This is a collection of ruffus pipelines and R scripts used for the cribbs group at the botnar research centre Oxford.
I recommend using miniconda to install a conda environment followed by mamba:
conda install mamba
mamba env create -f conda/environments/cribbslab.yml
The repository can also be installed manually, but dependancies will need to be installed seperately::
python setup.py develop
cribbslab --help
Run the ``cribbslab --help`` command view the help documentation for how to run the available workflows.
To run a pipeline first generate a configuration file::
cribbslab <workflow> config
Then run the pipeline::
cribbslab <workflow> make full -v5