Quickstart

This page is the shortest route from source tree to a useful .2me archive.

What epi4you is for

The most important workflow today is:

  1. take an existing command-line Nextflow run,

  2. package it as a portable .2me archive, and

  3. import that archive into an EPI2ME-style environment elsewhere.

This is especially useful for:

  • training courses,

  • classroom laptops,

  • demo machines,

  • conference booths,

  • disconnected or low-bandwidth environments, and

  • sharing representative analyses with colleagues.

Build the binary

Clone the repository and build it with Cargo:

cargo build

Or run the CLI without a separate install:

cargo run -- --help

Package a local Nextflow run

If you already have a directory containing prior Nextflow runs, list them first:

cargo run -- nextflow-run \
    --nxf_work /data/nextflow_runs \
    --list

Once you know the run_name you want, bundle it:

cargo run -- nextflow-run \
    --nxf_work /data/nextflow_runs \
    --runid clever_ampere \
    --twome /tmp/clever_ampere.2me.tar

What happens during bundling

The CLI capture flow does more than tar up a folder.

It:

  • resolves the original analysis output directory,

  • finds the matching .nextflow.log entry,

  • extracts the log lines needed to reconstruct workflow metadata,

  • synthesizes helper files such as nextflow.stdout and progress.json,

  • stages output files into an EPI2ME-like layout, and

  • writes a manifest-driven .2me tarball.

Import the archive

On the target machine, import the bundle:

cargo run -- import --twome /tmp/clever_ampere.2me.tar

At import time, epi4you verifies the embedded manifest before unpacking and then routes the payload into local EPI2ME-style storage.

Install Sphinx docs locally

cargo build is now wired to generate the Sphinx documentation as part of the build process. The build tries local sphinx-build first and then falls back to a dedicated AlmaLinux 9 container image defined in docs/Dockerfile.docs.

To build the documentation directly yourself:

python3 -m venv .venv
. .venv/bin/activate
pip install -r docs/requirements.txt
make -C docs html

The generated HTML will be in docs/build/html.

If you explicitly need to skip documentation generation for one build, set:

EPI4YOU_SKIP_DOCS=1 cargo build