This repositiory contains the code required to reproduce the copy number analysis presented in the publication The copy number and mutational landscape of recurrent ovarian high-grade serous carcinoma (Smith & Bradley et al. 2023 - Nature Communications).
Clone this git repository and cd into the directory
git clone https://github.com/BRITROC/britroc-1-cn-analysis.git
cd britroc-1-cn-analysis
Provided conda is installed and available on the $PATH run the following line. This will downloaded the pre-processed data from zenodo, install the required conda environment, and install packages which are not available via conda channels.
./install_env.sh {CONDA_INSTALL}
Where {CONDA_INSTALL} is the path to your conda directory, such as /home/username/resources/miniconda/.
conda activate britroc
Given all the previous steps were completed without issue, the entire copy number analysis can be reproduced by running the following bash script
./run_analysis_pipeline.sh
This will generate html markdown documents for all analyses performed as part of this publication excluding the compilation of main figures which is dependent on additional repositories.