This is a bare R project template that can be directly imported in Renku.
(See the Importing in Renku section below)
This is an R project and the .Rproj file is located in the main directory.
The entire environment required for this project is described in the Dockerfile located in the main directory.
It allows to generate a docker image that runs an instance of R Studio server in which the R project can be open.
You can change the R version that will be installed on the docker image by editing the FROM statement that specifies a base image in the Dockerfile:
FROM renku/renkulab-r:4.0.0-renku0.10.4-0.6.3
A list of available base images can be found at https://hub.docker.com/r/renku/renkulab-r/tags.
Chose one with the R version you want. For example, for R 3.6.2, you can chose the 3.6.2-renku0.10.4-0.6.3 image.
Don't forget to also update the R version in the renv.lock file (see the R dependencies section below).
This project uses the renv R package to manage R packages dependencies.
The renv.lock file is located in the main directory.
Renv has been set to install R packages on this project's docker image.
Therefore, the renv/ directory in the main directory of this project has been set as a symbolic link to the renv library located on the docker image, in the /home/rstudio directory.
To change this behavior, edit the install.R file located in the main directory. Don't forget to also change the renv link into an actual renv/ directory.
The prefered way to install additional R packages and manage them with renv is to use the install.packages()
command within an R session and to update the renv.lock file using the renv::snapshot(type="all") command.
As alternatives, you could :
- directly edit the
renv.lockfile -⚠️ be sure to know what you are doing though.
OR - add the
install.packages()command to theinstall.Rfile. However, this will not update the project'srenv.lockfile unless you userenv::snapshot()in an R session.
The required python packages can be listed in the requirements.txt file located in the main directory.
They will be installed on the docker image with pip3 (see the Dockerfile in the main directory).
- Go to
GitLab->New Project->Import Project->Repo by URL - Fill-in the essential fields:
- Git repository URL: https://github.com/auwerxlab/renku-r-template.git
- Project name: your-project-name
- Project slug: your-project-slug
- Click on
Create Project. - In your new project, update this README.md file with an appropriate description and commit your changes.
You will find a template for this purpose in the README.md template section below.
Also consider adding an appropriate license to the project. - After completing a first commit, the project interactive environment gets accessible in the Renku UI.
👍 That's it!
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Description of the project goals, applications and steps.
$ git clone <this_project_url>.git
This is an R project and the .Rproj file is located in the main directory.
The entire environment required for this project is described in the Dockerfile located in the main directory.
It allows to generate a docker image that runs an instance of R Studio server in which the R project can be open.
You can change the R version that will be installed on the docker image by editing the FROM statement that specifies a base image in the Dockerfile:
FROM renku/renkulab-r:4.0.0-renku0.10.4-0.6.3
A list of available base images can be found at https://hub.docker.com/r/renku/renkulab-r/tags.
Chose one with the R version you want. For example, for R 3.6.2, you can chose the 3.6.2-renku0.10.4-0.6.3 image.
This project uses the renv R package to manage R packages dependencies.
The renv.lock file is located in the main directory.
Renv has been set to install R packages on this project's docker image.
Therefore, the renv/ directory in the main directory of this project has been set as a symbolic link to the renv library located on the docker image, in the /home/rstudio directory.
To change this behavior, edit the install.R file located in the main directory. Don't forget to also change the renv link into an actual renv/ directory.
The prefered way to install additional R packages and manage them with renv is to use the install.packages()
command within an R session and to update the renv.lock file using the renv::snapshot(type="all") command.
As alternatives, you could :
- directly edit the
renv.lockfile -⚠️ be sure to know what you are doing though.
OR - add the
install.packages()command to theinstall.Rfile. However, this will not update the project'srenv.lockfile unless you userenv::snapshot()in an R session.
The required python packages can be listed in the requirements.txt file located in the main directory.
They will be installed on the docker image with pip3 (see the Dockerfile in the main directory).
This project uses Git to track files versions.
Description of the directory tree structure.
data/: Contains raw and processed data and metadata, including initial, intermediate data and final data and metadata.notebooks/: Contains computational notebooks used to process the data and metadata.bin/: Contains executable code.figs/: Contains figures..renku/: Contains files used by the Renku platform and its associatedrenkupython package.
Description of the data, metadata and code used in this project. For example:
- Data: How are data organized and used in this project? What is their source?
- Metadata: How are metadata organized and used in this project? What is their source?
- Code: How is the code organized and used in this project?
Reference and description to any associated study. For example:
- Study title
- Principal investigator: Name, contact and affiliation of the principal investigator.
- Associated funding: Reference to any funding.
- Associated publications: Links to any associated publications.
Names, contacts, affiliations and respective contributions of the project authors.
Description of any method associated to the code or datasets used in the project, any related ontologies and external references.
Mention of licenses associated with the project and/or part of the project.
- This project is based on the following template: https://github.com/auwerxlab/renku-r-template.git v1.0.1