:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'checkm2'
.. highlight: bash

checkm2
=======

.. conda:recipe:: checkm2
   :replaces_section_title:
   :noindex:

   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 <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/checkm2>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/checkm2/meta.yaml>`_

   


.. conda:package:: checkm2

   |downloads_checkm2| |docker_checkm2|

   :versions:
      
      

      ``1.1.0-1``,  ``1.1.0-0``,  ``1.0.2-0``,  ``1.0.1-0``

      

   
   :depends diamond: ``2.1.11.*``
   :depends keras: 
   :depends lightgbm: 
   :depends numpy: 
   :depends packaging: 
   :depends pandas: 
   :depends prodigal: ``>=2.6.3``
   :depends python: ``>3.12``
   :depends requests: 
   :depends scikit-learn: ``1.6.1.*``
   :depends scipy: 
   :depends tensorflow: ``2.17.*``
   :depends tqdm: 
   :requirements:

   :additional platforms:
      

   .. rubric:: Installation

  You need a conda-compatible package manager
  (currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
  and the Bioconda channel already activated (see :ref:`set-up-channels`).

  While any of above package managers is fine, it is currently recommended to use either
  micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ 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 <https://mamba.readthedocs.io>`_ 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>``)


.. |downloads_checkm2| image:: https://img.shields.io/conda/dn/bioconda/checkm2.svg?style=flat
   :target: https://anaconda.org/bioconda/checkm2
   :alt:   (downloads)
.. |docker_checkm2| image:: https://quay.io/repository/biocontainers/checkm2/status
   :target: https://quay.io/repository/biocontainers/checkm2
.. _`checkm2/tags`: https://quay.io/repository/biocontainers/checkm2?tab=tags


.. raw:: html

    <script>
        var package = "checkm2";
        var versions = ["1.1.0","1.1.0","1.0.2","1.0.1"];
    </script>





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


Download stats
-----------------

.. raw:: html
    :file: ../../templates/package_dashboard.html

Link to this page
-----------------

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

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/checkm2/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/checkm2/README.html