Active learning benchmarking

To reproduce the analysis in this repository and the associated paper follow these steps:

1. Install pipenv using pip install pipenv
2. Clone this repository git clone git@github.com:camlab-bioml/active-learning-benchmarking.git
3. Move into the folder that was created as part of the previous step: cd active-learning-benchmarking
4. Install the environment required for this analysis to work using pipenv install
5. Create a snakemake profile by following these instructions: https://github.com/Snakemake-Profiles/slurm
6. 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