Accessing Green Data

Using Google Cloud console

You can use the Google Cloud console to inspect or download the green library's contents or your files released from Sandbox by download request:

1. Open your web browser (Google Chrome is recommended) and navigate to https://console.cloud.google.com/storage/browser/<bucket-name>/ (replace bucket-name with your bucket, for instance finngen-production-library-green).

2. Sign in with your FinnGen account.

3. Find the file you are looking for and download it to your local system by clicking on the three dots on the right-hand side of the file, and select Download.

For more help on downloading files, see the instructions on How to download results from your IVM using the bucket-name that you receive by email after your download request from Sandbox has been approved.

Storage

The majority of the green data is stored in the green data library, which exists as a Google Cloud storage bucket named finngen-production-library-green. This data consists of aggregate-level results and is accessible to anyone with an @finngen.fi account (see How to request an account).

You can use the Google Cloud console to inspect or download the green library's contents by visiting the green library.

Using Google Cloud SDK

Alternatively, you can use the gsutil toolkit (Google Cloud SDK) to access the green library or your released files from download requests directly from the command line.

Directions for command-line access:

1. To install the Google Cloud SDK follow the install directions, or ask your IT support to install it for you if you're having trouble.

2. Authenticate using the command line by typing gcloud auth login.

3. A link will appear on your screen. Follow it with your web browser and sign in with your account when prompted.

A few examples for command-line access:

• List the files "gsutil ls gs://<bucket-name>/" .

  • gsutil ls gs://finngen-production-library-green will list the contents of the entire green library.

• Copy the files "gsutil cp gs://<bucket-name>/path/to/file/file.txt /path/to/your/incoming_folder/

  • gsutil cp will download any file from the green library to your local system. If the folder(s) in the path doesn't exist, the gsutil cp command will create it.

• Remove your credentials with gcloud auth revoke.

In all cases, you must be logged in with your @finngen.fi account to use these tools.

For more information about gsutil, please see the gsutil tool page.

The FinnGen PheWeb browser is also considered part of the green data. To access it, visit the PheWeb result page. From there, you will be prompted to login with your @finngen.fi account.