The ELIXIR-on-Cloud project is an initiative from the ELIXIR Compute Platform. Our goal is to support scientists across Europe in using cloud environments for their research activities. We support the use of ELIXIR services as well as open-source software, and the project has close connections with various academic cloud providers. One of our key focuses is developing and providing software that implements the specifications defined by the Global Alliance for Genomics and Health (GA4GH) for federated processing of workloads ([GA4GH Cloud Work Stream][ga4gh-cloud-ws]). This documentation offers guidance and best practices on how to use the services, further develop our services, and deploy services within the ELIXIR-on-Cloud Framework.