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Encrypt your data with the crypt4gh CLI

Encrypting your data with the crypt4gh command line interface (CLI) is good when:

  • You are comfortable working with a terminal
  • You are encrypting a lot of files

You must encrypt your data if you want to use the PGS calculation service.

Encrypting your data on your computer before uploading it is important to keep your data safe.

tip

Users unfamiliar with terminals and CLIs might prefer to use crypt4gh-gui

Step by step guide​

1. Install the crypt4gh utility​

crypt4gh is a Python tool to encrypt, decrypt or re-encrypt files, according to the GA4GH encryption file format.

You can install it from the Python Package Index (PyPI):

$ pipx install crypt4gh  # preferred - installs into an isolated environment
$ pip install --user crypt4gh  # if pipx is not installed
tip

You only need to install the crypt4gh utility once

caution

You need Python 3.6 or higher installed on your computer to use the crypt4gh utility

2. Download your unique public key from the platform​

tip
  • Each public key has a linked secret key, which we store securely on the platform
  • We use the secret key to temporarily decrypt your data and calculate PGS when you submit jobs
  • The secret key automatically expires 2 weeks after it's created to keep your data safe
  • Any encrypted data with an expired secret key cannot be decrypted and are automatically deleted on the platform
  • You'll need to restart the data encryption process with a new public key if more than 2 weeks have passed since you started the data upload process

3. Use the public key to encrypt your files​

$ cd /path/to/your/genomes
$ crypt4gh encrypt --recipient_pk ~/Downloads/INTD00000000024.pub < hapnest.pvar > hapnest.pvar.c4gh
$ crypt4gh encrypt --recipient_pk ~/Downloads/INTD00000000024.pub < hapnest.pgen > hapnest.pgen.c4gh
$ crypt4gh encrypt --recipient_pk ~/Downloads/INTD00000000024.pub < hapnest.psam > hapnest.psam.c4gh
caution
  • It's important to include the .c4gh suffix on the new encrypted files
  • Don't forget to include the original suffix (e.g. .pvar) or we won't be able to recognise your files

4. Continue to upload your encrypted data​

You're now ready to upload your encrypted data.

danger
  • Always encrypt your data, even if the data are not sensitive and publicly available (e.g. 1000 Genomes)
  • If you submit jobs using unencrypted data, they will always fail after some time