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

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

parascopy
=========

.. conda:recipe:: parascopy
   :replaces_section_title:
   :noindex:

   Calling paralog\-specific copy number and sequence variants in duplicated genes using short\-read whole\-genome sequencing.

   :homepage: https://github.com/tprodanov/parascopy
   :documentation: https://github.com/tprodanov/parascopy/blob/v1.18.0/README.md
   
   :license: MIT / MIT
   :recipe: /`parascopy <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/parascopy>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/parascopy/meta.yaml>`_
   :links: doi: :doi:`10.1038/s41467-022-30930-3`, doi: :doi:`10.1093/bioinformatics/btad268`, biotools: :biotools:`parascopyvc`

   


.. conda:package:: parascopy

   |downloads_parascopy| |docker_parascopy|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.18.0-1</code>,  <code>1.18.0-0</code>,  <code>1.17.4-0</code>,  <code>1.17.2-1</code>,  <code>1.17.2-0</code>,  <code>1.17.1-1</code>,  <code>1.17.1-0</code>,  <code>1.17.0-0</code>,  <code>1.16.3-0</code>,  </span></summary>
      

      ``1.18.0-1``,  ``1.18.0-0``,  ``1.17.4-0``,  ``1.17.2-1``,  ``1.17.2-0``,  ``1.17.1-1``,  ``1.17.1-0``,  ``1.17.0-0``,  ``1.16.3-0``,  ``1.16.2-0``,  ``1.16.0-0``,  ``1.15.1-2``,  ``1.15.1-1``,  ``1.15.1-0``,  ``1.15.0-0``,  ``1.14.1-0``,  ``1.14.0-0``,  ``1.13.9-0``,  ``1.12.0-0``,  ``1.11.0-2``,  ``1.11.0-1``,  ``1.11.0-0``,  ``1.10.6-0``,  ``1.9.7-1``,  ``1.9.7-0``,  ``1.9.1-0``,  ``1.7.6-0``,  ``1.7.4-0``,  ``1.7.3-0``,  ``1.7.1-0``,  ``1.7.0-0``,  ``1.6.2-0``,  ``1.6.1-0``,  ``1.5.0-0``,  ``1.4.0-0``,  ``1.3.4-0``,  ``1.3.3-0``,  ``1.3.2-0``,  ``1.3.1-0``,  ``1.3.0-0``,  ``1.2.6-0``,  ``1.2.4-0``,  ``1.2.3-0``,  ``1.2.2-0``,  ``1.2.1-0``,  ``1.2.0-0``,  ``1.1.2-0``,  ``1.1.0-0``,  ``1.0.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends biopython: ``>=1.70``
   :depends bwa: ``>=0.7``
   :depends bzip2: ``>=1.0.8,<2.0a0``
   :depends construct: ``>=2.10``
   :depends htslib: ``>=1.21,<1.23.0a0``
   :depends intervaltree: ``>=3.0``
   :depends libgcc: ``>=13``
   :depends liblzma: ``>=5.8.1,<6.0a0``
   :depends libstdcxx: ``>=13``
   :depends libzlib: ``>=1.3.1,<2.0a0``
   :depends numpy: ``>=1.15``
   :depends parasail-python: ``>=1.2``
   :depends pysam: ``>=0.17``
   :depends python: ``>=3.10,<3.11.0a0``
   :depends python_abi: ``3.10.* *_cp310``
   :depends samtools: ``>=1.11``
   :depends scipy: ``>=1.5``
   :depends simpleeval: ``>=0.9``
   :depends tabixpp: ``>=1.1.2,<1.1.3.0a0``
   :requirements:

   :additional platforms:
      
      .. raw:: html

         <span class="additional-platforms"><code>linux-aarch64</code></span>
      

   .. 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 parascopy

   and update with::

      mamba update parascopy

  To create a new environment, run::

      mamba create --name myenvname parascopy

  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/parascopy:<tag>

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


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


.. raw:: html

    <script>
        var package = "parascopy";
        var versions = ["1.18.0","1.18.0","1.17.4","1.17.2","1.17.2"];
    </script>






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

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

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