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

.. title:: Package Recipe 'gmwi2'
.. highlight: bash

gmwi2
=====

.. conda:recipe:: gmwi2
   :replaces_section_title:
   :noindex:

   Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles

   :homepage: https://github.com/danielchang2002/GMWI2
   :license: MIT / MIT
   :recipe: /`gmwi2 <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/gmwi2>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/gmwi2/meta.yaml>`_

   GMWI2 \(Gut Microbiome Wellness Index 2\) is a robust and biologically interpretable predictor of health status based on gut microbiome taxonomic profiles. 
   On a stool metagenome sample\, this command\-line tool performs four major steps\:
   \(1\) Quality control\;
   \(2\) Taxonomic profiling using MetaPhlAn3 \(v3.0.13\) with the mpa\\\_v30\\\_CHOCOPhlAn\_201901 marker database\;
   \(3\) Transformation of taxonomic relative abundances into a binary presence\/absence profile\;
   \(4\) Computation of the GMWI2 score using a Lasso\-penalized logistic regression model trained on a meta\-dataset of 8\,069 health status labeled stool shotgun metagenomes.


.. conda:package:: gmwi2

   |downloads_gmwi2| |docker_gmwi2|

   :versions:
      
      

      ``1.5-0``

      

   
   :depends bbmap: 
   :depends bedtools: 
   :depends fastqc: 
   :depends halo: 
   :depends metaphlan: ``3.0.13.*``
   :depends pandas: 
   :depends python: ``>=3.7``
   :depends samtools: 
   :depends scikit-learn: ``1.2.2.*``
   :depends trimmomatic: 
   :requirements:

   .. 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 gmwi2

   and update with::

      mamba update gmwi2

  To create a new environment, run::

      mamba create --name myenvname gmwi2

  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/gmwi2:<tag>

   (see `gmwi2/tags`_ for valid values for ``<tag>``)


.. |downloads_gmwi2| image:: https://img.shields.io/conda/dn/bioconda/gmwi2.svg?style=flat
   :target: https://anaconda.org/bioconda/gmwi2
   :alt:   (downloads)
.. |docker_gmwi2| image:: https://quay.io/repository/biocontainers/gmwi2/status
   :target: https://quay.io/repository/biocontainers/gmwi2
.. _`gmwi2/tags`: https://quay.io/repository/biocontainers/gmwi2?tab=tags


.. raw:: html

    <script>
        var package = "gmwi2";
        var versions = ["1.5"];
    </script>






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

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

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