Pvalue Match

Calculate pvalue match tables for use with SStar

Installation and setup

  1. Clone the workflow

    git clone
  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.yml
    source activate abwolf_match_pvalue_simulations
  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 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 "$@"