Usage

Installation

This document covers the installation requirements and dependency management for the PopMAG pipeline. It explains how to set up the required software environment, configure container systems, and manage external databases needed for population genomics analysis based on metagenome-assembled genomes.

For basic usage instructions after installation, see Basic Usage. For detailed configuration of pipeline parameters, see Global Parameters.

Prerequisites

  • Nextflow ≥ 24.04.2

  • Java ≥ 17

  • Bash ≥ 3.2

  • Container Engine: Docker, Singularity, Podman, or Apptainer

  • Conda/Mamba (optional alternative to containers)

Installation Steps

Install Nextflow

Nextflow official installation instructions can be found in https://www.nextflow.io/docs/latest/install.html

Self-Install

curl -s https://get.nextflow.io | bash
chmod +x nextflow
sudo mv nextflow /usr/local/bin/

Mamba/Conda

mamba create --name nf-env bioconda::nextflow
source activate nf-env

Verify installation

nextflow info

2. Choose Execution Profile

PopMAG supports multiple containerization and environment management systems for reproducible execution. The pipeline provides several execution profiles that configure different container engines and dependency management approaches:

  • Docker (recommended): -profile docker

  • Singularity (HPC systems): -profile singularity

  • Apptainer: -profile apptainer

  • Mamba: -profile mamba

  • Conda: -profile conda