+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
+
+{% include 'install_nginx_workbench' %}