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Pvalue Match

Calculate pvalue match tables for use with SStar

Installation and setup

  1. Clone the workflow

    git clone https://lance_parsons@bitbucket.org/lance_parsons/abwolf_match_pvalue_simulations.git
    
  2. Setup Bioconda

    Install Miniconda and setup Bioconda if you have not already done so.

  3. Install dependencies and archaic_match

    Bioconda is used to install the various dependencies. We then install the development version of archaic_match using pip.

    conda env create -n abwolf_match_pvalue_simulations -f environment.yaml
    source activate abwolf_match_pvalue_simulations
    pip install --no-deps --ignore-installed git+https://github.com/lparsons/archaic_match
    
  4. Prepare input data

  5. Edit config.yaml

  6. Run workflow

    This workflow uses Snakemake to manage the steps of the workflow.

    To see a dry run of the workflow:

    snakemake -nrp
    

    To run the workflow locally (not using cluster resources):

    snakemake --use-conda -rp -j $num_threads
    

    To run the workflow configured for cetus/gen-comp1 use run_cetus.sh which executes the following:

    snakemake --cluster-config 'cetus_cluster.yaml' \
            --drmaa " --cpus-per-task={cluster.n} --mem={cluster.memory} --qos={cluster.qos}" \
            --use-conda -w 60 -rp -j 250 "$@"