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A Structural Variant Post-Processing Package

Project description

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About

MAVIS is python command-line tool for the post-processing of structural variant calls. The general MAVIS pipeline consists of six main stages

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

mavis -h

Help sub-menus can be found by giving the pipeline step followed by no arguments or the -h options

mavis cluster -h

Common problems and questions are addressed on the wiki. 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 or contact us by email at mavis@bcgsc.ca

Install Instructions

There are 3 major steps to setting up and installing MAVIS.

1. Install Aligner

In addition to the python package dependencies, MAVIS also requires an aligner to be installed. Currently the only aligners supported are blat and bwa mem. 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

export PATH=/path/to/directory/containing/blat/binary:$PATH

blat is the default aligner. To configure MAVIS to use bwa mem as a default instead, use the MAVIS environment variables. Make sure to specify BOTH of the variables below to change the default aligner.

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

2. Install MAVIS

Install using pip

The easiest way to install MAVIS is through the python package manager, pip. If you do not have python3 installed it can be found here

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

pip install --upgrade pip setuptools

or (for Anaconda users)

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

Then install mavis itself

pip install mavis

This will install mavis and its python dependencies.

Install using Buildout

Alternatively you can use the bootstrap/buildout to install mavis into bin/mavis

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 is installed the reference 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.

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 is ready to be run. See the MAVIS tutorial to learn about running MAVIS.

Build the Sphinx Documentation

pip install .[docs]
sphinx-build docs/source/ html

Deploy to PyPi

Install m2r to ensure the README is converted nicely

pip install m2r

Install to build the egg

python setup.py install

Build the other distribution files

python setup.py sdist

Use twine to upload

twine upload -r pypi dist/*

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