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Install Instructions

Once the install steps are complete MAVIS is ready to be run. See the MAVIS tutorial to learn about running MAVIS.

For either install option you will want to install the main Snakefile. It is best to use a tag to specify the version of interest but you can download the latest version from the master branch

wget -O Snakefile

Install for Docker/Singularity

The simplest way to use MAVIS is via Singularity. The MAVIS docker container used by singularity will take care of installing the aligner as well.

pip install -U setuptools pip wheel
pip install mavis_config  # also installs snakemake

Now you will run mavis via Snakemake as follows

snakemake \
    -j <MAX JOBS> \
    --configfile <YOUR CONFIG> \
    --use-singularity \
    -s Snakefile

Install (Python Only)

MAVIS can also be run with just python. However you will need to install the aligner(s) required by MAVIS separately and ensure they are availble on the default PATH variable when MAVIS is run

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 it must be specified in the config JSON 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
cd mavis
pip install zc.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

Finally you will need to Build/Download the necessary reference files

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 is provided under mavis/tools for convenience.

Download Hg19 Files

cd /path/to/where/you/want/to/put/the/files

You should now see the reference files in the current directory

|-- cytoBand.txt
|-- ensembl69_hg19_annotations.json
|-- hg19.2bit
|-- hg19.fa

Download Hg38 Files

cd /path/to/where/you/want/to/put/the/files

You should now see the reference files in the current directory

|-- cytoBand.txt
|-- ensembl79_hg38_annotations.json
|-- GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
`-- hg38.2bit