recipe whokaryote

Classify metagenomic contigs as eukaryotic or prokaryotic

Homepage:

https://github.com/LottePronk/whokaryote

Developer docs:

https://git.wageningenur.nl/lotte.pronk/whokaryote

License:

GPL / AGPL-3.0

Recipe:

/whokaryote/meta.yaml

Links:

doi: https://doi.org/10.1099/mgen.0.000823

Whokaryote uses a random forest classifier that uses gene-structure based features and optionally Tiara predictions to predict whether a contig is from a eukaryote or from a prokaryote. You can use Whokaryote to determine which contigs need eukaryotic gene prediction and which need prokaryotic gene prediction.

package whokaryote

(downloads) docker_whokaryote

versions:

1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.1-0

depends biopython:

depends joblib:

depends numpy:

1.19.4.*

depends pandas:

depends pathlib:

depends prodigal:

depends python:

3.8.*

depends scikit-learn:

1.0.2.*

depends tiara:

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 whokaryote

and update with::

   mamba update whokaryote

To create a new environment, run:

mamba create --name myenvname whokaryote

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/whokaryote:<tag>

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

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