Run your first analysis

Create a TRE

From the Submission Layer navigation bar, go to TREs -> Create New Tre

Enter the name for the TRE and the admin username. The default Keycloak TRE admin username is accessfromtretosubmission

These are the TRE Agent user credentials, created in the Submission Layer Keycloak realm & are the same credentials set in the TRE Agent

Create a User

Create a user by navigating to People-> Create New User. The default Keycloak Submission admin user is globaladminuser

The username has to match the an existing keycloak user account.

Create a Project

Navigate to the Projects -> Create Project.

Once a Project is created, assign a TRE and a user that will be associated with the submissions.

TRE layer

The TRE Agent will sync any Projects created in the submission layer every 10 minutes by default. To adjust how long between each sync change the syncSchedule setting.

Approve Project and Membership

Once the TRE Agent is in sync the Project will appear in the TRE Agent UI.

Approve Project

Navigate to the Project Approval section to approve the Project

Approve Project User Membership

Navigate to the Memberships section to approve the users that can submit to that Project.

Run Analysis

Get Access Token

From the Submission Layer navigate to API Access Token -> Copy to Clipboard

Authorise request

You can make the request from the swagger API hosted at http://localhost:5034/swagger. Authorise the request with the Token from the Authorise button on the top right.

Get Project Output Bucket

The output bucket for a project can be found in the Submission UI. Go to Project -> About page and hover over Output Bucket. The naming pattern is: <projectName> + <projectUniqueID> + output. Then add tre to the end of it. For example the submission output bucket is: demoproject2367output then you need to set it to: demoproject2367outputtre

 
POST localhost:5034/v1/tasks
{
    "state": 0,
    "name": "Hello World",
    "inputs": [],
    "outputs": [
        {
            "name": "Stdout",
            "description": "Stdout results",
            "url": "s3://<outputBucketName>", // Set the output bucket
            "path": "/outputs",
            "type": "DIRECTORY"
        }
    ],
    "executors": [
        {
            "image": "ubuntu",
            "command": [
                "echo",
                "Hello World"
            ],
            "workdir": "/outputs",
            "stdout": "/outputs/stdout",
        }
    ],
    "volumes": null,
    "tags": {
        "project": "<ProjectName>", // Project that you would like to submit to.
        "tres": "<TREName>" // TRE related to that Project
    },
    "logs": null,
    "creation_time": null
}

More information on the TES payload can be found at the TES API specification website.

Actors Submission