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Proxying Galaxy with NGINX

In a production environment, it is recommended to run Galaxy behind a proxy web server for performance and security reasons. The proxy server sits between clients and your Galaxy server, relaying requests between them and offloading some of the more menial and resource-intensive tasks.

NGINX is a lightweight HTTP server designed with high performance proxying in mind. The Galaxy Project’s public servers, usegalaxy.org (“Main”) and Test, as well as the Docker Galaxy project use NGINX, rather than Apache, to proxy Galaxy. NGINX was chosen for its simple, fast load balancing and other proxy-oriented features.

Instructions for proxying with Apache are also available.

Prerequisites

This documentation should be used in conjunction with the Scaling and Load Balancing documentation, which you should familiarize yourself with prior to setting up your proxy.

You will need to ensure that inbound (and outbound) traffic on the HTTP (TCP port 80) and HTTPS (TCP port 443) ports is permitted by your server’s firewall/security.

Documentation Conventions:

For the purposes of this example, we assume that:

  • Debian refers to any Debian-based Linux distribution (including Ubuntu)
  • EL refers to any RedHat Enterprise Linux-based Linux distribution (including CentOS)
  • the Galaxy server is installed at /srv/galaxy/server
  • nginx runs as the user www-data (this is the default under Debian)
  • Galaxy runs as the user galaxy with primary group galaxy
  • Galaxy is served from the hostname galaxy.example.org

Throughout the configuration examples in this document, in order to avoid repetition, #... is used to denote a location where existing or previously given configuration statements would appear.

Danger

Please note that Galaxy’s files - code, datasets, and so forth - should never be located on disk inside nginx’s document root. By default, this would expose all of Galaxy (including datasets) to anyone on the web.

NGINX Proxy Prerequisities

If you plan to use nginx to handle your file uploads, you will (most likely) not be able to use your package manager’s version of nginx. The Receiving Files With NGINX section explains this in detail and provides some options for installing nginx + upload module packages maintained by the Galaxy Committers Team.

Otherwise, your system package manager’s version of nginx should be suitable. Under Debian, the nginx-light package contains all the necessary modules used in this guide. On EL, the EPEL version of nginx is suitable.

Basic Configuration

The use of SSL is strongly encouraged to avoid exposure of confidential information such as datasets and user credentials to eavesdroppers. The instructions in this document are for setting up an SSL-enabled Galaxy server.

When setting up an SSL server, simply enabling SSL with the default options is not enough to have a secure server. In most cases, the configuration is weak and vulnerable to one or more of the multitude of SSL attacks that have been recently prevalent. The Qualys SSL/TLS Deployment Best Practices is an excellent and up-to-date guide covering everything necessary for securing an SSL server. In addition, the Mozilla SSL Configuration Generator can provide you with a best practices config tailored to your desired security level and software versions.

Finally, Google’s PageSpeed Insights tool is helpful for determining how you can improve responsiveness as related to proxying, such as verifying that caching and compression are configured properly.

If you need to run more than one site on your Galaxy server, there are two options:

  • Run them on the same server but serve them on different hostnames
  • Serve them from different URL prefixes on a single hostname

The former option is typically cleaner, but if serving more than one SSL site, you will need an SSL certificate with subjectAltNames for each hostname served by the server.

Serving Galaxy at the Web Server Root

This configuration assumes that Galaxy will be the only site on your server using the given hostname (e.g. https://galaxy.example.org).

Beginning with Galaxy Release 18.01, the default application server that Galaxy runs under is uWSGI. Because of this, the native high performance uWSGI protocol should be used for communication between nginx and Galaxy, rather than HTTP. Legacy instructions for proxying via HTTP can be found in the Galaxy Release 17.09 proxy documentation.

Since nginx is more efficient than uWSGI at serving static content, it is best to serve it directly, reducing the load on the Galaxy process and allowing for more effective compression (if enabled), caching, and pipelining. Directives to do so are included in the example below.

uWSGI protocol support is built in to nginx, so (unlike Apache) no extra modules or recompiling should be required.

