Installation

Hoodini can be installed using several methods. Choose the one that best fits your workflow.

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Note: Hoodini requires downloading several databases on first run (~35GB uncompressed). Initial setup takes 5+ minutes depending on your internet connection and machine specs.

Installation Methods

Mamba (Recommended)

Mamba is the recommended method for most users. It handles all dependencies automatically.

Hoodini is not yet on Bioconda. For now, clone the repository and install from source.

Install Mamba

If you don’t have Mamba installed, get it via Miniforge :


curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

Clone the repository


git clone https://github.com/pentamorfico/hoodini.git
cd hoodini

Create environment and install


mamba env create -f environment.yml
mamba activate hoodini
pip install -e .

Verify installation


hoodini --help

Pixi

Pixi is a fast, modern package manager that’s great for reproducible environments.

Hoodini is not yet on conda-forge. For now, clone the repository and use the environment file.

Install Pixi


curl -fsSL https://pixi.sh/install.sh | bash

Clone and install


git clone https://github.com/pentamorfico/hoodini.git
cd hoodini
pixi install

Run Hoodini


pixi run hoodini --help

pip

pip installation works but requires external tools to be installed separately.

The pip installation requires you to manually install external dependencies like mmseqs2, diamond, mafft, veryfasttree, padloc, defense-finder, etc. We strongly recommend using Mamba instead.

Clone the repository


git clone https://github.com/pentamorfico/hoodini.git
cd hoodini

Install external tools first

Make sure all bioinformatics tools from environment.yml are available in your PATH.

Install Hoodini


pip install -e .

Verify installation


hoodini --help

Docker

Docker provides an isolated environment with all dependencies included.

Pull the image


docker pull pentamorfico/hoodini:latest

Run Hoodini


docker run -v $(pwd):/data pentamorfico/hoodini:latest hoodini --help

Run with your data

Mount your data directory to /data inside the container:


docker run -v /path/to/your/data:/data pentamorfico/hoodini:latest \
  hoodini run -i /data/input.fasta -o /data/output

Database Download

On first run, Hoodini will download the required databases. Here are the approximate sizes:

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Storage requirements: Make sure you have at least 40GB of free disk space for all databases.

Database	Size	Description
eggNOG-mapper	~24 GB	Functional annotation (largest)
MetaCerberus HMMs	~4.5 GB	Domain annotation (Pfam, COG, KEGG, etc.)
Contig lengths	~3.8 GB	NCBI assembly metadata
geNomad	~1.4 GB	Virus/plasmid detection
PADLOC	~1 GB	Defense system detection
DefenseFinder	~350 MB	Defense system detection

You can skip specific databases during download:


hoodini download databases --skip-emapper --skip-genomad

Verify Installation

After installation, verify everything works:


# Check version
hoodini --version
 
# Run with test data (will download databases on first run)
hoodini run -i test.fasta -o test_output --threads 4

Tip: Use the --threads flag to speed up processing. Hoodini scales well with multiple cores.