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

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

rappas
======

.. conda:recipe:: rappas
   :replaces_section_title:
   :noindex:

   RAPPAS \(Rapid Alignment\-free Phylogenetic PLacement via Ancestral Sequences\) is a program dedicated to Phylogenetic Placement of \(meta\)genomic reads on a reference tree. As apposed to previous PP programs\, RAPPAS is based on the phylo\-kmers idea\, detailed in tis manuscript and uses a 2 step approach divided into a\) the database build\, and b\) the placement itself. The main advantage of RAPPAS is that it is alignment free\, which means that after step \(a\) \(the DB build\) is performed\, metagenomic reads can be directly placed on a referene tree WITHOUT aligning them to the reference alignment on which the tree was built \(as required by other approaches\). The second advantage of RAPPAS is its algorithm based on phylo\-kmers matches\, making its execution time linear with respect to the length of the placed sequences.

   :homepage: https://github.com/blinard-BIOINFO/RAPPAS
   :license: GPL3
   :recipe: /`rappas <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/rappas>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/rappas/meta.yaml>`_

   


.. conda:package:: rappas

   |downloads_rappas| |docker_rappas|

   :versions:
      
      

      ``1.22-0``,  ``1.21-0``,  ``1.20-0``,  ``1.12-0``

      

   
   :depends font-ttf-dejavu-sans-mono: 
   :depends openjdk: ``>=8.0.144``
   :depends phyml: ``3.3.20190909.*``
   :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 rappas

   and update with::

      mamba update rappas

  To create a new environment, run::

      mamba create --name myenvname rappas

  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/rappas:<tag>

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


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


.. raw:: html

    <script>
        var package = "rappas";
        var versions = ["1.22","1.21","1.20","1.12"];
    </script>






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

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

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