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

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

pmdtools
========

.. conda:recipe:: pmdtools
   :replaces_section_title:
   :noindex:

   Compute postmortem damage patterns and decontaminate ancient genomes

   :homepage: https://github.com/pontussk/PMDtools
   :license: GPL-3.0
   :recipe: /`pmdtools <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/pmdtools>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/pmdtools/meta.yaml>`_
   :links: doi: :doi:`10.1073/pnas.1318934111`

   


.. conda:package:: pmdtools

   |downloads_pmdtools| |docker_pmdtools|

   :versions:
      
      

      ``0.60-5``,  ``0.60-4``,  ``0.60-3``,  ``0.60-2``,  ``0.60-1``

      

   
   :depends python: 
   :depends r-base: ``>=4.0``
   :depends samtools: ``>=1.13``
   :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 pmdtools

   and update with::

      mamba update pmdtools

  To create a new environment, run::

      mamba create --name myenvname pmdtools

  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/pmdtools:<tag>

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


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


.. raw:: html

    <script>
        var package = "pmdtools";
        var versions = ["0.60","0.60","0.60","0.60","0.60"];
    </script>






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-----------------

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

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