The following configuration is not exhaustive, only the portions most relevant to serving Galaxy are shown, these should be incorporated with your existing/default nginx config as is appropriate for your server. Notably, the nginx package you installed most likely has a multi-file config layout. If you are not already familiar with that layout and where best to place your configuration, you can learn more in the Proxy Package Layouts documentation.

http {

    #...

    # compress responses whenever possible
    gzip on;
    gzip_http_version 1.1;
    gzip_vary on;
    gzip_comp_level 6;
    gzip_proxied any;
    gzip_types text/plain text/css application/json application/x-javascript text/xml application/xml application/xml+rss text/javascript;
    gzip_buffers 16 8k;

    # allow up to 3 minutes for Galaxy to respond to slow requests before timing out
    uwsgi_read_timeout 180;

    # maximum file upload size
    client_max_body_size 10g;

    # allowable SSL protocols
    ssl_protocols TLSv1 TLSv1.1 TLSv1.2;

    # use secure ciphers
    ssl_ciphers
    ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-ECDSA-AES128-SHA:ECDHE-ECDSA-AES256-SHA:ECDHE-ECDSA-AES128-SHA256:ECDHE-ECDSA-AES256-SHA384:ECDHE-RSA-AES128-GCM-SHA256:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-RSA-AES128-SHA:ECDHE-RSA-AES256-SHA:ECDHE-RSA-AES128-SHA256:ECDHE-RSA-AES256-SHA384:DHE-RSA-AES128-GCM-SHA256:DHE-RSA-AES256-GCM-SHA384:DHE-RSA-AES128-SHA:DHE-RSA-AES256-SHA:DHE-RSA-AES128-SHA256:DHE-RSA-AES256-SHA256;
    ssl_dhparam /etc/nginx/ssl/dhparams.pem;
    ssl_prefer_server_ciphers on;

    # enable session reuse
    ssl_session_cache shared:SSL:8m;
    ssl_session_timeout 5m;

    # cert/key
    ssl_certificate /etc/nginx/ssl/server.crt;
    ssl_certificate_key /etc/nginx/ssl/server.key;

    # OCSP stapling
    ssl_stapling on;
    ssl_stapling_verify on;
    ssl_trusted_certificate /etc/nginx/ssl/ca.crt;


    server {
        listen 80 default_server;
        listen [::]:80 default_server;
        server_name _;

        return 301 https://$host$request_uri;
    }

    server {
        listen 443 default_server;
        listen [::]:443 default_server;
        server_name _;

        # use a variable for convenience
        set $galaxy_root /srv/galaxy/server;

        # Enable HSTS
        add_header Strict-Transport-Security "max-age=15552000; includeSubdomains";

        # proxy all requests not matching other locations to uWSGI
        location / {
            uwsgi_pass unix:///srv/galaxy/var/uwsgi.sock
            uwsgi_param UWSGI_SCHEME $scheme;
            include uwsgi_params;
        }

        # serve framework static content
        location /static/style {
            alias $galaxy_root/static/style/blue;
            expires 24h;
        }
        location /static {
            alias $galaxy_root/static;
            expires 24h;
        }
        location /robots.txt {
            alias $galaxy_root/static/robots.txt;
            expires 24h;
        }
        location /favicon.ico {
            alias $galaxy_root/static/favicon.ico;
            expires 24h;
        }

        # serve visualization and interactive environment plugin static content
        location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ {
            alias $galaxy_root/config/plugins/$plug_type/$vis_name/static/$static_file;
            expires 24;
        }
    }
}

Be sure to set $galaxy_root to the path to your copy of Galaxy and modify the value of uwsgi_pass to match your uWSGI socket path. With the default configuration, uWSGI will bind to a random TCP socket, so you will need to set it to a fixed value as described in the Scaling and Load Balancing documentation. If using a UNIX domain socket, be sure to pay particular attention to the discussion of users and permissions.

