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Snakemake demonstration

Reproduces some tables and graphs from Angrist & Krueger (1991).

How to compile

The project is set up so that snakemake handles the installation of the required dependencies into a local virtual environment. The following external dependencies have to be manually installed:

  • A TeX distribution with pdflatex and latexmk available on the path
  • The snakemake workflow management system

A TeX distribution can be installed using your preferred method (TeX Live for Linux, MikTeX for Windows and MacTeX for MacOS are good default choices, installable via apt/rpm/etc., scoop/chocolately and homebrew, respectively). It is recommended to install snakemake in its own separate conda virtual environment (e.g. conda create -c conda-forge -c bioconda -n snakemake snakemake).

The steps to build the project are described in its snakemake file. If snakemake is installed it can be compiled from scratch by running the snakemake command in its root directory:

    cd /path/to/project-for-pp4rs
    conda activate snakemake
    snakemake --cores all --use-conda

assuming that snakemake is available in the conda environment names snakemake. --cores all sets the number of parallel jobs equal to the number of your logical cpu cores. If you wish to run N jobs in parallel, replace it with --cores N.