+h3. Other options
+
+Consult @application.default.yml@ for a full list of configuration options. Always put your local configuration in @application.yml@ instead of editing @application.default.yml@.
+
+h2. Configure Piwik
+
+In @/var/www/arvados-workbench/current/config@, copy @piwik.yml.example@ to @piwik.yml@ and edit to suit.
+
+h2. Prepare the Workbench deployment
+
+Now that all your configuration is in place, run @/usr/local/bin/arvados-workbench-upgrade.sh@. This will install and check your configuration, and install necessary gems.
+
+{% include 'notebox_begin' %}
+You can safely ignore the following error message you may see when installing gems:
+<notextile>
+<pre><code>themes_for_rails at /usr/local/rvm/gems/ruby-2.1.1/bundler/gems/themes_for_rails-1fd2d7897d75 did not have a valid gemspec.
+This prevents bundler from installing bins or native extensions, but that may not affect its functionality.
+The validation message from Rubygems was:
+ duplicate dependency on rails (= 3.0.11, development), (>= 3.0.0) use:
+ add_runtime_dependency 'rails', '= 3.0.11', '>= 3.0.0'
+Using themes_for_rails (0.5.1) from https://github.com/holtkampw/themes_for_rails (at 1fd2d78)
+</code></pre>
+</notextile>
+{% include 'notebox_end' %}
+
+This command aborts when it encounters an error. It's safe to rerun multiple times, so if there's a problem with your configuration, you can fix that and try again.
+
+h2. Set up Web server
+
+For best performance, we recommend you use Nginx as your Web server front-end, with a Passenger backend to serve Workbench. To do that:
+
+<notextile>
+<ol>
+<li>Install Nginx via your distribution or a backports repository.</li>
+
+<li><a href="https://www.phusionpassenger.com/documentation/Users%20guide%20Nginx.html">Install Phusion Passenger for Nginx</a>.</li>
+
+<li><p>Edit the http section of your Nginx configuration to run the Passenger server, and act as a front-end for it. You might add a block like the following, adding SSL and logging parameters to taste:</p>
+
+<pre><code>server {
+ listen 127.0.0.1:9000;
+ server_name localhost-workbench;
+
+ root /var/www/arvados-workbench/current/public;
+ index index.html index.htm index.php;
+
+ passenger_enabled on;
+ # If you're using RVM, uncomment the line below.
+ #passenger_ruby /usr/local/rvm/wrappers/default/ruby;
+}
+
+upstream workbench {
+ server 127.0.0.1:9000 fail_timeout=10s;
+}
+
+proxy_http_version 1.1;
+
+server {
+ listen <span class="userinput">[your public IP address]</span>:443 ssl;
+ server_name workbench.<span class="userinput">uuid-prefix.your.domain</span>;
+
+ ssl on;
+
+ index index.html index.htm index.php;
+
+ location / {
+ proxy_pass http://workbench;
+ proxy_redirect off;
+
+ proxy_set_header X-Forwarded-Proto https;
+ proxy_set_header Host $http_host;
+ proxy_set_header X-External-Client $external_client;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ }
+}
+</code></pre>
+</li>
+
+<li>Restart Nginx.</li>
+
+</ol>
+</notextile>