This is the complete use case described in the manuscript "Language-Agnostic Reproducible Data Analysis Using Literate Programming".

To get the source and data and change to the directory:

$ git clone https://github.com/borisvassilev/endobrca.git
$ cd endobrca

You will already have access to the generated display items and final documentation in tcga.html. The links to data files from within tcga.html however will not work. You need to re-run the analysis!

If you have already installed lir and want to regenerate all data and documentation, after cloning the repository, run:

$ make

In addition to standard command line tools, the analysis requires R and SQLite, so you need reasonably recent versions of both installed on your computer.