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

.. title:: Package Recipe 'sra-tools'
.. highlight: bash

sra-tools
=========

.. conda:recipe:: sra-tools
   :replaces_section_title:
   :noindex:

   SRA Toolkit and SDK from NCBI

   :homepage: https://github.com/ncbi/sra-tools
   :documentation: https://github.com/ncbi/sra-tools/wiki
   
   :license: Public Domain
   :recipe: /`sra-tools <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/sra-tools>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/sra-tools/meta.yaml>`_

   The SRA Toolkit and SDK from NCBI is a collection of tools and libraries
   for using data in the INSDC Sequence Read Archives.



.. conda:package:: sra-tools

   |downloads_sra-tools| |docker_sra-tools|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>3.1.0-1</code>,  <code>3.1.0-0</code>,  <code>3.0.10-0</code>,  <code>3.0.9-0</code>,  <code>3.0.8-0</code>,  <code>3.0.7-0</code>,  <code>3.0.6-0</code>,  <code>3.0.5-1</code>,  <code>3.0.5-0</code>,  </span></summary>
      

      ``3.1.0-1``,  ``3.1.0-0``,  ``3.0.10-0``,  ``3.0.9-0``,  ``3.0.8-0``,  ``3.0.7-0``,  ``3.0.6-0``,  ``3.0.5-1``,  ``3.0.5-0``,  ``3.0.3-0``,  ``3.0.0-1``,  ``3.0.0-0``,  ``2.11.0-3``,  ``2.11.0-2``,  ``2.11.0-1``,  ``2.11.0-0``,  ``2.10.9-0``,  ``2.10.8-0``,  ``2.10.7-2``,  ``2.10.7-1``,  ``2.10.7-0``,  ``2.10.3-0``,  ``2.10.1-0``,  ``2.10.0-0``,  ``2.9.6-0``,  ``2.9.1_1-0``,  ``2.9.1-0``,  ``2.9.0-1``,  ``2.8.2-1``,  ``2.8.2-0``,  ``2.8.1-0``,  ``2.8.0-0``,  ``2.7.0-0``,  ``2.6.3-0``,  ``2.6.2-0``

      
      .. raw:: html

         </details>
      

   
   :depends ca-certificates: 
   :depends curl: 
   :depends libgcc-ng: ``>=12``
   :depends libstdcxx-ng: ``>=12``
   :depends ncbi-vdb: ``>=3.1.0``
   :depends ncbi-vdb: ``>=3.1.0,<4.0a0``
   :depends ossuuid: 
   :depends perl: 
   :depends perl-uri: 
   :depends perl-xml-libxml: 
   :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 sra-tools

   and update with::

      mamba update sra-tools

  To create a new environment, run::

      mamba create --name myenvname sra-tools

  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/sra-tools:<tag>

   (see `sra-tools/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "sra-tools";
        var versions = ["3.1.0","3.1.0","3.0.10","3.0.9","3.0.8"];
    </script>





Notes
-----
After installation\, you should run the configuration tool\: .\/vdb\-config \-i. This tool will setup your download\/cache area for downloaded files and references.


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/sra-tools/README.html)

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