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

.. title:: Package Recipe 'bcbio-nextgen-vm'
.. highlight: bash

bcbio-nextgen-vm
================

.. conda:recipe:: bcbio-nextgen-vm
   :replaces_section_title:
   :noindex:

   Run bcbio\-nextgen genomic sequencing analyses using isolated containers and virtual machines

   :homepage: https://github.com/chapmanb/bcbio-nextgen-vm
   :license: MIT
   :recipe: /`bcbio-nextgen-vm <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bcbio-nextgen-vm>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bcbio-nextgen-vm/meta.yaml>`_

   


.. conda:package:: bcbio-nextgen-vm

   |downloads_bcbio-nextgen-vm| |docker_bcbio-nextgen-vm|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>0.1.6-3</code>,  <code>0.1.6-2</code>,  <code>0.1.6-1</code>,  <code>0.1.6-0</code>,  <code>0.1.5-0</code>,  <code>0.1.3-1</code>,  <code>0.1.2a-1</code>,  <code>0.1.1-1</code>,  <code>0.1.1-0</code>,  </span></summary>
      

      ``0.1.6-3``,  ``0.1.6-2``,  ``0.1.6-1``,  ``0.1.6-0``,  ``0.1.5-0``,  ``0.1.3-1``,  ``0.1.2a-1``,  ``0.1.1-1``,  ``0.1.1-0``,  ``0.1.0a-136``,  ``0.1.0a-135``,  ``0.1.0a-134``,  ``0.1.0a-133``,  ``0.1.0a-132``,  ``0.1.0a-131``,  ``0.1.0a-130``,  ``0.1.0a-129``,  ``0.1.0a-128``,  ``0.1.0a-127``,  ``0.1.0a-126``,  ``0.1.0a-125``,  ``0.1.0a-124``,  ``0.1.0a-123``,  ``0.1.0a-122``,  ``0.1.0a-121``,  ``0.1.0a-120``,  ``0.1.0a-119``,  ``0.1.0a-118``,  ``0.1.0a-117``,  ``0.1.0a-116``,  ``0.1.0a-115``,  ``0.1.0a-114``,  ``0.1.0a-113``,  ``0.1.0a-112``,  ``0.1.0a-111``,  ``0.1.0a-110``,  ``0.1.0a-109``,  ``0.1.0a-108``,  ``0.1.0a-107``,  ``0.1.0a-106``,  ``0.1.0a-105``,  ``0.1.0a-104``,  ``0.1.0a-103``,  ``0.1.0a-102``,  ``0.1.0a-101``,  ``0.1.0a-100``,  ``0.1.0a-99``,  ``0.1.0a-98``,  ``0.1.0a-97``,  ``0.1.0a-96``,  ``0.1.0a-95``,  ``0.1.0a-94``,  ``0.1.0a-93``,  ``0.1.0a-92``,  ``0.1.0a-91``,  ``0.1.0a-90``,  ``0.1.0a-89``,  ``0.1.0a-88``,  ``0.1.0a-87``,  ``0.1.0a-86``,  ``0.1.0a-85``,  ``0.1.0a-84``,  ``0.1.0a-83``,  ``0.1.0a-82``,  ``0.1.0a-81``,  ``0.1.0a-80``,  ``0.1.0a-79``,  ``0.1.0a-78``,  ``0.1.0a-77``,  ``0.1.0a-76``,  ``0.1.0a-75``,  ``0.1.0a-74``,  ``0.1.0a-73``,  ``0.1.0a-72``,  ``0.1.0a-71``,  ``0.1.0a-70``,  ``0.1.0a-69``

      
      .. raw:: html

         </details>
      

   
   :depends arvados-cwl-runner: ``>=1.3.1.20190301150258``
   :depends bcbio-nextgen: ``>1.1.4``
   :depends boto3: 
   :depends cachecontrol: ``0.11.7``
   :depends cromwell: ``>=0.36``
   :depends cwltool: 
   :depends dx-cwl: ``>=0.1.0a20180820``
   :depends dxpy: 
   :depends google-cloud-sdk: 
   :depends ipyparallel: ``>=6.0.2``
   :depends nodejs: 
   :depends nose: 
   :depends pathlib2: ``2.3.2``
   :depends pysam: ``>=0.15.2``
   :depends python: 
   :depends python-dateutil: ``>=2.5.0``
   :depends rabix-bunny: ``>=1.0.4``
   :depends ruamel.yaml: ``>=0.13.0``
   :depends sevenbridges-python: ``>=0.17.5``
   :depends six: 
   :depends synapseclient: 
   :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 bcbio-nextgen-vm

   and update with::

      mamba update bcbio-nextgen-vm

  To create a new environment, run::

      mamba create --name myenvname bcbio-nextgen-vm

  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/bcbio-nextgen-vm:<tag>

   (see `bcbio-nextgen-vm/tags`_ for valid values for ``<tag>``)


.. |downloads_bcbio-nextgen-vm| image:: https://img.shields.io/conda/dn/bioconda/bcbio-nextgen-vm.svg?style=flat
   :target: https://anaconda.org/bioconda/bcbio-nextgen-vm
   :alt:   (downloads)
.. |docker_bcbio-nextgen-vm| image:: https://quay.io/repository/biocontainers/bcbio-nextgen-vm/status
   :target: https://quay.io/repository/biocontainers/bcbio-nextgen-vm
.. _`bcbio-nextgen-vm/tags`: https://quay.io/repository/biocontainers/bcbio-nextgen-vm?tab=tags


.. raw:: html

    <script>
        var package = "bcbio-nextgen-vm";
        var versions = ["0.1.6","0.1.6","0.1.6","0.1.6","0.1.5"];
    </script>






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

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

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