recipe kmerfinder

Prediction of bacterial species using a fast K-mer algorithm.

Homepage:

https://bitbucket.org/genomicepidemiology/kmerfinder

License:

APACHE / APACHE-2.0

Recipe:

/kmerfinder/meta.yaml

package kmerfinder

versions:

3.0.2-0

depends kma:

depends python:

>=3.5

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 kmerfinder

and update with::

   mamba update kmerfinder

To create a new environment, run:

mamba create --name myenvname kmerfinder

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/kmerfinder:<tag>

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

Notes

KmerFinder requires a database that can be downloaded with download-db.sh.

Download stats

Link to this page

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