recipe pathogist

Calibrated multi-criterion genomic analysis for public health microbiology






package pathogist

(downloads) docker_pathogist



depends coincbc:


depends khmer:

depends kwip:

depends matplotlib:

depends mentalist:

depends networkx:

depends numpy:


depends pandas:


depends prince:

depends pulp:


depends python:

depends pyyaml:


depends scikit-learn:


depends scipy:


depends snippy:


depends spotyping3:

depends vcflib:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install pathogist

and update with::

   mamba update pathogist

To create a new environment, run:

mamba create --name myenvname pathogist

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `pathogist/tags`_ for valid values for ``<tag>``)

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