Installation

Multiple installation options are available depending on your context. We recommend Bioconda, which installs FlavoTyper and its external tools (BLAST+, fastANI) in a single step. The PyPI and from-source installs require you to install those external tools yourself.

Option 1 — Bioconda (recommended)

New to conda?

It is recommended to install a conda package manager, create a separate environment, and activate it before installing and running FlavoTyper. See the First time with conda? walkthrough for detailed steps.

conda create -n flavotyper -c conda-forge -c bioconda flavotyper
conda activate flavotyper

Option 2 — PyPI

First time with Python/pip?

This option requires a working Python installation, then creating a virtual environment and activating it before installing FlavoTyper. See the step-by-step setup guide.

python3 -m venv .venv
source .venv/bin/activate
pip install flavotyper

Option 3 — From source

git clone https://forge.inrae.fr/eric.duchaud/flavotyper.git
cd flavotyper
python3 -m venv .venv
source .venv/bin/activate
pip install .

External dependencies

Required only for the PyPI and from-source installs:

Dependency	Minimum version	Purpose
BLAST+ (blastn, makeblastdb)	2.12	Marker alignment and locus comparison
fastANI	1.3	Species validation (ANI-based QC)

The simplest way to get them is conda:

conda install -c conda-forge -c bioconda blast fastani

Verify the installation

flavotyper --version
flavotyper data-dir
blastn -version
fastANI --version