Installation

Conda installation

MiST and all associated dependencies can be installed through conda.

conda create -n mist python=3.11
conda activate mist
conda install bioconda::mist_typing -c bioconda -c conda-forge

Alternatively, faster package managers such as mamba or pixi can be used.

mkdir mist
cd mist
pixi init
pixi config set default-channels '["conda-forge", "bioconda"]'
pixi add mist

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Manual installation

Dependencies

The following dependencies are required.

• Minimap2
• CD-HIT
• MUMmer4

The corresponding binaries should be in your PATH to run the workflow.

export PATH=$PATH:/path/to/minimap2_dir

Installing MiST from pip

Python >=3.11 is recommended for manual installation via Pip.

virtualenv mist_env --python=python3.11
source mist_env/bin/activate
pip install mist_typing

Installing MiST from source

git clone https://github.com/BioinformaticsPlatformWIV-ISP/MiST.git
cd MiST
virtualenv mist_env --python=python3.11
source mist_env/bin/activate
pip install .

This method ensures you get the most recent updates and bug fixes.

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Verifying the installation

After installation, mist_query should be available in the PATH. The following command can be used to verify that the installation was successful.

mist_index --version # checks the dependencies required for indexing
mist_query --version # checks the dependencies required for querying

Note: MLST and cgMLST databases are not included in the installation and must be downloaded separately, see Downloading schemes for more information.