recipe checkm2

Assessing the quality of metagenome-derived genome bins using machine learning.

Homepage:

https://github.com/chklovski/CheckM2

License:

GPL / GPL-3.0-only

Recipe:

/checkm2/meta.yaml

package checkm2

versions:

1.0.2-0,  1.0.1-0

depends diamond:

2.0.4.*

depends h5py:

2.10.0.*

depends lightgbm:

3.2.1.*

depends numpy:

1.19.2.*

depends packaging:

depends pandas:

<=1.4.0

depends prodigal:

>=2.6.3

depends python:

>=3.6,<3.9

depends requests:

depends scikit-learn:

0.23.2.*

depends scipy:

depends setuptools:

depends tensorflow:

>=2.1.0,<2.6.0

depends tqdm:

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 checkm2

and update with::

   mamba update checkm2

To create a new environment, run:

mamba create --name myenvname checkm2

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/checkm2:<tag>

(see `checkm2/tags`_ for valid values for ``<tag>``)

Notes

CheckM2 requries the DIAMOND database that can be downloaded with `checkm2 database --download`.

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Link to this page

Render an badge with the following MarkDown:

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