+
+h2. Prepare the API server deployment
+
+Now that all your configuration is in place, run @/usr/local/bin/arvados-api-server-upgrade.sh@. This will install and check your configuration, install necessary gems, and run any necessary database setup.
+
+{% include 'notebox_begin' %}
+You can safely ignore the following messages if they appear while this script runs:
+<pre>Don't run Bundler as root. Bundler can ask for sudo if it is needed, and installing your bundle as root will
+break this application for all non-root users on this machine.</pre>
+<pre>fatal: Not a git repository (or any of the parent directories): .git</pre>
+{% 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.
+