Installation

Requirements

• Nextflow >= 23.04.0 (requires Java 11+)
• A container engine: Docker, Singularity, Apptainer, Podman, or Conda

Install Nextflow

curl -s https://get.nextflow.io | bash
mv nextflow ~/bin/  # or any directory on your $PATH

Container engine

Docker

# Install Docker: https://docs.docker.com/get-docker/
docker --version

Singularity / Apptainer

# Install Apptainer: https://apptainer.org/docs/admin/main/installation.html
apptainer --version

Conda

# Install Conda: https://docs.conda.io/en/latest/miniconda.html
conda --version

Bakta database

Bakta requires a pre-built database. The pipeline will download it automatically if --bakta_db is not provided, but you can pre-download it for faster runs:

bakta_db download --output /path/to/bakta_db --type light

Or for the full database:

bakta_db download --output /path/to/bakta_db --type full

Then pass --bakta_db /path/to/bakta_db when running the pipeline.

Clone the repository

git clone https://github.com/exterex/janus.git
cd janus

Alternatively, Nextflow can pull the pipeline directly:

nextflow run exterex/janus --help