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

.. title:: Package Recipe 'braker2'
.. highlight: bash

braker2
=======

.. conda:recipe:: braker2
   :replaces_section_title:
   :noindex:

   BRAKER2 is an extension of BRAKER1

   :homepage: https://github.com/Gaius-Augustus/BRAKER
   :license: Other / Artistic License
   :recipe: /`braker2 <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/braker2>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/braker2/meta.yaml>`_
   :links: doi: :doi:`10.1093/nargab/lqaa108`

   BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark\-EX and AUGUSTUS from RNA\-Seq and\/or protein homology information\, and that integrates the extrinsic evidence from RNA\-Seq and protein homology information into the prediction.


.. conda:package:: braker2

   |downloads_braker2| |docker_braker2|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.1.6-5</code>,  <code>2.1.6-4</code>,  <code>2.1.6-3</code>,  <code>2.1.6-2</code>,  <code>2.1.6-1</code>,  <code>2.1.6-0</code>,  <code>2.1.5-3</code>,  <code>2.1.5-2</code>,  <code>2.1.5-1</code>,  </span></summary>
      

      ``2.1.6-5``,  ``2.1.6-4``,  ``2.1.6-3``,  ``2.1.6-2``,  ``2.1.6-1``,  ``2.1.6-0``,  ``2.1.5-3``,  ``2.1.5-2``,  ``2.1.5-1``,  ``2.1.5-0``,  ``2.1.4-1``,  ``2.1.4-0``,  ``2.1.2-2``,  ``2.1.2-1``,  ``2.1.2-0``

      
      .. raw:: html

         </details>
      

   
   :depends augustus: ``>=3.4.0``
   :depends bamtools: ``>=2.5.1``
   :depends biopython: 
   :depends blast: ``>=2.2.31``
   :depends cdbtools: ``>=0.99``
   :depends diamond: ``>=0.9.24``
   :depends exonerate: ``>=2.2.0``
   :depends gemoma: ``1.6.4``
   :depends genomethreader: ``>=1.7.0``
   :depends makehub: 
   :depends perl: 
   :depends perl-app-cpanminus: 
   :depends perl-class-data-inheritable: 
   :depends perl-exception-class: 
   :depends perl-file-homedir: 
   :depends perl-file-spec: 
   :depends perl-file-which: 
   :depends perl-hash-merge: 
   :depends perl-list-moreutils: 
   :depends perl-list-util: 
   :depends perl-logger-simple: 
   :depends perl-math-utils: 
   :depends perl-mce: 
   :depends perl-module-load-conditional: 
   :depends perl-parallel-forkmanager: 
   :depends perl-posix: 
   :depends perl-scalar-util-numeric: 
   :depends perl-test-pod: 
   :depends perl-yaml: 
   :depends python: ``>=3.3``
   :depends samtools: ``>=1.7``
   :depends spaln: ``>=2.3.3``
   :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 braker2

   and update with::

      mamba update braker2

  To create a new environment, run::

      mamba create --name myenvname braker2

  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/braker2:<tag>

   (see `braker2/tags`_ for valid values for ``<tag>``)


.. |downloads_braker2| image:: https://img.shields.io/conda/dn/bioconda/braker2.svg?style=flat
   :target: https://anaconda.org/bioconda/braker2
   :alt:   (downloads)
.. |docker_braker2| image:: https://quay.io/repository/biocontainers/braker2/status
   :target: https://quay.io/repository/biocontainers/braker2
.. _`braker2/tags`: https://quay.io/repository/biocontainers/braker2?tab=tags


.. raw:: html

    <script>
        var package = "braker2";
        var versions = ["2.1.6","2.1.6","2.1.6","2.1.6","2.1.6"];
    </script>





Notes
-----
- GeneMark software can be used for free\, but requires a license file and should be additionally installed on the machine where the BRAKER2 environment is.

- ProtHint software can be used for free\, but doesn\'t allow redistribution and should be additionally installed on the machine where the BRAKER2 environment is.


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

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

Link to this page
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