

  • yum-utils, git, jq, and packer from yum repository.
  • AWS CLI V2, AWS CDK V1.0 and V2.0
  • NVM, NodeJs V14.17.0 and V16.15.0
  • NPM packages pnpm, serverless
  • GO