# A computationally reproducible manuscript
This git repository contains the code and text for a totally computationally
reproducible manuscript. It is organized following the principles detailed in
"A quick guide to organizing your computational biology project," Noble.
- data:
Should contain the scripts to download the data (Not demoed).
- doc:
Contains all documents related to the project. In particular,
`doc/manuscript_Rmd/manuscript.Rmd` contains the manuscript.
- scripts:
Contains the code. In this very small example, the only code outside of
the manuscript is a small script to simulate data.
- results:
Should contain the labnoteboo (Not demoed).
Every time anyone pushes to this repository *or* creates a pull request, the
code will be ran, and the manuscript will be compiled from scratch.
## How does it work?
The code and manuscript are built using travis-CI. In order to do this, I rely
on a set of R scripts automated through makefile and a bash script and a bash
script. The first element executed is the makefile in data. For this
particular project, no external data is needed. Thus, the makefile does
nothing. The second element executed is the makefile in scripts. This one only
has one command: it runs the `generate_gaussian_data.R` file, that outputs a
generated data set. The third element executed is the makefile in doc. This
Makefile also does only one thing: compiles the file `compile.R`, which itself
compiles the document manuscript.Rmd