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S3 Imports

S3 Integration Guide

You must grant Gencove permission to access your AWS account in which it will be able to list and read objects from S3 buckets. Gencove uses a cross-account role with external ID enabled.

Step 1: Configure your Gencove account

  1. Login to your Gencove account and go to the fastqs page.
  2. Click the S3 tab.
  3. Click Connect to Amazon S3 and follow the instructions.
    1. Copy the AWS Account ID, it is needed for the next step.
    2. Generate a new External ID and copy it, you will need it for the next step.

Connect to Amazon S3

Step 2: Create a cross-account role and an access policy on AWS

  1. In the AWS Console, go to the IAM service.
  2. Click the Roles tab in the sidebar.
  3. Click Create role.

    • In Select type of trusted entity, click the Another AWS account tile.
    • In the Account ID field, enter the Gencove account ID from Step 1
    • Paste the External ID generated in Step 1 into the corresponding field.

      Create AWS Role

  4. Then click on Next to set permissions.

    • Create a custom policy using the template below. Click the JSON tab, paste the template and replace "${BucketName}" with the name of the bucket you want to give access to.
        "Version": "2012-10-17",
        "Statement": [
                "Action": [
                "Effect": "Allow",
                "Resource": "arn:aws:s3:::${BucketName}"
                "Effect": "Allow",
                "Action": "s3:GetObject",
                "Resource": "arn:aws:s3:::${BucketName}/*"
  5. Click on Next to set the Role name.

  6. Click on Create Role. Then the list of roles is displayed, click on the role you just created and copy the role ARN. It takes some time for AWS to propagate changes, it could take a couple minutes until the role is ready to be used, we recommend waiting at least 5 minutes before continuing.
  7. Go to Roles list and select the role you created.

    Role detail view

    Copy Role ARN

  8. Go back to your Gencove fastqs S3 configuration page and paste the role ARN in the corresponding field and click "Connect".

Connect to Amazon S3

Step 3: Import samples from S3

  1. Login to your Gencove account and go to the fastqs page.
  2. Click the S3 tab.
  3. Click "Import from S3" and paste the S3 uri that you want to import, then click "Import".

    Import from S3

  4. Choose a project to assign the imported samples.

    Assign to Gencove Project

  5. Finally you will see an overview. You can assign metadata to the samples. When you're done, click "Run analysis".

    Run Analysis

  6. You will be redirected to the project page and you will find the new samples there in importing state.

    Project Samples

  7. After the sample is imported it will be sent to analysis.

Sample details view

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