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Installation

Prerequisites

mlstdb is designed to work alongside the mlst tool. You'll need:

  • Python >= 3.8
  • mlst — install via bioconda
  • BLAST+ — comes with mlst, or install separately via bioconda/apt

Create a conda environment with mlst, then install mlstdb via pip:

conda create -n mlst -c bioconda mlst
conda activate mlst
pip install mlstdb

This is the most reliable method and avoids dependency conflicts.

Alternative Methods

conda install -c conda-forge -c bioconda mlstdb

Note

Include the -c conda-forge channel to resolve all dependencies. If you see errors like nothing provides rauth >=0.7.3, this is the fix.

conda create -n mlst -c conda-forge -c bioconda mlst mlstdb

pip install mlstdb

Warning

You'll need to install mlst and BLAST+ separately if using pip only.

Verify Installation

mlstdb --version
mlstdb --help

You should see the version number and the available commands (connect, update, fetch).

Next Steps

Head to the Getting Started guide to connect to the databases and download your first MLST schemes.