recipe dodge

Dynamic Outbreak Detection for Genomic Epidemiology. Automated point source bacterial outbreak detection using cumulative long term genomic surveillance.

Homepage:

https://github.com/LanLab/dodge

License:

GPL-3.0-or-later

Recipe:

/dodge/meta.yaml

package dodge

versions:

1.0.1-0,  1.0.0-0,  0.1.0-0

depends pandas:

>=1.3

depends python:

>=3.8

depends scikit-learn:

>=1.0

requirements:

Installation

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 dodge

and update with::

   mamba update dodge

To create a new environment, run:

mamba create --name myenvname dodge

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 quay.io/biocontainers/dodge:<tag>

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

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