System Requirements

COWSNPhR has been tested with Debian-based Linux systems, but should in principle work on any flavour of Linux, as well as MacOSX. Windows isn't supported, but it may very well be installable via bioconda.

COWSNPhR should run on any regular desktop/laptop with 8 GB or RAM or more.

Download DeepVariant Docker image

You must have docker installed, and be a member of the 'docker' users group

To install docker, follow this guide

To create the docker group and add your user:

- Create the docker group. $ sudo groupadd docker.
- Add your user to the docker group. $ sudo usermod -aG docker $USER.
- Log out and log back in so that your group membership is re-evaluated. ...
- Verify that you can run docker commands without sudo .

Download the DeepVariant image

docker pull gcr.io/deepvariant-docker/deepvariant:1.0.0

Installing Using Conda

COWSNPhR is available as a conda package.

To install conda, as well as the COWSNPhR:

Download and run the conda installation scrips

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
bash miniconda.sh -b -p $HOME/miniconda
export PATH="$HOME/miniconda/bin:$PATH"
conda update -q conda

Add the necessary channels to your conda installation

conda config --add channels olcbioinformatics
conda config --add channels conda-forge
conda config --add channels bioconda

Install the COWSNPhR conda package

conda install -c olcbioinformatics cowsnphr

With that done, typing cowsnphr.py, cowsnphr or python -m cowsnphr_src.cowsnphr launch the COWSNPhR pipeline. See the Usage section for instructions on how to use the COWSNPhR.