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        "description": ".. image:: http://mavis.bcgsc.ca/docs/latest/_static/acronym.svg\n\n|\n\n\n\n.. image:: https://img.shields.io/pypi/v/mavis.svg\n   :target: https://img.shields.io/pypi/v/mavis.svg\n   :alt: PyPi\n\n.. image:: https://travis-ci.org/bcgsc/mavis.svg?branch=master\n   :target: https://travis-ci.org/bcgsc/mavis.svg?branch=master\n   :alt: Travis\n\n.. image:: https://readthedocs.org/projects/pip/badge/\n   :target: https://readthedocs.org/projects/pip/badge/\n   :alt: ReadTheDocs\n\n\nAbout\n=====\n\n`MAVIS <http://mavis.bcgsc.ca>`__ is python command-line tool for the post-processing of structural variant calls.\nThe general `MAVIS <http://mavis.bcgsc.ca>`__ pipeline consists of six main stages\n\n\n* convert\n* `cluster <http://mavis.bcgsc.ca/docs/latest/mavis.cluster.html#mavis-cluster>`_\n* `validate <http://mavis.bcgsc.ca/docs/latest/mavis.validate.html#mavis-validate>`_\n* `annotate <http://mavis.bcgsc.ca/docs/latest/mavis.annotate.html#mavis-annotate>`_\n* `pairing <http://mavis.bcgsc.ca/docs/latest/mavis.pairing.html#mavis-pairing>`_\n* `summary <http://mavis.bcgsc.ca/docs/latest/mavis.summary.html#mavis-summary>`_\n\nGetting Help\n------------\n\nAll steps in the MAVIS pipeline are called following the main mavis entry point. The usage menu can be viewed\nby running without any arguments, or by giving the -h/--help option\n\n.. code-block:: bash\n\n   mavis -h\n\nHelp sub-menus can be found by giving the pipeline step followed by no arguments or the -h options\n\n.. code-block:: bash\n\n   mavis cluster -h\n\nCommon problems and questions are addressed on the `wiki <https://github.com/bcgsc/mavis/wiki/Help-and-Frequently-Asked-Questions>`_.\nIf you have a question or issue that is not answered there (or already a github issue) please submit\na 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>`_\n\nInstall Instructions\n--------------------\n\nThere 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\n\n1. Install Aligner\n^^^^^^^^^^^^^^^^^^\n\nIn addition to the python package dependencies, `MAVIS <http://mavis.bcgsc.ca>`__ also requires an aligner to be installed.\nCurrently 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>`_.\nFor MAVIS to run successfully the aligner must be installed and accessible on the path.\nIf you have a non-standard install you may find it useful to edit the PATH environment variable. For example\n\n.. code-block:: bash\n\n   export PATH=/path/to/directory/containing/blat/binary:$PATH\n\n`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\n`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.\n\n.. code-block:: bash\n\n   export MAVIS_ALIGNER='bwa mem'\n   export MAVIS_ALIGNER_REFERENCE=/path/to/mem/fasta/ref/file\n\nAfter this has been installed MAVIS itself can be installed through `pip <https://pypi.org/project/mavis/>`_\n\n2. Install MAVIS\n^^^^^^^^^^^^^^^^\n\nInstall using pip\n~~~~~~~~~~~~~~~~~\n\nThe 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>`_\n\nEnsuring 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\n\n.. code-block:: bash\n\n   pip install --upgrade pip setuptools\n\nor (for Anaconda users)\n\n.. code-block:: bash\n\n   conda update pip setuptools\n\nIf 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>`_\n\nThen install mavis itself\n\n.. code-block:: bash\n\n   pip install mavis\n\nThis will install mavis and its python dependencies.\n\nInstall using Buildout\n~~~~~~~~~~~~~~~~~~~~~~\n\nAlternatively you can use the `bootstrap/buildout <http://www.buildout.org/en/latest/>`__ to install mavis into bin/mavis\n\n.. code-block:: bash\n\n   git clone https://github.com/bcgsc/mavis.git\n   cd mavis\n   pip install zc.buildout\n   python bootstrap.py\n   bin/buildout\n\nThis will install mavis and its python dependencies into eggs inside the cloned mavis directory which can be used by simply running bin/mavis\n\n3. Build or Download Reference Files\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nAfter `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.\n\n.. code-block:: bash\n\n   cd /path/to/where/you/want/to/put/the/files\n   wget https://raw.githubusercontent.com/bcgsc/mavis/master/tools/get_hg19_reference_files.sh\n   bash get_hg19_reference_files.sh\n   source reference_inputs/hg19_env.sh\n\nOnce the above 3 steps are complete `MAVIS <http://mavis.bcgsc.ca>`__ is ready to be run.\nSee the MAVIS `tutorial <http://mavis.bcgsc.ca/docs/latest/pipeline.html#mavis-mini-tutorial>`__ to learn about running MAVIS.\n\nCitation\n--------\n\nIf you use MAVIS as a part of your project please cite\n\n`Reisle,C. et al. (2018) MAVIS: Merging, Annotation, Validation, and Illustration of Structural variants. Bioinformatics. <https://doi.org/10.1093/bioinformatics/bty621>`_\n\n\n",
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