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

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

gpatch
======

.. conda:recipe:: gpatch
   :replaces_section_title:
   :noindex:

   Starting with alignments of contigs to a reference genome\, produce a chromosome\-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference. Download the github repository for helper scripts to automate GPatch workflows\, identify and correct misjoins in the contig assembly\, produce dot\-plots of patched pseudoassemblies to a reference assembly\, and generate chrom.sizes and liftover chains for patched pseudoassemblies.\"

   :homepage: https://github.com/adadiehl/GPatch.git
   :license: MIT / MIT
   :recipe: /`gpatch <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/gpatch>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/gpatch/meta.yaml>`_

   


.. conda:package:: gpatch

   |downloads_gpatch| |docker_gpatch|

   :versions:
      
      

      ``0.4.0-0``,  ``0.3.8-0``,  ``0.3.6-0``,  ``0.3.5-0``,  ``0.3.4-0``

      

   
   :depends biopython: ``>=1.84``
   :depends pysam: ``>=0.22.1``
   :depends python: ``>=3.7,<3.13``
   :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 gpatch

   and update with::

      mamba update gpatch

  To create a new environment, run::

      mamba create --name myenvname gpatch

  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/gpatch:<tag>

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


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


.. raw:: html

    <script>
        var package = "gpatch";
        var versions = ["0.4.0","0.3.8","0.3.6","0.3.5","0.3.4"];
    </script>






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

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

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
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