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oxo-flow package#

Package a workflow into a container image definition (Dockerfile or Singularity definition file).

Usage#

oxo-flow package [OPTIONS] <WORKFLOW>

Arguments#

Argument Description
<WORKFLOW> Path to the .oxoflow workflow file

Options#

Option Short Default Description
--format -f docker Container format: docker or singularity
--output -o stdout Output file path
--verbose -v — Enable debug-level logging

Examples#

Generate a Dockerfile#

oxo-flow package pipeline.oxoflow

Write Dockerfile to a file#

oxo-flow package pipeline.oxoflow -o Dockerfile

Generate a Singularity definition#

oxo-flow package pipeline.oxoflow -f singularity -o pipeline.def

Build the container#

# Docker
oxo-flow package pipeline.oxoflow -o Dockerfile
docker build -t my-pipeline:1.0.0 .

# Singularity
oxo-flow package pipeline.oxoflow -f singularity -o pipeline.def
singularity build pipeline.sif pipeline.def

Output#

Dockerfile example#

FROM ubuntu:22.04
LABEL maintainer="oxo-flow"
LABEL version="1.0.0"

RUN apt-get update && apt-get install -y \
    wget curl

# Install conda
RUN wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
    bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
    rm Miniconda3-latest-Linux-x86_64.sh

ENV PATH="/opt/conda/bin:$PATH"

COPY . /workflow
WORKDIR /workflow

Singularity definition example#

Bootstrap: docker
From: ubuntu:22.04

%labels
    maintainer oxo-flow
    version 1.0.0

%post
    apt-get update && apt-get install -y wget curl

%files
    . /workflow

%runscript
    cd /workflow
    exec oxo-flow run pipeline.oxoflow "$@"

Notes#

  • The package command generates container definitions, not built images — you must run docker build or singularity build separately
  • If --output is not specified, the definition is printed to stdout
  • The generated containers include all workflow files, environment specs, and scripts needed for self-contained execution
  • Container packaging is key for reproducibility: the same container produces the same results regardless of the host system