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.