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Proxying Galaxy with Apache

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.

The Apache HTTP Server is a widely deployed and very featureful general purpose web server with mature proxying capabilities.

Instructions for proxying with NGINX, which is the proxy server used by The Galaxy Project’s public servers, usegalaxy.org (“Main”) and Test, as well as the Docker Galaxy project, 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

• Apache 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 Apache’s document root. By default, this would expose all of Galaxy (including datasets) to anyone on the web.

Apache Proxy Prerequisites

Currently, the only recommended way to proxy Galaxy with Apache is using mod_rewrite, mod_proxy, and mod_proxy_uwsgi. These modules must be enabled in the Apache config. The main proxy directives, ProxyRequests and ProxyVia do not need to be enabled.

Additionally, these directions are written for Apache 2.4+. Apache 2.4 for EL 6 can be obtained from the CentOS SCLo SIG Repo. Otherwise, your system package manager’s version of Apache should be suitable. On EL, you will need to enable the EPEL repository to obtain the mod_proxy_uwsgi package.

Caution

mod_uwsgi is not the same module as mod_proxy_uwsgi. The former is the old and unsupported module. Be sure that you have installed mod_proxy_uwsgi.

Ensure that the mod_headers, mod_rewrite, mod_proxy, and mod_proxy_uwsgi modules are loaded. Although not required, the configuration examples also use mod_deflate and mod_expires for increased client/server performance, so these should also be enabled.

On Debian you can install the necessary packages and enable the modules this with the following:

# apt-get install apache2 libapache2-mod-proxy-uwsgi
# a2enmod headers deflate expires rewrite proxy proxy_uwsgi
Enabling module headers.
Considering dependency filter for deflate:
Module filter already enabled
Module deflate already enabled
Enabling module expires.
Enabling module rewrite.
Enabling module proxy.
Considering dependency proxy for proxy_uwsgi:
Module proxy already enabled
Enabling module proxy_uwsgi.
To activate the new configuration, you need to run:
  service apache2 restart

And on EL:

# yum install httpd mod_proxy_uwsgi
# echo "LoadModule proxy_uwsgi_module modules/mod_proxy_uwsgi.so" > /etc/httpd/conf.modules.d/10-proxy-uwsgi.conf

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 Apache and Galaxy, rather than HTTP. Legacy instructions for proxying via HTTP can be found in the Galaxy Release 17.09 proxy documentation.

Since Apache 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.

The following configuration is not exhaustive, only the portions most relevant to serving Galaxy are shown, these should be incorporated with your existing/default Apache config as is appropriate for your server. Notably, the Apache 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.

SSLProtocol             all -SSLv3
SSLCipherSuite          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
SSLHonorCipherOrder     on
SSLCompression          off
SSLSessionTickets       off

# OCSP stapling
SSLUseStapling          on
SSLStaplingResponderTimeout 5
SSLStaplingReturnResponderErrors off
SSLStaplingCache        shmcb:/var/run/ocsp(128000)

<VirtualHost _default_:80> 
    Redirect permanent / https://galaxy.example.org
</VirtualHost>

<VirtualHost _default_:443>
    SSLEngine on
    SSLCertificateFile      /etc/apache2/ssl/server.crt
    SSLCertificateKeyFile   /etc/apache2/ssl/server.key

    # Enable HSTS
    Header always set Strict-Transport-Security "max-age=15552000; includeSubdomains"

    # use a variable for convenience
    Define galaxy_root /srv/galaxy/server

    # don't decode encoded slashes in path info
    AllowEncodedSlashes NoDecode

    # enable compression on all relevant types
    AddOutputFilterByType DEFLATE text/html text/plain text/xml
    AddOutputFilterByType DEFLATE text/css
    AddOutputFilterByType DEFLATE application/x-javascript application/javascript application/ecmascript
    AddOutputFilterByType DEFLATE application/rss+xml
    AddOutputFilterByType DEFLATE application/xml
    AddOutputFilterByType DEFLATE application/json

    # allow access to static content
    <Directory "${galaxy_root}/static">
        AllowOverride None
        Require all granted
    </Directory>

    # Galaxy needs to know that this is https for generating URLs
    RequestHeader set X-URL-SCHEME "%{REQUEST_SCHEME}e"

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

    # proxy all requests not matching other locations to uWSGI
    ProxyPass / unix:///srv/galaxy/var/uwsgi.sock|uwsgi://
    # or uWSGI on a TCP socket
    #ProxyPass / uwsgi://127.0.0.1:4001/

    # serve framework static content
    RewriteEngine On
    RewriteRule ^/static/(.*) ${galaxy_root}/static/$1 [L]
    RewriteRule ^/favicon.ico ${galaxy_root}/static/favicon.ico [L]
    RewriteRule ^/robots.txt ${galaxy_root}/static/robots.txt [L]

    # enable caching on static content
    <Location "/static">
        ExpiresActive On
        ExpiresDefault "access plus 24 hours"
    </Location>

    # serve visualization and interactive environment plugin static content
    <Directory "${galaxy_root}/config/plugins/(.+)/(.+)/static">
        AllowOverride None
        Require all granted
    </Directory>
    RewriteRule ^/plugins/(.+)/(.+)/static/(.*)$ ${galaxy_root}/config/plugins/$1/$2/static/$3 [L]
</VirtualHost>

Be sure to set galaxy_root to the path to your copy of Galaxy and modify the value of ProxyPass / 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 Apache configuration contains a line or included config file defining a default server, be sure to disable it by commenting its <VirtualHost> or preventing its inclusion (under Debian this is done by removing its symlink from /etc/apache2/sites-enabled).

