wbuild 1.0

Automtic build tool for R Reports

wBuild

Automatic build tool for R Reports

Features

• Enables reproducible research by appending every R-markdown script to the global analysis pipeline written in snakemake

• All R scripts using R-markdown get compiled via Rmarkdown and rendered in a navigable web-page

• This is achieved by writing the snakemake rules directly in the header of your R scripts * Headers allow the same flexibility (i.e. usage of python) as in the traditional Snakefile

Installation

• pip install wBuild

Within the Gagneurlab, load python version /opt/modules/i12g/anaconda/3-4.1.1/ using module system..

Getting started

• Navigate to an empty directory

• Run wbuild demo. This will create a wBuild demo project with various examples.

• Explore the files in Scripts/

• View the compiled version of the demo project: <https://i12g-gagneurweb.in.tum.de/project/wBuild/>

• Run snakemake to compile the projects

• Open Output/html/index.html in your web browser.

Usage

• Navigate to the root of your project (new or existing)

• Run wbuild init

• Run snakemake

Documentation

• Run wbuild –help or wbuild <command> –help to learn more about available wBuild commands.

• See the documentation/demo page at <https://i12g-gagneurweb.in.tum.de/project/wBuild/>

Credits

Leonhard Wachutka

History

0.1.0 (2017-06-23)

• First release on PyPI.

1.0 (2017-12-15)

• Improved Demo

• Many fixes