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

.. title:: Package Recipe 'jbrowse2'
.. highlight: bash

jbrowse2
========

.. conda:recipe:: jbrowse2
   :replaces_section_title:
   :noindex:

   The JBrowse 2 Genome Browser

   :homepage: https://jbrowse.org/
   :license: Apache / Apache-2.0
   :recipe: /`jbrowse2 <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/jbrowse2>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/jbrowse2/meta.yaml>`_
   :links: biotools: :biotools:`jbrowse`, doi: :doi:`10.1101/gr.094607.109`

   


.. conda:package:: jbrowse2

   |downloads_jbrowse2| |docker_jbrowse2|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.11.0-0</code>,  <code>2.10.3-0</code>,  <code>2.10.2-0</code>,  <code>2.10.1-0</code>,  <code>2.10.0-0</code>,  <code>2.9.0-0</code>,  <code>2.8.0-0</code>,  <code>2.7.2-0</code>,  <code>2.7.1-0</code>,  </span></summary>
      

      ``2.11.0-0``,  ``2.10.3-0``,  ``2.10.2-0``,  ``2.10.1-0``,  ``2.10.0-0``,  ``2.9.0-0``,  ``2.8.0-0``,  ``2.7.2-0``,  ``2.7.1-0``,  ``2.7.0-0``,  ``2.6.3-0``,  ``2.6.2-0``,  ``2.6.1-0``,  ``2.5.0-1``,  ``2.5.0-0``,  ``2.4.2-0``,  ``2.4.1-0``,  ``2.4.0-0``,  ``2.3.4-0``,  ``2.3.3-0``,  ``2.3.2-0``,  ``2.3.1-0``,  ``2.2.2-0``,  ``2.2.1-0``,  ``2.2.0-0``,  ``2.1.6-0``,  ``2.1.5-0``,  ``2.1.4-0``,  ``2.1.2-0``,  ``2.1.0-0``,  ``2.0.1-0``,  ``2.0.0-0``,  ``1.7.11-0``,  ``1.7.10-0``,  ``1.7.9-0``,  ``1.7.8-0``,  ``1.7.7-0``,  ``1.7.6-0``,  ``1.7.4-0``,  ``1.7.3-0``,  ``1.6.9-0``,  ``1.6.7-0``,  ``1.6.6-0``,  ``1.6.5-0``,  ``1.6.4-1``,  ``1.6.4-0``,  ``1.5.9-1``,  ``1.5.9-0``,  ``1.5.8-0``,  ``1.5.5-0``,  ``1.5.3-0``,  ``1.5.1-0``,  ``1.5.0-0``,  ``1.4.4-0``,  ``1.4.1-0``,  ``1.3.5-0``,  ``1.3.3-0``,  ``1.3.2-0``

      
      .. raw:: html

         </details>
      

   
   :depends bcftools: 
   :depends gff3sort: 
   :depends htslib: 
   :depends nodejs: 
   :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 jbrowse2

   and update with::

      mamba update jbrowse2

  To create a new environment, run::

      mamba create --name myenvname jbrowse2

  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/jbrowse2:<tag>

   (see `jbrowse2/tags`_ for valid values for ``<tag>``)


.. |downloads_jbrowse2| image:: https://img.shields.io/conda/dn/bioconda/jbrowse2.svg?style=flat
   :target: https://anaconda.org/bioconda/jbrowse2
   :alt:   (downloads)
.. |docker_jbrowse2| image:: https://quay.io/repository/biocontainers/jbrowse2/status
   :target: https://quay.io/repository/biocontainers/jbrowse2
.. _`jbrowse2/tags`: https://quay.io/repository/biocontainers/jbrowse2?tab=tags


.. raw:: html

    <script>
        var package = "jbrowse2";
        var versions = ["2.11.0","2.10.3","2.10.2","2.10.1","2.10.0"];
    </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/jbrowse2/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/jbrowse2/README.html