• ProxyTimeout can be adjusted as appropriate for your site. This is the amount of time allowed for communication between Apache 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.

• If your Apache server is set up to use mod_security, you may need to modify the value of the SecRequestBodyLimit. The default value on some systems will limit uploads to only a few kilobytes.

• Some Galaxy URLs contain encoded slashes (%2F) in the path and Apache will not serve these URLs by default, which is the reason for inclusion of the AllowEncodedSlashes directive. Note: The NoDecode value was added in Apache2 2.2.18, which is newer than EL 6’s provided 2.2.15.

• If you must serve Galaxy without SSL, you would simply replace the 443 with 80 in the SSL VirtualHost block and remove the non-SSL block and all SSL directives.

• If the proxy works but you are getting 404 errors for Galaxy’s static content, be sure that the user that Apache 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 Apache config, prefix all of the location directives with your prefix, like so:

       #...
   
       # proxy all requests not matching other locations to uWSGI
       ProxyPass /galaxy unix:///srv/galaxy/var/uwsgi.sock|uwsgi://
       # or uWSGI on a TCP socket
       #ProxyPass /galaxy uwsgi://127.0.0.1:4001/
   
       # serve framework static content
       RewriteEngine On
       RewriteRule ^/galaxy/$ /galaxy [R,L]
       RewriteRule ^/galaxy/static/(.*) ${galaxy_root}/static/$1 [L]
       RewriteRule ^/galaxy/favicon.ico ${galaxy_root}/static/favicon.ico [L]
   RewriteRule ^/galaxy/robots.txt ${galaxy_root}/static/robots.txt [L]
   

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 (the uwsgi section in config/galaxy.yml) like so and restarting Galaxy:

   uwsgi:
       #...
       socket: /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()
   

   Note

   Older versions of Galaxy required you to set the cookie_path option. This is no longer necessary as of Galaxy release 19.05 as it is now set automatically, but the (now undocumented) option still remains and overrides the automatic setting. If you have this option set, unset it unless you know what you’re doing.

   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 Apache

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).

Apache can assume this task instead and, as an added benefit, speed up downloads. In addition, both the IGV genome browser and JBrowse tool (run within Galaxy) require support for the HTTP Range header, and this is only available if the proxy serves datasets. This is accomplished through the use of mod_xsendfile, a 3rd-party Apache module. Dataset security is maintained in this configuration because Apache will still check with Galaxy to ensure that the requesting user has permission to access the dataset before sending it.

To enable it, you must first install mod_xsendfile. This is usually available via your package manager (libapache2-mod-xsendfile on Debian and mod_xsendfile from EPEL on EL). Once installed, add the appropriate LoadModule directive to your Apache configuration (LoadModule xsendfile_module /path/to/mod_xsendfile.so, but both the Debian and EPEL packages do this for you upon installation).

The, add XSendFile directives to your proxy configuration:

<Location "/">
     XSendFile on
     XSendFilePath /
</Location>

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

galaxy:
    # ...
    apache_xsendfile: true

For this to work, the user under which your Apache 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 Apache 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 Apache user to the Galaxy group as shown above.

External user authentication

• Apache for External Authentication

• Built-in Galaxy External Authentication

Display Sites

Display sites such as UCSC work not by sending data directly from Galaxy to UCSC via the client’s browser, but by sending UCSC a URL to the data in Galaxy that the UCSC server will retrieve data from. Since enabling authentication will place all of Galaxy behind authentication, such display sites will no longer be able to access data via that URL. If display_servers is set to a non-empty value in $galaxy_root/config/galaxy.yml, this tells Galaxy it should allow the named servers access to data in Galaxy. However, you still need to configure Apache to allow access to the datasets. An example config is provided here that allows the UCSC Main/Test backends:

<Location "/root/display_as">
    Satisfy Any
    Order deny,allow
    Deny from all
    Allow from hgw1.cse.ucsc.edu
    Allow from hgw2.cse.ucsc.edu
    Allow from hgw3.cse.ucsc.edu
    Allow from hgw4.cse.ucsc.edu
    Allow from hgw5.cse.ucsc.edu
    Allow from hgw6.cse.ucsc.edu
    Allow from hgw7.cse.ucsc.edu
    Allow from hgw8.cse.ucsc.edu
</Location>

PLEASE NOTE that this introduces a security hole , the impact of which depends on whether you have restricted access to the dataset via Galaxy’s internal dataset permissions.

• By default, data in Galaxy is public. Normally with a Galaxy server behind authentication in a proxy server this is of little concern since only clients who’ve authenticated can access Galaxy. However, if display site exceptions are made as shown above, anyone could use those public sites to bypass authentication and view any public dataset on your Galaxy server. If you have not changed from the default and most of your datasets are public, you should consider running your own display sites that are also behind authentication rather than using the public ones.

• For datasets for which access has been restricted to one or more roles (i.e. it is no longer “public”), access for reading via external browsers is only allowed for a brief period, when someone with access permission clicks the “display at…” link. During this period, anyone who has the dataset ID would then be able to use the browser to view this dataset. Although such a scenario is unlikely, it is technically possible.