External Authentication


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

objectives 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.

requirements Requirements

time Time estimation: 30 minutes

Supporting Materials

last_modification Last modification: Nov 26, 2020


For this exercise we will use a basic password file method for authenticating - this is probably not a very useful method in production, but it demonstrates how the proxy server can be configured to provide the correct header to Galaxy, and how Galaxy integrates with upstream authentication providers. This same method can be used with NGINX and Apache modules for CAS or SAML authentication.


  1. Configuring Authentication
  2. Testing
  3. API access
  4. Reverting

Configuring Authentication

hands_on Hands-on: Configuring everything

  1. Edit the galaxy.j2 template file in the templates/nginx directory and update the main location block defined for serving galaxy. Add the parameters:
    • auth_basic galaxy;
    • auth_basic_user_file /etc/nginx/passwd;
    • uwsgi_param HTTP_REMOTE_USER $remote_user;

    It should look like:

    @@ -14,6 +14,10 @@
             uwsgi_param UWSGI_SCHEME $scheme;
             include uwsgi_params;
    +        auth_basic           galaxy;
    +        auth_basic_user_file /etc/nginx/passwd;
    +        uwsgi_param          HTTP_REMOTE_USER $remote_user;
    +        uwsgi_param          HTTP_GX_SECRET SOME_SECRET_STRING;
         # Static files can be more efficiently served by Nginx. Why send the

    auth_basic enables validation of username and password using the “HTTP Basic Authentication” protocol. Its value galaxy is used as a realm name to be displayed to the user when prompting for credentials. auth_basic_user_file specifies the file that keeps usernames and passwords. uwsgi_param adds HTTP_REMOTE_USER to the special variables passed by nginx to uwsgi, with value $remote_user, which is a nginx embedded variable containing the username supplied with the Basic authentication.

    GX_SECRET is added as a header for security purposes, to prevent any other users on the system impersonating nginx and sending requests to Galaxy. NGINX and other webservers like Apache will strip any user-sent REMOTE_USER headers, as that header defines the authenticated user. If you can talk directly to Galaxy (e.g. via curl) and provide the REMOTE_USER header, you can impersonate any other use. While having Galaxy listen on prevents any requests from outside of the system reaching Galaxy, anyone on the system can still send requests to that port. Here you can choose to switch to a unix socket with permissions only permitting Galaxy and Nginx to connect. GX_SECRET adds additional security as it needs to match remote_user_secret in your galaxy configutation.

    tip Proxy bypass

    Users can bypass the authentication only if they can talk directly to the uWSGI processes (if you have socket/http:, or if it is directly responsible for serving galaxy, and there is no proxy.) This can happen mostly when some users have command line access to the Galaxy server, which is considered a bad practice.

  2. Add a pre_task using the pip module which installs the library passlib, which is required for htpasswd.

    Add a pre_task using the htpasswd module which sets up a password file in /etc/nginx/passwd, with owner and group set to root, and a name and password, and a mode of 0640.

    question Question

    How does your final configuration look?

    solution Solution

    @@ -7,6 +7,15 @@
             name: galaxy
             state: restarted
    +    - pip:
    +        name: passlib
    +    - htpasswd:
    +        path: /etc/nginx/passwd
    +        name: user1        # Pick a username
    +        password: changeme # and a password
    +        owner: www-data    # nginx on centos
    +        group: root
    +        mode: 0640
         - name: Install Dependencies
             name: ['git', 'make', 'python3-psycopg2', 'virtualenv']
  3. Galaxy needs to be instructed to expect authentication to come from the upstream proxy. In order to do this, set the following two options in your Galaxy group variables:

        use_remote_user: true
        remote_user_maildomain: "{{ inventory_hostname }}"
        remote_user_secret: SOME_SECRET_STRING

    Set the remote_user_maildomain option to the appropriate domain name for your site.

  4. Run the playbook

comment Access denied

If you see this message, it is because nginx is not correctly sending the REMOTE_USER or the GX_SECRET values.

access denied message


You should now be presented with a password dialog when attempting to load the Galaxy UI.

hands_on Hands-on: Testing

  1. Log in using the username and password you provided when creating the passwd file. If your username and the value of remote_user_maildomain match an existing user, you will be logged in to that account. If not, a new account will be created for that user.

  2. Click on the “User” menu at the top, to see how the username appears.

  3. Note that some user features are not available when remote user support is enabled.

    Try logging out by selecting User -> Logout. You will discover that when returning to the user interface, you are still logged in. This is because Galaxy has no way of logging you out of the proxy’s authentication system. Instead, you should set remote_user_logout_href in galaxy.yml to point to the URL of your authentication system’s logout page.

API access

If you wish your Galaxy to be accessible to command line clients (e.g. bioblend, blend4j, parsec), you will need to add an exception for authentication on the API. Galaxy will still be secure and protected, but non-browser access will be permitted with an API key.

location /api/ {
    satisfy any;
    allow all;

tip Notification of Registration

There is no built-in way to be notified if users are registered, with external authentication or built-in. However, you could automate this easily. There is a gxadmin command we use called gxadmin query latest-users which Björn uses often. Other sites have other methods, e.g. Nicola’s cron script which runs daily on his server, to add new users to a group according to their email domain name.


We don’t want to leave Galaxy this way for the rest of our workshop.

hands_on Hands-on: Reverting the changes

  1. Edit your group variables file and comment out:

    • the NGINX changes
    • use_remote_user: true
  2. Run the playbook

keypoints Key points

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


Did you use this material as an instructor? Feel free to give us feedback on how it went.

Click here to load Google feedback frame

Citing this Tutorial

  1. Nate Coraor, Nicola Soranzo, Helena Rasche, 2020 External Authentication (Galaxy Training Materials). /training-material/topics/admin/tutorials/external-auth/tutorial.html Online; accessed TODAY
  2. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

details BibTeX

    author = "Nate Coraor and Nicola Soranzo and Helena Rasche",
    title = "External Authentication (Galaxy Training Materials)",
    year = "2020",
    month = "11",
    day = "26"
    url = "\url{/training-material/topics/admin/tutorials/external-auth/tutorial.html}",
    note = "[Online; accessed TODAY]"
        doi = {10.1016/j.cels.2018.05.012},
        url = {https://doi.org/10.1016%2Fj.cels.2018.05.012},
        year = 2018,
        month = {jun},
        publisher = {Elsevier {BV}},
        volume = {6},
        number = {6},
        pages = {752--758.e1},
        author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{\i}}rez and Devon Ryan and Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Björn Grüning},
        title = {Community-Driven Data Analysis Training for Biology},
        journal = {Cell Systems}

congratulations Congratulations on successfully completing this tutorial!