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

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

mvip
====

.. conda:recipe:: mvip
   :replaces_section_title:
   :noindex:

   MVP v.1.0\, a user\-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification\, characterization of genome quality\, filtering\, clustering\, taxonomic and functional annotation\, genome binning\, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall\, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large\-scale sequencing data including metagenomes\, metatranscriptomes\, viromes and isolate genomes.

   :homepage: https://gitlab.com/ccoclet/mvp
   :license: GNU GENERAL PUBLIC LICENSE
   :recipe: /`mvip <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/mvip>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/mvip/meta.yaml>`_

   


.. conda:package:: mvip

   |downloads_mvip| |docker_mvip|

   :versions:
      
      

      ``1.1.5-1``,  ``1.1.5-0``,  ``1.1.4-0``,  ``1.1.3-0``,  ``1.1.2-0``,  ``1.1.1-0``,  ``1.1.0-1``,  ``1.1.0-0``,  ``1.0.0-0``

      

   
   :depends bowtie2: 
   :depends checkv: 
   :depends coverm: 
   :depends dos2unix: 
   :depends fasttree: 
   :depends flit: 
   :depends genomad: ``1.7.4``
   :depends importlib_resources: 
   :depends mafft: 
   :depends minimap2: 
   :depends mmseqs2: 
   :depends numpy: ``1.23``
   :depends pandas: 
   :depends parallel: 
   :depends python: ``>=3.7``
   :depends rpy2: 
   :depends samtools: 
   :depends scikit-learn: ``0.23``
   :depends seqtk: 
   :depends table2asn: 
   :depends taxopy: 
   :depends tqdm: 
   :depends trimal: 
   :depends vrhyme: 
   :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 mvip

   and update with::

      mamba update mvip

  To create a new environment, run::

      mamba create --name myenvname mvip

  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/mvip:<tag>

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


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


.. raw:: html

    <script>
        var package = "mvip";
        var versions = ["1.1.5","1.1.5","1.1.4","1.1.3","1.1.2"];
    </script>






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/mvip/README.html)

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