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

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

riboseed
========

.. conda:recipe:: riboseed
   :replaces_section_title:
   :noindex:

   riboSeed\: assemble across rDNA regions

   :homepage: https://github.com/nickp60/riboSeed
   :license: MIT / MIT License
   :recipe: /`riboseed <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/riboseed>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/riboseed/meta.yaml>`_

   Genome assembly polisher to bridge rDNA gaps


.. conda:package:: riboseed

   |downloads_riboseed| |docker_riboseed|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>0.4.90-0</code>,  <code>0.4.89-0</code>,  <code>0.4.88-0</code>,  <code>0.4.87-0</code>,  <code>0.4.86-0</code>,  <code>0.4.73-1</code>,  <code>0.4.73-0</code>,  <code>0.4.71-0</code>,  <code>0.4.70-2</code>,  </span></summary>
      

      ``0.4.90-0``,  ``0.4.89-0``,  ``0.4.88-0``,  ``0.4.87-0``,  ``0.4.86-0``,  ``0.4.73-1``,  ``0.4.73-0``,  ``0.4.71-0``,  ``0.4.70-2``,  ``0.4.68-2``,  ``0.4.67-2``,  ``0.4.65-1``,  ``0.4.47-1``,  ``0.4.47-0``,  ``0.4.16-0``

      
      .. raw:: html

         </details>
      

   
   :depends barrnap: 
   :depends bcbiogff: 
   :depends bcftools: 
   :depends biopython: 
   :depends blast: 
   :depends bwa: 
   :depends coverage: 
   :depends jenkspy: 
   :depends mafft: 
   :depends matplotlib: 
   :depends networkx: 
   :depends numpy: 
   :depends pandas: 
   :depends prank: 
   :depends pyaml: 
   :depends pysam: 
   :depends python: ``3.5.*``
   :depends quast: ``>=4.6.3``
   :depends samtools: 
   :depends skesa: 
   :depends spades: ``3.9.1``
   :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 riboseed

   and update with::

      mamba update riboseed

  To create a new environment, run::

      mamba create --name myenvname riboseed

  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/riboseed:<tag>

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


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


.. raw:: html

    <script>
        var package = "riboseed";
        var versions = ["0.4.90","0.4.89","0.4.88","0.4.87","0.4.86"];
    </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/riboseed/README.html)

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