superphy/kmer

Using machine learning to predict E. coli phenotypes

Setup

1. Clone repository (run git clone https://github.com/superphy/kmer.git)

2. Download anaconda or miniconda (python 3.7), instructions for that are here

3. Install dependecies: run conda env create -f data/envi.yaml

4. Start conda environment: run source activate skmer

5. Run the following command to prepare the data, where 'X' is the number of cores you wish to use

   snakemake -j X -s src/setup.smk

6. Run the following command to run all of the tests

   snakemake -s src/run_tests.smk or snakemake -s src/slurm_run_tests.smk(if using slurm)

7. Run for dir in results/*; do python src/figures.py $dir/; done to save all the results as figures

Manually Running Tests

If you do not want to run all tests in step 6 of setup, run src/model.py --help to see how to run the model for a specific set of parameters.