1. Installation

Installation Guide for FlexTaxD

Welcome to the installation guide for FlexTaxD. Follow these steps to set up FlexTaxD and get started with your taxonomy database management.

Preferred Method: Bioconda Installation

FlexTaxD can be installed via Bioconda using Mamba or Conda. We recommend creating a new environment specifically for FlexTaxD to avoid any dependency conflicts.

mamba create -n flextaxd flextaxd ncbi-genome-download ncbi-datasets-cli

Activate the new environment with:

mamba activate flextaxd

Optional Dependencies

Visualization Tools

To enable database visualization features in FlexTaxD, the following additional libraries are required. They can be installed through Conda:

mamba install inquirer biopython matplotlib

Downstream Read Classifiers

For compiling ready-to-use databases, you may choose to install downstream read classifiers. These can be added to the FlexTaxD environment using Conda:

mamba install kraken2
# or
mamba install krakenuniq
# or
mamba install ganon

Note: Kraken2 and Krakenuniq are based on different versions of the same codebase and should not be installed simultaneously in the same environment.

FlexTaxD also supports exporting formatted data for other read classifiers and allows custom formatting.

Installation from Source

For those who prefer or require installation from the source, FlexTaxD is developed in Python 3 and can be installed directly from the GitHub repository:

git clone https://github.com/FOI-Bioinformatics/flextaxd
cd flextaxd
pip insatll .