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README.md

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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.