BOSH operates at a lower level, working with VMs. Flynn is higher level and allows deployment and management of applications and databases in containers.

Instead of relying on a lower layer like BOSH, Flynn is self-bootstrapping and self-hosting. It runs everything except the container runner in containers managed by the platform. The same APIs and tools are used to manage user applications and Flynn components.

For more information, check out our Architecture page: https://flynn.io/docs/architecture

You can bring your own lower level infrastructure, like IaaS or bare metal. There is a cloud installer that can spin up a cluster to try out on EC2, Azure, or Digital Ocean, but most production users are using whatever management tools they are comfortable with to deploy and scale Flynn hosts out.

Also, what's the difference to dokku or deis?

Both Dokku and Deis focus on stateless webapps.

Dokku is explicitly single-host. Flynn can run in a single-host configuration but typically deployed in a highly available configuration with three or more hosts.

Flynn is designed to tackle some much bigger problems and supports running and managing highly available databases inside the platform out of the box in addition to stateless web apps.

As Titanous said, BOSH operates at a lower level than Flynn. You could use BOSH to deploy Flynn, hypothetically. A more direct comparison would be Cloud Foundry.

BOSH would be ideal for managing a Flynn cluster.

At Pivotal we're seeing multi-thousand VM instances of Cloud Foundry that BOSH deploys and updates gracefully.