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

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

haystack_bio
============

.. conda:recipe:: haystack_bio
   :replaces_section_title:
   :noindex:

   Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

   :homepage: https://github.com/pinellolab/haystack_bio
   :license: GPLv3
   :recipe: /`haystack_bio <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/haystack_bio>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/haystack_bio/meta.yaml>`_

   


.. conda:package:: haystack_bio

   |downloads_haystack_bio| |docker_haystack_bio|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>0.5.5-1</code>,  <code>0.5.5-0</code>,  <code>0.5.4-1</code>,  <code>0.5.3-1</code>,  <code>0.5.3-0</code>,  <code>0.5.2-8</code>,  <code>0.5.2-7</code>,  <code>0.5.2-6</code>,  <code>0.5.2-5</code>,  </span></summary>
      

      ``0.5.5-1``,  ``0.5.5-0``,  ``0.5.4-1``,  ``0.5.3-1``,  ``0.5.3-0``,  ``0.5.2-8``,  ``0.5.2-7``,  ``0.5.2-6``,  ``0.5.2-5``,  ``0.5.2-4``,  ``0.5.2-3``,  ``0.5.2-2``,  ``0.5.2-1``,  ``0.5.2-0``,  ``v0.5.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bedtools: 
   :depends bx-python: 
   :depends jinja2: 
   :depends matplotlib: 
   :depends meme: ``4.11.2.*``
   :depends numpy: ``1.15.*``
   :depends openjdk: 
   :depends pandas: 
   :depends python: ``>=2.7,<3.0a0``
   :depends sambamba: 
   :depends scipy: 
   :depends tqdm: 
   :depends ucsc-bedgraphtobigwig: 
   :depends ucsc-bigwigaverageoverbed: 
   :depends weblogo: 
   :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 haystack_bio

   and update with::

      mamba update haystack_bio

  To create a new environment, run::

      mamba create --name myenvname haystack_bio

  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/haystack_bio:<tag>

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


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


.. raw:: html

    <script>
        var package = "haystack_bio";
        var versions = ["0.5.5","0.5.5","0.5.4","0.5.3","0.5.3"];
    </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/haystack_bio/README.html)

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