TRE-FX Documentation

Run analysis with All In One Demo

Install Funnel

In the All In One repository change these settings:

Change these settings in the .env file:

.env

UseTESK = true

In the docker-compose.yml set:

docker-compose.yml

// Set all instances of DemoMode and KeycloakDemoMode in the file to:
DemoMode = false
KeyCloakDemoMode = true
 
// Set TESKAPIURL to the URL where Funnel is hosted:
TESKAPIURL = "http://localhost:8000/v1/tasks"
 
// Set the prefix for GenericS3 storage:
TESKOutputBucketPrefix = "s3://"

Submit a TES message

Once the Funnel is running and the All In One is up and configured, you can submit a TES payload to the Submission Layer.

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.

Make submission

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

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
}

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