Authentication

Galaxy supports the following authentication mechanisms:

Galaxy Database

Without any additional configuration Galaxy will simply use its database to maintain usernames and passwords. The Galaxy user interface and API provide functions allowing users to register accounts, change passwords, etc....

If deploying Galaxy using the default authentication option, user activation can be enabled also. This is documented below.

Authentication Framework

Galaxy is distributed with a plugin-driven authentication framework for which the default database authentication is just one (and the default plugin). This framework can be used to allow Galaxy to delegate authentication to an LDAP server, an Active Directory server, or to PAM.

These same mechanisms can also be configured by proxies serving Galaxy (e.g. nginx or Apache), but configuring them within Galaxy allows users to use the Galaxy UI for logging in instead of relying on a proxy.

To configure one or more authentication plugins, simply copy config/auth_conf.xml.sample to config/auth_conf.xml. The provided sample configuration file has numerous commented out examples and serves as the most up-to-date source of documentation on configuring these plugins.

OpenID

OpenID is becoming less popular and probably shouldn’t be used the primary mechanism for authentication in Galaxy but it is an available option.

Enabling OpenID requires you to edit Galaxy’s configuration file and set enable_openid to True. This file is likely located in config/galaxy.ini and can be created by copying Galaxy’s sample config/galaxy.ini.sample.

Enabling this option enables OpenID and causes the OpenID form to be displayed on the login screen.

Remote User Authentication

If Galaxy is deployed with either nginx or Apache serving as a front-end proxy for Galaxy requests, they can be configured to authenticate users and pass this authentication information along to Galaxy using the HTTP remote user mechanism. See, for example, the authentication and authorization guide for the Apache Web server for an impression of the possibilities. Thus, by the time Galaxy is aware of a request, the user identity will have been determined and there will be no need for Galaxy to do any additional authentication work, such as showing a login screen or checking user credentials.

However, accepting an identity asserted by the Web server does not relieve Galaxy from having to create a user account for such an identity. Thus, Galaxy automatically creates a user for each identity of this kind, recording that the user is “external” and also creating a random password in order to effectively disable traditionally performed logins for the user, although the remote user mechanism should normally prohibit any login mechanism other than that imposed by the Web server, and the “external” flag should itself prohibit the traditional mechanism being used with the user concerned. When a remote user returns to Galaxy and is not already logged in, the details of the user are retrieved according to the identity information supplied by the Web server.

Enabling remote user authentication requires you to edit Galaxy’s configuration file and set use_remote_user to True. This file is likely located in config/galaxy.ini and can be created by copying Galaxy’s sample config/galaxy.ini.sample.

Additional Galaxy configuration options related to remote user authentication are documented in Galaxy’s sample configuration file. The options remote_user_maildomain, remote_user_header, and normalize_remote_user_email can adapt Galaxy to different responses from the proxy, while remote_user_secret can be used to provide added security, and remote_user_logout_href can be used to fix Galaxy’s logout for the deployed setup.

User Activation

Galaxy admins using the default authentication mechanism have an option to turn on the email verification feature to force users to provide working email during the registration. You can also turn on the disposable email domains filter to disable registration for users using known disposable email provider.

How to set up this config is presented here.

Note: SQLite database is not supported with this feature. Please use PostgreSQL.

Account activation feature

In the Galaxy config file config/galaxy.ini there is the user activation setting that you have to turn on.

user_activation_on = True

There is also the option for tracking jobs in database that is required to be turned on for the account activation to be effective. By default it is off.

track_jobs_in_database = True

After you turn on both of these every user that will try to register after this configuration file takes effect will have the verification email sent to the email address provided. Unless the Grace period (see below) is set, the user won’t be able to login before the verification happens.

Furthermore in order for this to work correctly smtp server and admin email should be set:

#smtp_server = some.server.edu:587
#smtp_username = example_username
#smtp_password = example_passsword
#activation_email = activation-noreply@example.com
#error_email_to = admin@example.com

Smtp server takes care of the email sending and the activation_email email is used as the From address in the verification email. Furthermore the error_email_to is being shown to the user if the Galaxy detects its own misconfiguration.

You can also set the instance_resource_url which is shown in the activation emails so you can point users to your wiki or other materials.

instance_resource_url = http://wiki.galaxyproject.org/

The final activation email looks like this:

Hello <user_name>,

In order to complete the activation process for <user_email> begun on <date> at <hostname>, please click on the following link to verify your account:

test.galaxyproject.org/activate?activation_token=46701ecdbbf2a79a7348ddae33062774edadef59&email=example%40example.com

By clicking on the above link and opening a Galaxy account you are also confirming that you have read and agreed to Galaxy's Terms and Conditions for use of this service (<link_to_terms_config>). This includes a quota limit of one account per user. Attempts to subvert this limit by creating multiple accounts or through any other method may result in termination of all associated accounts and data.

Please contact us if you need help with your account at: <error_email_to_config>. You can also browse resources available at: <instance_resources_url_config>.

More about the Galaxy Project can be found at galaxyproject.org

Your Galaxy Team

Changing email address

If an activated user changes email address in user settings, his/her account will be deactivated. A new activation link will be sent and the user will have to visit it to activate the account again.

Grace period

In case you want the account activation feature but don’t want to disable login completely you can set the activation_grace_period parameter. It specifies, in hours, the period in between registration time and the login time that the user will be allowed to log in even with an inactive account.

# Activation grace period. Activation is not forced (login is not disabled) until 
# grace period has passed. Users under grace period can't run jobs (see inactivity_box_content).
# In hours. Default is 3. Enter 0 to disable grace period. 
# Users with OpenID logins have grace period forever. 
#activation_grace_period = 3

However with inactive account the user won’t be able to run jobs and warning message will be shown to him at the top of the page. It is customizable via the inactivity_box_content parameter.

# Used for warning box for inactive accounts (unable to run jobs).
# In use only if activation_grace_period is set.
#inactivity_box_content = Your account has not been activated yet. Please activate your account by verifying your email address. For now you can access everything at Galaxy but your jobs won't run.

Disposable email address filtering

To prevent users from using disposable email addresses as a workaround for the email verification the domain blacklist can be turned on through the blacklist_file path parameter. Users that use disposable email domains defined at the file in this provided path will be refused registration.

# E-mail domains blacklist is used for filtering out users that are using disposable email address
# during the registration. If their address domain matches any domain in the BL they are refused the registration.
blacklist_file = config/disposable_email_blacklist.conf

Disposable domains blacklist file for download and modification is at GitHub

In the file each domain is on its own line and without the @ sign. Example of the blacklist file format:

drdrb.com
mailinator.com
sogetthis.com
spamgourmet.com
trashmail.net
kurzepost.de
objectmail.com
proxymail.eu
rcpt.at
trash-mail.at
trashmail.at
trashmail.me
wegwerfmail.de
wegwerfmail.net
wegwerfmail.org