Additional Notes

  • Do not simply copy the SSL configuration directives and expect them to work on your server or to be secure! These are provided as examples of some of the best practices as of the time of writing, but will not always be up to date. Use the guides referenced in basic configuration section to configure SSL properly.
  • If your existing nginx configuration contains a line or included config file defining a default server, be sure to disable it by commenting its server {} or preventing its inclusion (under Debian this is done by removing its symlink from /etc/nginx/sites-enabled).
  • uwsgi_read_timeout can be adjusted as appropriate for your site. This is the amount of time allowed for communication between nginx and uWSGI to block while waiting for a response from Galaxy, and is useful for holding client (browser) connections while uWSGI is restarting Galaxy subprocesses or Galaxy is performing a slow operation.
  • The parameter client_max_body_size specifies the maximum upload size that can be handled by POST requests through nginx. You should set this to the largest file size that you wish to allow for upload and that could be reasonably handled by your site. It defaults to 1MB, so it will need to be increased if you are dealing with genome sized datasets.
  • If you must serve Galaxy without SSL, you would simply replace the listen directives in the SSL server {} block with the listen directives from the non-SSL server {} block and remove the non-SSL block and SSL directives from the http {} block.
  • If the proxy works but you are getting 404 errors for Galaxy’s static content, be sure that the user that nginx runs as has access to Galaxy’s static/ directory (and all its parent directories) on the filesystem. You can test this on the command line with e.g. sudo -u www-data ls /srv/galaxy/server/static.

Serving Galaxy at a URL Prefix

It may be necessary to serve Galaxy from an address other than the web server root (https://www.example.org/galaxy), instead of https://galaxy.example.org). To do this, you need to make the following changes to the configuration in the previous section:

  1. In the nginx config, prefix all of the location directives with your prefix and redirect requests from /prefix to /prefix/ like so:

            #...
    
            # proxy all requests not matching other locations to uWSGI
            location /galaxy {
                uwsgi_pass unix:///srv/galaxy/var/uwsgi.sock
                uwsgi_param UWSGI_SCHEME $scheme;
                include uwsgi_params;
            }
    
            # serve framework static content
            location /galaxy/static/style {
                alias $galaxy_root/static/style/blue;
                expires 24h;
            }
    
            # additional static locations...
    
            # redirect /prefix -> /prefix/
            rewrite ^/galaxy$ /galaxy/ last;
    
  2. The Galaxy application needs to be aware that it is running with a prefix (for generating URLs in dynamic pages). This is accomplished by configuring uWSGI and Galaxy (the uwsgi and galaxy sections in config/galaxy.yml respectively) like so and restarting Galaxy:

    uwsgi:
        #...
        socket: unix:///srv/galaxy/var/uwsgi.sock
        mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
        manage-script-name: true
        # `module` MUST NOT be set when `mount` is in use
        #module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
    
    galaxy:
        #...
        cookie_path: /galaxy
    

    cookie_path should be set to prevent Galaxy’s session cookies from clobbering each other if you are running more than one instance of Galaxy under different URL prefixes on the same hostname.

    Be sure to consult the Scaling and Load Balancing documentation, other options unrelated to proxying should also be set in the uwsgi section of the config.

Advanced Configuration Topics

Sending Files With Nginx

Galaxy sends files (e.g. dataset downloads) by opening the file and streaming it in chunks through the proxy server. However, this ties up the Galaxy process, which can impact the performance of other operations (see Production Server Configuration for a more in-depth explanation).

Nginx can assume this task instead and as an added benefit, speed up downloads. This is accomplished through the use of the special X-Accel-Redirect header. Dataset security is maintained in this configuration because nginx will still check with Galaxy to ensure that the requesting user has permission to access the dataset before sending it.

