I am not sure whether to run with Docker or run locally. Which one should I choose?

Use this quick comparison to choose a run mode.

Mode	Good	Bad	Best for
Docker run	Fastest setup; reproducible environment; fewer dependency/version issues; easier onboarding for new users	Docker install required; container startup overhead; file mounts/permissions can be confusing; less convenient for editing internals	First-time users, tutorials, shared team workflows, reproducible reruns
Local run	Direct access to local files/tools; easier debugging and profiling; no container boundary; easier to customize and extend	More setup effort; dependency conflicts are more likely; environments can drift across machines	Power users, developers, custom pipelines, tight integration with local tooling/HPC modules

Quick decision rule

• Choose Docker if your priority is getting started quickly and reproducibly.

• Choose local if your priority is deep customization, debugging, or development.

• Docker guide: Run with Docker

• Local guide: Run Locally

Choosing an interface (not a run mode)

This page is about where to run (Docker vs local). For which command to drive the pipeline — run_together vs run_xenium/run_visiumhd vs individual modules — see Which interface should I use?.