To reproduce the analysis in this repository and the associated paper follow these steps:
- Install
pipenv
usingpip install pipenv
- Clone this repository
git clone git@github.com:camlab-bioml/active-learning-benchmarking.git
- Move into the folder that was created as part of the previous step:
cd active-learning-benchmarking
- Install the environment required for this analysis to work using
pipenv install
- Create a snakemake profile by following these instructions: https://github.com/Snakemake-Profiles/slurm
- Inside the root directory of this repository run the following commands
module load singularity
snakemake --profile [your_snakemake_profile] -j [n_jobs] --rerun-incomplete
where
- [your_snakemake_profile] is the name of the snakemake profile you generated in step 5
- [n_jobs] is the total number of jobs you would like to be submitted at a time