PROJECT NAME

• Contributors:
  • YOUR NAME (YOUR GH HANDLE) [cre, aut]

Cool Documentation

IN PROGRESS

TO DO:

1. add an all rule to the ROOT Snakefile
2. Add Snakefile skeletons to each of the directories where work is likley to take place

How to Run

1. Open a terminal and navigate to this directory
2. run snakemake all

Install instructions

The goal is to make our entire workflow reproducible. To do this we want (i) the steps we need to take to process everything (our workflow) should be explicitly stated; (ii) any packages we load in our R code to be stored so everyone who tries to run our code has the same versions installed

Installing R

• Install the latest version of R by following the instructions here.
  • You can ignore the RStudio instructions for the purpose of this project.

Documenting and Executing the Workflow

This project uses Snakemake to execute our research workflow. You can install snakemake as follows:

• Install Snakemake from the command line (needs pip, and Python)

  pip install snakemake
  

  • If you haven't got Python installed click here for instructions

Archiving our R packages

To ensure that the same output is returned whenever our code is run we want to ensure that the same R packages are used, and that the save version of the package is used. Packrat is a package manager that facilitates this task for us.

packrat is itself an R package. Once you have installed R and Snakemake we can install packrat as follows:

• Open a terminal and navigate to this folder.

• Install packrat by entering the following into the terminal, and pressing Return:

  snakemake packrat_install
  

  This opens an R session to install packrat for us.

• If you are starting a new project, which is likely if you are using this template, you need to initialize a new packrat instance to track your R packages and store them. Enter the following command into the same terminal as above and press Return.

  snakemake packrat_init
  

LICENSE

TBD

Suggested Citation:

Deer, Lachlan and Julian Langer. 2018. Reproducible Economics Research Workflows with Snakemake.