Getting Started

Getting Started#

Downloading the package#

CanSig can be downloaded directly from github.

   git clone https://github.com/BoevaLab/CanSig-benchmark.git
   cd CanSig-benchmark

Installing the enviorments#

This repository provides conda environments for reproducing our benchmarking. We provide two installation options for different reproducibility needs.

Option 1: Exact Reproducibility Use environments from envs/with_build/:

   conda env create -f envs/with_build/CanSig-R.yml
   conda env create -f envs/with_build/CanSig-python.yml
   conda env create -f envs/with_build/cansig-benchmark.yml

Option 2: Flexible installation

Use environments from envs/without_build/:

   conda env create -f envs/without_build/CanSig-R.yml
   conda env create -f envs/without_build/CanSig-python.yml
   conda env create -f envs/without_build/cansig-benchmark.yml

The whole benchmark is run with the cansig-benchmark environment and snakemake activates the other environments.

   conda activate cansig-benchmark

Running the snakemake pipeline#

   snakemake --configfile <path_to_your_config> -c <number_of_cores>

To reproduce the results from the paper run

   snakemake --configfile config/config_gbm.yml -c <number_of_cores>
   snakemake --configfile config/config_breast.yml -c <number_of_cores>
   snakemake --configfile config/config_scc.yml -c <number_of_cores>
   snakemake --configfile config/config_luad.yml -c <number_of_cores>