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

.. title:: Package Recipe 'cap-mirseq'
.. highlight: bash

cap-mirseq
==========

.. conda:recipe:: cap-mirseq
   :replaces_section_title:
   :noindex:

   A comprehensive analysis pipeline for deep microRNA sequencing

   :homepage: http://bioinformaticstools.mayo.edu/research/cap-mirseq/
   :license: GPL
   :recipe: /`cap-mirseq <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/cap-mirseq>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/cap-mirseq/meta.yaml>`_

   


.. conda:package:: cap-mirseq

   |downloads_cap-mirseq| |docker_cap-mirseq|

   :versions:
      
      

      ``version-0``

      

   
   :depends bedtools: ``>=2.17.0``
   :depends bioconductor-edger: ``>=3.14.0``
   :depends bowtie: ``>=1.1.2``
   :depends fastqc: ``>=0.11.5``
   :depends java-jdk: 
   :depends mirdeep2: ``>=2.0.0.7``
   :depends perl-threaded: 
   :depends picard: ``>=1.97``
   :depends r-base: ``3.2.2*``
   :depends r-essentials: 
   :depends samtools: ``>=0.1.19``
   :depends vcftools: ``>=0.1.11``
   :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 cap-mirseq

   and update with::

      mamba update cap-mirseq

  To create a new environment, run::

      mamba create --name myenvname cap-mirseq

  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/cap-mirseq:<tag>

   (see `cap-mirseq/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "cap-mirseq";
        var versions = ["version"];
    </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/cap-mirseq/README.html)

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