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

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

tetrimmer
=========

.. conda:recipe:: tetrimmer
   :replaces_section_title:
   :noindex:

   TETrimmer is designed to replace and assist TE manual curation.

   :homepage: https://github.com/qjiangzhao/TETrimmer.git
   :license: GPL3 / GPL-3.0-only
   :recipe: /`tetrimmer <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/tetrimmer>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/tetrimmer/meta.yaml>`_

   


.. conda:package:: tetrimmer

   |downloads_tetrimmer| |docker_tetrimmer|

   :versions:
      
      

      ``1.4.0-0``

      

   
   :depends bedtools: ``>=2.31.1``
   :depends biopython: 
   :depends blast: 
   :depends cd-hit: 
   :depends click: 
   :depends dataclasses: 
   :depends dill: 
   :depends emboss: 
   :depends ghostscript: 
   :depends hmmer: 
   :depends iqtree: 
   :depends joblib: 
   :depends mafft: 
   :depends matplotlib-base: 
   :depends multiprocess: 
   :depends nseg: 
   :depends numpy: 
   :depends pandas: 
   :depends perl: 
   :depends pfam_scan: 
   :depends plotly: 
   :depends pypdf2: 
   :depends python: ``>=3.8,<3.11``
   :depends r-base: 
   :depends recon: 
   :depends regex: 
   :depends repeatmasker: 
   :depends repeatmodeler: 
   :depends requests: 
   :depends samtools: 
   :depends scikit-learn: 
   :depends tk: 
   :depends trf: 
   :depends urllib3: 
   :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 tetrimmer

   and update with::

      mamba update tetrimmer

  To create a new environment, run::

      mamba create --name myenvname tetrimmer

  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/tetrimmer:<tag>

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


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


.. raw:: html

    <script>
        var package = "tetrimmer";
        var versions = ["1.4.0"];
    </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/tetrimmer/README.html)

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