recipe crocodeel

CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data

Homepage:

https://github.com/metagenopolis/crocodeel

License:

GPL3 / GPL-3.0-or-later

Recipe:

/crocodeel/meta.yaml

CroCoDeEL is a tool that detects cross-sample (aka well-to-well) contamination in shotgun metagenomic data. It accurately identifies contaminated samples but also pinpoints contamination sources and estimates contamination rates. CroCoDeEL relies only on species abundance tables and does not need negative controls.

package crocodeel

(downloads) docker_crocodeel

versions:

1.0.5-0,  1.0.4-0,  1.0.3-0,  1.0.2-0

depends joblib:

>=1.4

depends matplotlib-base:

>=3.8

depends numpy:

>=1.26

depends pandas:

>=2.2

depends python:

>=3.12

depends scikit-learn:

>=1.3,<1.4

depends scipy:

>=1.13

depends tqdm:

>=4.66

requirements:

additional platforms:

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 crocodeel

and update with::

   mamba update crocodeel

To create a new environment, run:

mamba create --name myenvname crocodeel

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/crocodeel:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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