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

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

reparation_blast
================

.. conda:recipe:: reparation_blast
   :replaces_section_title:
   :noindex:

   A pipeline that detects novel open reading frames with ribseq data for bacteria.

   :homepage: https://github.com/RickGelhausen/REPARATION_blast
   :license: GPL3
   :recipe: /`reparation_blast <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/reparation_blast>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/reparation_blast/meta.yaml>`_

   A pipeline that uses ribosome profiling data for a de novo open reading frame delineation in prokaryotic \(bacterial\) genomes. I changed the original reparation project to use the open\-source blast tool \(https\:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi\) instead of the commercial usearch \-\-ublast tool \(https\:\/\/drive5.com\/usearch\/manual\/ublast\_algo.html\). I did this in order to add this tool to bioconda without having licensing issues with the commercial usearch \-ublast tool. The original software was created at VIB\-UGent Center for Medical Biotechnology and Lab of Bioinformatics and Computational Genomics \(Biobix\)\, University of Gent\, Belgium\, by Elvis Ndah. \(https\:\/\/github.com\/Biobix\/REPARATION\). Be advised that the adapted version has slightly different results and is slower than the original reparation software.


.. conda:package:: reparation_blast

   |downloads_reparation_blast| |docker_reparation_blast|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.0.9-3</code>,  <code>1.0.9-2</code>,  <code>1.0.9-1</code>,  <code>1.0.9-0</code>,  <code>1.0.8-0</code>,  <code>1.0.7-2</code>,  <code>1.0.7-0</code>,  <code>v1.0.7-1</code>,  <code>v1.0.7-0</code>,  </span></summary>
      

      ``1.0.9-3``,  ``1.0.9-2``,  ``1.0.9-1``,  ``1.0.9-0``,  ``1.0.8-0``,  ``1.0.7-2``,  ``1.0.7-0``,  ``v1.0.7-1``,  ``v1.0.7-0``,  ``v1.0.6-0``,  ``v1.0.5-0``,  ``v1.0.4-0``,  ``v1.0.3-2``,  ``v1.0.2-1``,  ``v1.0.1-0``

      
      .. raw:: html

         </details>
      

   
   :depends biopython: ``1.77.*``
   :depends blast: 
   :depends glimmer: 
   :depends openssl: ``>=1.1.0,<=1.1.1``
   :depends perl: ``>=5.32.1,<6.0a0 *_perl5``
   :depends perl-bioperl: ``>=1.7.2``
   :depends perl-posix: 
   :depends plastid: 
   :depends prodigal: 
   :depends pysam: ``0.16.0.1.*``
   :depends r-ggplot2: 
   :depends r-prroc: 
   :depends r-randomforest: 
   :depends r-rocr: 
   :depends r-sizer: 
   :depends samtools: 
   :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 reparation_blast

   and update with::

      mamba update reparation_blast

  To create a new environment, run::

      mamba create --name myenvname reparation_blast

  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/reparation_blast:<tag>

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


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


.. raw:: html

    <script>
        var package = "reparation_blast";
        var versions = ["1.0.9","1.0.9","1.0.9","1.0.9","1.0.8"];
    </script>






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

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

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
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