qbicsoftware/qbic-r-analysis repository overview

⁠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.