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

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

colombo
=======

.. conda:recipe:: colombo
   :replaces_section_title:
   :noindex:

   A software framework equipped with a GUI for the prediction of genomic islands \(GIs\) in prokaryotes.

   :homepage: https://www.uni-goettingen.de/en/research/185810.html
   :license: Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
   :recipe: /`colombo <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/colombo>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/colombo/meta.yaml>`_

   COLOMBO is a software framework equipped with a GUI for the prediction of genomic islands \(GIs\) in prokaryotes. It can be equipped with different plugins that actually perform the prediction. 
   The current version of COLOMBO is supplied with

   SIGI\-HMM that uses hidden Markov models and codon usage bias\;

   SIGi\-CRF utilizing conditional random fields and tetramer\-based order\-3 Markov chain transition probabilities. In particular\, SIGI\-CRF analyzes non\-annotated genomic sequences.

   https\:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471\-2105\-7\-142

   SIGI\_CRF\-AUTO

   SIGI\_CRF\-AUTO is an alternative front\-end to the SIGI\-CRF processing core. First\, it allows to batch process a large number of genome sequences and\/or to run a variety of parameter combinations. 
   Second\, it can collect all individual prediction results generated by varying parameter combinations and combine them into a single graphical representation. Once rendered\, images can be saved very 
   flexible with a broad variety of format options.


.. conda:package:: colombo

   |downloads_colombo| |docker_colombo|

   :versions:
      
      

      ``4.0-1``,  ``4.0-0``,  ``3.8-1``,  ``3.8-0``,  ``v4.0-1``,  ``v4.0-0``,  ``v3.8-0``

      

   
   :depends openjdk: 
   :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 colombo

   and update with::

      mamba update colombo

  To create a new environment, run::

      mamba create --name myenvname colombo

  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/colombo:<tag>

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


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


.. raw:: html

    <script>
        var package = "colombo";
        var versions = ["4.0","4.0","3.8","3.8","v4.0"];
    </script>





Notes
-----
Wrapper scripts are provided to handle Colombo needing to be run with the working directory in its own folder


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/colombo/README.html)

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