External Authentication

Contributors

Authors: Martin Čech Nicola Soranzo

Questions

• How can I connect Galaxy with CAS, SAML, etc.

Objectives

• be familiar with configuring Galaxy to use an upstream (proxy) authentication provider

• be able to log in to your Galaxy server with a file-configured user.

Auth Mechanisms supported

• Galaxy-specific account database
• HTTP remote user provided by a reverse proxy server
• Galaxy authentication framework (LDAP/AD, PAM)

Galaxy account

• Stored in the Galaxy DB
  • Unique in both email and username
  • Passwords hashed and salted, using PBKDF2 (default)
  • Table galaxy_user
  • Abstracted as User in lib/galaxy/model/mapping.py
• Session cookie expires after 3 months
  • Configurable with session_duration
• Password reset uses ‘visit-link’ mechanism
• require_login can be set to disable anonymous access

Authentication tweaks

In galaxy.yml:

• Activation
  • user_activation_on will prevent accounts from running jobs until they visit activation link
  • activation_grace_period gives users some time before their jobs are ignored
  • inactivity_box_content defines the message shown to inactive users
• Expiration
  • password_expiration_period forces users to change password
• Disposable domain blacklist
  • blacklist_file defines domains (e.g. example.org) that will be rejected as user emails

Speaker Notes https://github.com/martenson/disposable-email-domains

Reverse proxy

In galaxy.yml:

• Set use_remote_user: true to delegate authentication to the upstream proxy server
  • The proxy server should set the REMOTE_USER HTTP header
  • Disables regular logins

Dedicated Galaxy external auth documentation.

General configuration

• If the proxy server returns only usernames, set remote_user_maildomain to a default mail domain to be appended
• If a client can bypass the proxy, it can impersonate any user by forging the REMOTE_USER HTTP header:
  • Configure the proxy server to define a GX_SECRET header and set remote_user_secret to the same value
• Set remote_user_logout_href to point to your logout URL

Nginx

• Modules exist for PAM, Kerberos and LDAP.
• Most likely you’ll need to recompile Nginx as none of them are included by default.

Example PAM stack

• You need to set up your system’s PAM stack (very site-specific)
• A PAM configuration that would be suitable for authentication with Kerberos (placed in /etc/pam.d/nginx) might look like:

  auth  [success=1 default=ignore]  pam_krb5.so minimum_uid=1000 ignore_k5login
  auth  requisite                   pam_deny.so
  auth  required                    pam_permit.so
  

Example nginx.conf

location / {
    auth_pam "Basic Auth Realm Name";
    auth_pam_service_name "nginx";
    ...
    proxy_set_header REMOTE_USER $remote_user;
}

The value of auth_pam_service_name must match the filename of the pam configuration you created in /etc/pam.d/ .

Dedicated Galaxy with Nginx documentation.

Apache httpd

The authentication module (basic authentication, mod_auth_kerb, mod_authnz_ldap, mod_auth_cas, Cosign, etc.) is responsible for providing a username, which we will pass through the proxy to Galaxy as $REMOTE_USER.

In addition to the modules above, mod_headers must be enabled in the Apache config, for some types of authentication.

Dedicated Galaxy with Apache documentation.

Galaxy Authentication Framework

Authenticate to external services directly in Galaxy

Available provider modules for:

• Local Galaxy DB (default)
• LDAP/Active Directory
• System (Linux) PAM

Key Points

• Remote auth is not complex to set up and can help you meet institutional requirements

Thank you!