Installation

pip install mgnifam        # or: uv tool install mgnifam

Or from bioconda, into its own environment:

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

Channel order matters — put conda-forge before bioconda, per the bioconda setup. The package is noarch, and conda pulls in a Python 3.13 interpreter itself, so it does not have to be the one already on your PATH. mamba/micromamba work the same way with the same flags.

Requires Python >= 3.13. Verify with mgnifam --version.

To work on the package itself, or to reproduce published results byte-for-byte, install from the repository against the committed lockfile instead — see Reproducibility, which is scoped to that resolved dependency set:

git clone https://github.com/vagkaratzas/mgnifam && cd mgnifam
uv sync --frozen

Commands in these docs are written uv run mgnifam ... for the cloned checkout. On a pip or conda install, drop the uv run prefix.

mgnifam --help lists the subcommands, and python -m mgnifam is equivalent to the console script.