Sharing individual-level data within the Sandbox

Other users can't access your IVM but you can still share individual-level data with other Sandbox users. Please keep in mind that you can't download individual-level data outside of the Sandbox environment.

There are two scenarios for sharing individual-level data with other Sandbox users:

• Sharing within your organization (between Sandbox users)

• Sharing outside your organization (between all FinnGen Sandbox users)

Sharing within your organization

You can share individual-level data within your organization by copying files into the "red" bucket. Each organization has its own "red" bucket that is shared between all users of the organization.

When you are logged into your IVM, you can find the "red" bucket path in the IVM background image next to the red bucket:

To keep your organization's data organized and easy to find, we recommend that users create their own folder/directory in the "red" bucket.

Please follow these steps to share data within your organization using the gsutil command:

1. Open the "Applications" menu

2. Click the "Terminal Emulator"

3. Use the following command to copy <your file(s)> into the "red" bucket in <your folder> directory. If the folder doesn't exist yet it will be created for you with the same command.

gsutil cp <your file(s)> gs://fg-production-sandbox-<sandbox number>-red/<your folder>/

You can get the <sandbox number> from your sandbox URL. For example, if the sandbox URL is https://sandbox.finngen.fi/fg-production-sandbox-6/vm then the <sandbox number> is 6, and the "red" bucket is gs://fg-production-sandbox-6-red. Please remember to include the trailing '/' to create the <your folder> directory. If the folder(s) in the path doesn't exist, the gsutil cp command will create it.

Please follow these steps to share data within your organization using the File Manager:

1. Open the "Applications" menu

2. Click the "File Manager"

3. Right-click a file and select "Upload to red bucket" from the pop-up menu. Please note that when using the File Manager files can only be copied to the "red" bucket root directory.

Sharing outside your organization

There is two ways to share data outside your organisation:

1) Shared bucket via share request

2) Shared network disk

Shared bucket via share request:

You can share individual-level data outside your organization by first copying files into your organization's "red" bucket and then requesting these files to be shared with all FinnGen users.

Data shared outside your organization is always available to all Sandbox users in all organizations and can't be shared only with specific users.

Please follow these steps to share data outside your organization:

1. Copy files to your organization's "red" bucket. Please follow the instructions in the 'Sharing within your organization' section to do this.

2. Use the file browser to browse a file's location in the "red" bucket.

3. Right-click on the file and select "Share with all FinnGen Users".

4. You will then be asked to provide information about the data you are sharing with other Sandbox users

5. Usually a few minutes after you have requested your files to be shared, you will get an email containing a path to the data. You can send this email to colleagues looking for the files so they know how to find them. A unique identifier is added to each share with encoded information about the data. This can be a bit unwieldy and it is possible to copy and paste these back into your IVM to make things easier.

Shared network disk:

The shared network disk is read/write accessible to all Sandbox users. Please be cautious not to erase data generated by others!

Use an informative folder structure for your data. It is recommended that the first folder describes the owner (e.g.: /finngen/shared_nfs/"user_name", /finngen/shared_nfs/"taskforce_name").

The primary purpose of the shared network disk is to share code and documentation. Therefore, there is a strict 100 MB size limit for files.

Note: Files larger than 100 MB will be deleted when the disk is full, without separate warning.

The shared network disk is not intended for permanent storage and is not backed up. please move your static data into red bucket or other storage media.

Practicalities:

You can find the network disk in folder /finngen/shared_nfs/ folder.

The disk can be accessed as normal linux folder using tools from the IVM.