Metadata-Version: 1.2
Name: mavis
Version: 1.6.10
Summary: A Structural Variant Post-Processing Package
Home-page: https://github.com/bcgsc/mavis.git
Author: Caralyn Reisle
Author-email: creisle@bcgsc.ca
License: UNKNOWN
Download-URL: https://github.com/bcgsc/mavis/archive/v1.6.10.tar.gz
Project-URL: mavis, http://mavis.bcgsc.ca
Description-Content-Type: UNKNOWN
Description: .. image:: http://mavis.bcgsc.ca/docs/latest/_static/acronym.svg
        
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        *(master)* 
        
        
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        *(develop)* 
        
        `MAVIS <http://mavis.bcgsc.ca>`__ is python command-line tool for the post-processing of structural variant calls. 
        The general `MAVIS <http://mavis.bcgsc.ca>`__ pipeline consists of six main stages
        
        
        * convert
        * `cluster <http://mavis.bcgsc.ca/docs/latest/mavis.cluster.html#mavis-cluster>`_
        * `validate <http://mavis.bcgsc.ca/docs/latest/mavis.validate.html#mavis-validate>`_
        * `annotate <http://mavis.bcgsc.ca/docs/latest/mavis.annotate.html#mavis-annotate>`_
        * `pairing <http://mavis.bcgsc.ca/docs/latest/mavis.pairing.html#mavis-pairing>`_
        * `summary <http://mavis.bcgsc.ca/docs/latest/mavis.summary.html#mavis-summary>`_
        
        Getting started
        ---------------
        
        There are 3 major steps to setting up and installing `MAVIS <http://mavis.bcgsc.ca>`_
        
        
        #. **Install non-python dependencies**
        
        Before `MAVIS <http://mavis.bcgsc.ca>`__ can be installed, the `non-python dependencies <http://mavis.bcgsc.ca/docs/latest/about.html#non-python-dependencies>`__ will need to be installed.
        After these have been installed MAVIS itself can be installed through pip
        
        These include: an aligner (\ `blat <http://mavis.bcgsc.ca/docs/latest/glossary.html#term-blat>`__ or `bwa mem <http://mavis.bcgsc.ca/docs/latest/glossary.html#term-bwa>`_\ ) and `samtools <http://samtools.sourceforge.net>`_.
        
        
        #. **Install MAVIS**
        
        The easiest way to install `MAVIS <http://mavis.bcgsc.ca>`__ is through the python package manager, pip
        
        .. code-block::
        
           pip install mavis
        
        This will install mavis and its python dependencies.
        
        
        #. **Build reference files**
        
        After `MAVIS <http://mavis.bcgsc.ca>`__ is installed the `reference files <http://mavis.bcgsc.ca/docs/latest/reference.html>`__ must be generated (or downloaded) before it can be run.
        
        Once the above 3 steps are complete `MAVIS <http://mavis.bcgsc.ca>`__ is ready to be run. See `running the pipeline <http://mavis.bcgsc.ca/docs/latest/pipeline.html>`_.
        
        Help
        ----
        
        If you have a question or issue that is not answered in the `FAQs <http://mavis.bcgsc.ca/docs/latest/faqs.html>`__ please submit
        an issue to our `github page <https://github.com/bcgsc/mavis/issues>`__ or contact us by email at `mavis@bcgsc.ca <mailto:mavis@bcgsc.ca>`_
        
Platform: UNKNOWN
Requires-Python: >=3
