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

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

hapog
=====

.. conda:recipe:: hapog
   :replaces_section_title:
   :noindex:

   Haplotype\-Aware Polishing of Genomes

   :homepage: https://github.com/institut-de-genomique/HAPO-G
   :documentation: https://www.genoscope.cns.fr/hapog/
   
   :license: OTHER / CECILL-2.1
   :recipe: /`hapog <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/hapog>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/hapog/meta.yaml>`_
   :links: doi: :doi:`10.1093/nargab/lqab034`

   


.. conda:package:: hapog

   |downloads_hapog| |docker_hapog|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.3.8-0</code>,  <code>1.3.7-0</code>,  <code>1.3.6-0</code>,  <code>1.3.5-0</code>,  <code>1.3.4-3</code>,  <code>1.3.4-2</code>,  <code>1.3.4-1</code>,  <code>1.3.4-0</code>,  <code>1.3.3-0</code>,  </span></summary>
      

      ``1.3.8-0``,  ``1.3.7-0``,  ``1.3.6-0``,  ``1.3.5-0``,  ``1.3.4-3``,  ``1.3.4-2``,  ``1.3.4-1``,  ``1.3.4-0``,  ``1.3.3-0``,  ``1.3.2-0``

      
      .. raw:: html

         </details>
      

   
   :depends biopython: 
   :depends bwa: 
   :depends htslib: ``>=1.19.1,<1.21.0a0``
   :depends libgcc-ng: ``>=12``
   :depends libzlib: ``>=1.2.13,<1.3.0a0``
   :depends minimap2: 
   :depends python: ``>=3.10,<3.11.0a0``
   :depends python_abi: ``3.10.* *_cp310``
   :depends samtools: 
   :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 hapog

   and update with::

      mamba update hapog

  To create a new environment, run::

      mamba create --name myenvname hapog

  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/hapog:<tag>

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


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


.. raw:: html

    <script>
        var package = "hapog";
        var versions = ["1.3.8","1.3.7","1.3.6","1.3.5","1.3.4"];
    </script>






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

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

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

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