Metadata-Version: 2.1
Name: mavis
Version: 2.2.7
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/v2.2.7.tar.gz
Project-URL: mavis, http://mavis.bcgsc.ca
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        About
        =====
        
        `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 Help
        ------------
        
        All steps in the MAVIS pipeline are called following the main mavis entry point. The usage menu can be viewed
        by running without any arguments, or by giving the -h/--help option
        
        .. code-block:: bash
        
           mavis -h
        
        Help sub-menus can be found by giving the pipeline step followed by no arguments or the -h options
        
        .. code-block:: bash
        
           mavis cluster -h
        
        Common problems and questions are addressed on the `wiki <https://github.com/bcgsc/mavis/wiki/Help-and-Frequently-Asked-Questions>`_.
        If you have a question or issue that is not answered there (or already a github issue) please submit
        a github issue to our `github page <https://github.com/bcgsc/mavis/issues>`__ or contact us by email at `mavis@bcgsc.ca <mailto:mavis@bcgsc.ca>`_
        
        Install Instructions
        --------------------
        
        There are 3 major steps to setting up and installing `MAVIS <http://mavis.bcgsc.ca>`_. If you are a developer contributing to mavis, please see the `instructions for developers page <http://mavis.bcgsc.ca/docs/latest/development.html>`__ instead
        
        1. Install Aligner
        ^^^^^^^^^^^^^^^^^^
        
        In addition to the python package dependencies, `MAVIS <http://mavis.bcgsc.ca>`__ also requires an aligner to be installed.
        Currently the only aligners supported are `blat <http://mavis.bcgsc.ca/docs/latest/glossary.html#term-blat>`__ and `bwa mem <http://mavis.bcgsc.ca/docs/latest/glossary.html#term-bwa>`_.
        For MAVIS to run successfully the aligner must be installed and accessible on the path.
        If you have a non-standard install you may find it useful to edit the PATH environment variable. For example
        
        .. code-block:: bash
        
           export PATH=/path/to/directory/containing/blat/binary:$PATH
        
        `blat <http://mavis.bcgsc.ca/docs/latest/glossary.html#term-blat>`__ is the default aligner. To configure MAVIS to use `bwa mem <http://mavis.bcgsc.ca/docs/latest/glossary.html#term-bwa>`__ as a default instead, use the
        `MAVIS environment variables <http://mavis.bcgsc.ca/configuration.html#environment-variables>`_. Make sure to specify BOTH of the variables below to change the default aligner.
        
        .. code-block:: bash
        
           export MAVIS_ALIGNER='bwa mem'
           export MAVIS_ALIGNER_REFERENCE=/path/to/mem/fasta/ref/file
        
        After this has been installed MAVIS itself can be installed through `pip <https://pypi.org/project/mavis/>`_
        
        2. Install MAVIS
        ^^^^^^^^^^^^^^^^
        
        Install using pip
        ~~~~~~~~~~~~~~~~~
        
        The easiest way to install `MAVIS <http://mavis.bcgsc.ca>`__ is through the python package manager, pip. If you do not have python3 installed it can be found `here <https://www.python.org/downloads>`_
        
        Ensuring you have a recent version of pip and setuptools will improve the install experience. Older versions of pip and setuptools may have issues with obtaining some of the mavis python dependencies
        
        .. code-block:: bash
        
           pip install --upgrade pip setuptools
        
        or (for Anaconda users)
        
        .. code-block:: bash
        
           conda update pip setuptools
        
        If this is not a clean/new python install it may be useful to set up mavis in a `virtual python environment <https://docs.python.org/3/tutorial/venv.html>`_
        
        Then install mavis itself
        
        .. code-block:: bash
        
           pip install mavis
        
        This will install mavis and its python dependencies.
        
        Install using Buildout
        ~~~~~~~~~~~~~~~~~~~~~~
        
        Alternatively you can use the `bootstrap/buildout <http://www.buildout.org/en/latest/>`__ to install mavis into bin/mavis
        
        .. code-block:: bash
        
           git clone https://github.com/bcgsc/mavis.git
           cd mavis
           pip install zc.buildout
           python bootstrap.py
           bin/buildout
        
        This will install mavis and its python dependencies into eggs inside the cloned mavis directory which can be used by simply running bin/mavis
        
        3. Build or Download Reference Files
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        After `MAVIS <http://mavis.bcgsc.ca>`__ is installed the `reference files <http://mavis.bcgsc.ca/docs/latest/mavis_input.html#reference-input-files>`__ must be generated (or downloaded) before it can be run. A simple bash script to download the hg19 reference files and generate a MAVIS environment file is provided under mavis/tools for convenience.
        
        .. code-block:: bash
        
           cd /path/to/where/you/want/to/put/the/files
           wget https://raw.githubusercontent.com/bcgsc/mavis/master/tools/get_hg19_reference_files.sh
           bash get_hg19_reference_files.sh
           source reference_inputs/hg19_env.sh
        
        Once the above 3 steps are complete `MAVIS <http://mavis.bcgsc.ca>`__ is ready to be run.
        See the MAVIS `tutorial <http://mavis.bcgsc.ca/docs/latest/pipeline.html#mavis-mini-tutorial>`__ to learn about running MAVIS.
        
        Citation
        --------
        
        If you use MAVIS as a part of your project please cite
        
        `Reisle,C. et al. (2018) MAVIS: Merging, Annotation, Validation, and Illustration of Structural variants. Bioinformatics. <https://doi.org/10.1093/bioinformatics/bty621>`_
        
Platform: UNKNOWN
Requires-Python: >=3.2
Provides-Extra: dev
Provides-Extra: test
Provides-Extra: docs
Provides-Extra: deploy
