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

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

viroconstrictor
===============

.. conda:recipe:: viroconstrictor
   :replaces_section_title:
   :noindex:

   ViroConstrictor is a flexible pipeline for analysis of targeted viral sequencing data

   :homepage: https://rivm-bioinformatics.github.io/ViroConstrictor/
   :developer docs: https://github.com/RIVM-bioinformatics/ViroConstrictor
   :license: AGPL / GNU Affero General Public v3
   :recipe: /`viroconstrictor <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/viroconstrictor>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/viroconstrictor/meta.yaml>`_

   


.. conda:package:: viroconstrictor

   |downloads_viroconstrictor| |docker_viroconstrictor|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.6.5-0</code>,  <code>1.6.4-0</code>,  <code>1.6.3-0</code>,  <code>1.6.2-0</code>,  <code>1.6.1-0</code>,  <code>1.6.0-0</code>,  <code>1.5.5-0</code>,  <code>1.5.4-0</code>,  <code>1.5.3-0</code>,  </span></summary>
      

      ``1.6.5-0``,  ``1.6.4-0``,  ``1.6.3-0``,  ``1.6.2-0``,  ``1.6.1-0``,  ``1.6.0-0``,  ``1.5.5-0``,  ``1.5.4-0``,  ``1.5.3-0``,  ``1.5.2-0``,  ``1.5.1-0``,  ``1.5.0-0``,  ``1.4.6-0``,  ``1.4.5-1``,  ``1.4.5-0``,  ``1.4.4-0``,  ``1.4.3-0``,  ``1.4.2-0``,  ``1.4.1-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.3.1-0``,  ``1.3.0-0``,  ``1.2.6-0``,  ``1.2.5-0``,  ``1.2.4-0``

      
      .. raw:: html

         </details>
      

   
   :depends aminoextract: ``0.4.1``
   :depends bcbio-gff: ``0.7.1``
   :depends biopython: ``1.85``
   :depends biovalid: ``0.3.0``
   :depends conda: 
   :depends drmaa: ``0.7.9``
   :depends fpdf2: ``2.8.4``
   :depends mamba: ``>=1.5.0,<2.0.0``
   :depends openpyxl: ``3.1.5``
   :depends pandas: ``2.3.3``
   :depends python: ``>=3.10``
   :depends python-magic: ``0.4.27``
   :depends pyyaml: ``6.0.3``
   :depends rich: ``13.9.4``
   :depends snakemake-executor-plugin-drmaa: ``0.1.5``
   :depends snakemake-executor-plugin-lsf: ``0.2.6``
   :depends snakemake-executor-plugin-slurm: ``2.0.0``
   :depends snakemake-interface-logger-plugins: ``1.2.4``
   :depends snakemake-minimal: ``9.5.1``
   :depends urllib3: ``2.5.0``
   :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 viroconstrictor

   and update with::

      mamba update viroconstrictor

  To create a new environment, run::

      mamba create --name myenvname viroconstrictor

  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/viroconstrictor:<tag>

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


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


.. raw:: html

    <script>
        var package = "viroconstrictor";
        var versions = ["1.6.5","1.6.4","1.6.3","1.6.2","1.6.1"];
    </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/viroconstrictor/README.html)

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