TODO: Fill in details of planned experiments to be reproduced.
Additional details of the experiments, data, and conclusions can be found in the report/.
The source code is written in Python 3. We use snakemake to manage the workflow. We suggest using Conda to install dependencies, which you can do directly from the provided environment.yml file.
conda env create -f environment.yml
source activate reproducing-davies2017-env
We have included two git modules that you will need to download before you can run snakemake all
git submodule init
git submodule update
To download the input data files and reproduce the experiments and..., simply run:
snakemake all
TODO: insert some expectation of runtime.
Additional configuration options are detailed at the beginning of the Snakefile.
There are also various command-line options for the provided scripts in src/.
- Davies, et al. (2017) "HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures." Nature Medicine 23, pages 517-525. doi: 10.1038/nm.4292