Preliminary steps
Required before you can download GP data from TDR
- Create a TDR Google Billing Profile (for step-by-step instructions, see How to create a TDR Billing Profile (GCP).
- Set up a Mercury Research Project (RP) with correct inputs.
- Follow steps for PDO placement and data generation.
Create and export snapshot
Once your GP data is available in the Terra Data Repository, follow the steps below to export the data to a Terra workspace for analysis or storage.
1. Log into TDR at https://data.terra.bio/datasets and click on the dataset name (circled in orange below) to select it.
2. Click View Dataset Data (indicated with an orange arrow).
3. Once the PDO is completed, you’ll see the samples populate in the TDR Dataset page.
Make sure sample is selected in the dropdown.
Dataset name formatting (GP only)
- Note that datasets from GP will be formatted like RP_####.
4. Filter for samples using PDOs/other dropdowns.
5. Fill in the fields for snapshot name and description, and select the asset from the dropdown (orange highlight in the screenshot below). You’ll want to go through the snapshot process twice, selecting processing_inputs (for gVCF delivery) and then deliverables_singlesample (for crams delivery).
Example
- For BGE data, you would select the bge_stanley_deliverable asset.
If the asset you want isn't in the dropdown, you'll need to put in a Support ticket to have this added to the RP so that it shows up.
6. (non-GP datasets only) In the Share Snapshot popup, add steward and reader users/permissions. Note that custodians have access as stewards by default.
Users and roles to add
- Individual users who will be accessing the data (stewards and readers)
- <stanley_pms@firecloud.org> (stewards and readers)
- <SC_BGE_Analysis@firecloud.org> (stewards and readers)
Note that you will also need to add them later to the Terra workspace as readers.
7. Add groups to the dataset Custodian role to automatically get snapshot access as stewards.
8. Click the blue Create Snapshot button (bottom right) to finish.
9. Click on Export Snapshot to expose the export configuration page (screenshot below). Select the Convert DRS and add Workspace policy groups checkboxes (circled) and click the Export snapshot button (orange arrow).
10. Export snapshots to desired workspace. You will have the opportunity to use an existing workspace or create a new one.
To create a new workspace, complete the three parts of the Create a workspace screen.
Workspace delivery and Authorization DomainsDon’t enable the additional security monitoring or add Authorization Domain/Access groups unless you are certain they should be added! If Auth Domain groups are added, EVERYONE who needs access to the Workspace needs to be in ALL of them. They cannot be removed! See When you need an Authorization Domain for more details.
11. Go to your Terra workspace and add appropriate reference data.