epi4you documentation

epi4you is a toolkit for moving Oxford Nanopore EPI2ME assets between machines and contexts, especially when portability matters more than a perfect reproduction of the original workstation.

The original motivation for the project was practical: lifting over bioinformatics assets for training courses, demonstrations, workshops, and conference deployments. In those situations you often need more than a single results folder. You need the workflow context, the expected metadata shape, and sometimes the associated software artefacts as well.

This documentation is organized around that use case:

• get a quick success path first,

• understand why the archive model exists,

• see how the CLI maps a raw Nextflow run into something EPI2ME Desktop can import, and

• learn where the codebase stores those responsibilities.

Guide

• Quickstart
  • What epi4you is for
  • Build the binary
  • Package a local Nextflow run
  • What happens during bundling
  • Import the archive
  • Install Sphinx docs locally
  • What to read next
• Why epi4you exists
  • The practical problem
  • epi4you’s answer
  • Why the project is broader than the current CLI
  • Audience
• Training courses and asset liftover
  • Why training environments are awkward
  • How epi4you helps
  • Typical course-preparation pattern
  • What to package
  • What this does not replace
• CLI reference
  • Package a CLI Nextflow run
  • Import an archive
  • Notes on older capabilities
• The .2me archive model
  • What the archive contains
  • Manifest responsibilities
  • Payload types
  • Why manifests matter for liftover
  • Current integrity model
• Architecture
  • High-level flow
  • Main areas of the codebase
  • Design intent
  • Relationship to the broader repository
• Developer documentation builds
  • Build behavior
  • Why use a container
  • Skipping docs intentionally
  • Relevant files
  • Publishing to GitHub Pages

Indices and tables

• Index

• Search Page