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Storing secrets in the vault

Galaxy can be configured to store secrets in an external vault, which is useful for secure handling and centralization of secrets management. In particular, information fields in the “Manage information” section of the user profile, such as AWS credentials, can be configured to be stored in an encrypted vault instead of the database. Vault keys are generally stored as key-value pairs in a hierarchical fashion, for example: /galaxy/user/2/preferences/aws/client_secret.

Vault backends

There are currently 3 supported backends.




Hashicorp Vault is a secrets and encryption management system. https://www.vaultproject.io/


Custos is an NSF-funded project, backed by open source software that provides science gateways such as Galaxy with single sign-on, group management, and management of secrets such as access keys and OAuth2 access tokens. Custos secrets management is backed by Hashicorp’s vault, but provides a convenient, always-on ReST API service.


The database backend stores secrets in an encrypted table in the Galaxy database itself. It is a convenient way to get started with a vault, and while it supports basic key rotation, we recommend using one of the other options in production.

Configuring Galaxy

The first step to using a vault is to configure the vault_config_file setting in galaxy.yml.

  # Vault config file
  # The value of this option will be resolved with respect to
  # <config_dir>.
  vault_config_file: vault_conf.yml

Configuring vault_conf.yml

The vault_conf.yml file itself has two basic fields:

type: hashicorp  # required
path_prefix: /galaxy  # optional

The type must be a valid backend type: hashicorp, custos, or database. At present, only a single vault backend is supported. The path_prefix property indicates the root path under which to store all vault keys. If multiple Galaxy instances are using the same vault, a prefix can be used to uniquely identify the Galaxy instance. If no path_prefix is provided, the prefix defaults to /galaxy.

Vault configuration for Hashicorp Vault

type: hashicorp
path_prefix: /my_galaxy_instance
vault_address: http://localhost:8200
vault_token: vault_application_token

Vault configuration for Custos

type: custos
custos_host: service.staging.usecustos.org
custos_port: 30170
custos_client_id: custos-jeREDACTEDye-10000001
custos_client_sec: OGREDACTEDBSUDHn

Obtaining the Custos client id and client secret requires first registering your Galaxy instance with Custos. Visit usecustos.org for more information.

Vault configuration for database

type: database
path_prefix: /galaxy
# Encryption keys must be valid fernet keys
# To generate a valid key:
# Use the ascii string value as a key
# For more details, see: https://cryptography.io/en/latest/fernet/#
  - 5RrT94ji178vQwha7TAmEix7DojtsLlxVz8Ef17KWgg=
  - iNdXd7tRjLnSqRHxuhqQ98GTLU8HUbd5_Xx38iF8nZ0=
  - IK83IXhE4_7W7xCFEtD9op0BAs11pJqYN236Spppp7g=

Secrets stored in the database are encrypted using Fernet keys. Therefore, all listed encryption keys must be valid fernet keys. To generate a new Fernet key, use the following Python code:

from cryptography.fernet import Fernet

If multiple encryption keys are defined, only the first key is used to encrypt secrets. The remaining keys are tried in turn during decryption. This is useful for key rotation. We recommend periodically generating a new fernet key and rotating old keys. However, before removing an old key, make sure that any data encrypted using that old key is no longer present or the data will no longer be decryptable.

Configuring user preferences to use the vault

The user_preferences_extra_conf.yml can be used to automatically route secrets to a vault. An example configuration follows:

        description: Your NextCloud account
            - name: password
              label: password
              type: password
              store: vault
              required: False

Note the store: vault property, which results in the property being stored in the vault. Note also that if you use type: password, the secret is sent to the client front-end, but specifying type: secret would mean that the values cannot be retrieved by the client, only written to, providing an extra layer of security.

Configuring file sources to use (user) secrets stored in a vault

In a file source the password could be used as follows:

- type: webdav
  id: nextcloud
  label: NextCloud
  doc: UFZ NextCloud files (configure access in user preferences)
  url: https://some-nextcloud.org
  root: /remote.php/dav/files/${user.username}/
  login: ${user.username}
  password: ${user.user_vault.read_secret('preferences/ufz-nextcloud/password')}

This example assumes that the NextCloud username is identical to the Galaxy username. If this is not the case also the username could be a user preference that is stored in a vault.