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
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 email@example.com
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
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
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<58"
or (for Anaconda users)
conda update pip "setuptools<58"
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
If you use MAVIS as a part of your project please cite