From anaconda (complete pipeline)

This is the preferred way to install the complete MiCoNE pipeline.

First clone the public repository:

git clone git://

Then create a conda environment and install the required packages:

cd MiCoNE
mamba env create -n micone -f env.yml

Or you can directly install from the repository:

mamba env create -n micone -f

NOTE: 1. MiCoNE requires the mamba package manager, otherwise micone init will not work. 2. Direct installation via anaconda cloud will be available soon.

From pip (only Python package)

To install the MiCoNE Python package, run this command in your terminal:

pip install MiCoNE

If you don’t have pip installed, this Python installation guide can guide you through the process.


This does not install the nextflow related pipeline elements, and does not provide the functionality to execute pipelines. Those can be installed through anaconda (see above).

From sources (only Python package)

The sources for Microbial Interaction Database Pipeline can be downloaded from the Github repo.

You can either clone the public repository:

git clone git://

Or download the tarball:

curl  -OL

Once you have a copy of the source, you can install it with:

pip install .