To enable it, add the following to your Galaxy’s server {} block:

        location /_x_accel_redirect/ {
            internal;
            alias /;
        }

Next, edit galaxy.yml and make the following change before restarting Galaxy:

galaxy:
    #...
    nginx_x_accel_redirect_base: '/_x_accel_redirect'

For this to work, the user under which your nginx server runs will need read access to Galaxy’s files_path directory (by default, database/files/) and its contents. This is most easily done by adding the nginx user to the Galaxy user’s primary group and setting the umask(2) to create files with the group read permission set. If you start Galaxy from the command line, you can do this like so:

admin@server$ sudo usermod -a -G galaxy www-data    # add `www-data` user to `galaxy` group
admin@server$ sudo -iu galaxy
galaxy@server$ umask 027
galaxy@server$ sh run.sh

If you start Galaxy from supervisord, you can set the umask option in the program section after adding the nginx user to the Galaxy group as shown above.

Receiving Files With Nginx

Galaxy receives files (e.g. dataset uploads) by streaming them in chunks through the proxy server and writing the files to disk. However, this again ties up the Galaxy process. nginx can assume this task instead and as an added benefit, speed up uploads. This is accomplished through the use of nginx_upload_module, a 3rd-party nginx module.

To enable it, you must first download, compile and install nginx with the upload module, since prior to NGINX 1.11.5, nginx did not support shared modules, and the upload module is not yet shared-compatible. Because this is a tedious and complicated process, the Galaxy Committers team maintains (for some platforms) versions of nginx modified from their upstream package sources (APT, EPEL, etc.) to include the upload module:

To contribute support for additional platforms, please see the Galaxy Starforge project, which is used to do the repackaging.

Once nginx with the upload module is installed, create a directory in which to store uploads (ideally, for performance reasons, on the same filesystem as Galaxy’s datasets) and add the necessary directives to nginx.conf:

user galaxy;

http {

    #...

    server {

        #...

        # handle file uploads via the upload module
        location /_upload {
            upload_store /srv/galaxy/upload_store;
            upload_store_access user:rw group:rw;
            upload_pass_form_field "";
            upload_set_form_field "__${upload_field_name}__is_composite" "true";
            upload_set_form_field "__${upload_field_name}__keys" "name path";
            upload_set_form_field "${upload_field_name}_name" "$upload_file_name";
            upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path";
            upload_pass_args on;
            upload_pass /_upload_done;
        }

        # once upload is complete, redirect to the proper galaxy path
        location /_upload_done {
            set $dst /api/tools;
            if ($args ~ nginx_redir=([^&]+)) {
                set $dst $1;
            }
            rewrite "" $dst;
        }
}

Note the user directive at the top, outside of the http {} block. To ensure that Galaxy has write permission on the uploaded files, nginx’s workers will need to run as the same user as Galaxy.

When serving Galaxy at a URL prefix as described in the Serving Galaxy at a URL prefix section, you will need to change set $dst /api/tools; to set $dst /prefix/api/tools; (e.g. set $dst /galaxy/api/tools;).

Finally, edit galaxy.yml and make the following change before restarting Galaxy:

galaxy:
    #...
    nginx_upload_store: /srv/galaxy/upload_store
    nginx_upload_path: '/_upload'

Use Galaxy Authentication to Protect Custom Paths

You may find it useful to require authentication for access to certain paths on your server. For example, Galaxy can run a separate reports app which gives useful information about your Galaxy instance. See the Reports Configuration documentation and Peter Briggs’ blog post on the subject for more.

After succesfully following the blog post, Galaxy reports should be available at e.g. https://galaxy.example.org/reports. To secure this page to only Galaxy administrators, adjust your nginx config accordingly:

TODO: This is not valid for the uWSGI proxy method and needs to be updated. -nate 2018-01-11

        location /reports {
            #...
            satisfy any;            # only one auth method needs to succeed
            deny all;               # host-based auth is not allowed
            auth_request /_auth;    # forward authentication
        }

        location /_auth {
            #internal; probably?
            # The used galaxy api endpoint is only available to galaxy admins and thus limits the access
            # to only logged in admins.
            proxy_pass http://localhost/api/configuration/dynamic_tool_confs;
            proxy_pass_request_body off;
            proxy_set_header Content-Length "";
            proxy_set_header X-Original-URI $request_uri;
        }