R container library for reporanalysis

A collection of project-related Dockerfiles for a controlled R environment with defined R packages.

THIS IS WORK IN PROGRESS !

Build new R analysis projects from the template

We have a R analysis template and you can use the cookiecutter tool for that. Please check out https://github.com/qbicsoftware/qbic-r-analysis-template and follow the instructions shown in the README.

1. Fork this repo

Please check the GitHub help pages for that.

2. Clone the fork

As easy as:

git clone https://github.com/<yourname>/qbic-r-analysis

3. Create a new R analysis project using cookiecutter

Use cookiecutter and a project from a template with:

cookiekutter https://github.com/qbicsoftware/qbic-r-analysis-template

You will get asked to answer some questions, and cookiecutter will automatically put the information into the template!

> cookiekutter https://github.com/qbicsoftware/qbic-r-analysis-template
r_version [3.2.4]: 
author_name [Sven Fillinger]: 
author_email [[email protected]]: 
container_version [0.1dev]: 
project_code [QABCD]: 

The values in [] are the default values, that are taken if you just hit enter.

4. Modify the template

Next, you still need to make some adjustments. The current project structure looks like this:

projects/
    projectA/
        Dockerfile
        rpackages.txt
        scripts/
          myscript.R
    projectB/
        ...

When you have created your project, you have to replace the content of the rpackages.txt with the packages you want to have installed in your R container.

Export the packages from the R session variable

RCOMMAND

Author

This repo was created by Sven Fillinger (@sven1103), Quantitative Biology Center, University of Tübingen.