https://github.com/datasnakes/beRi

beRi "beri environments for R installations" is an R environment, R installation, and R package management system for R
https://github.com/datasnakes/beRi

biohackathon cli environment hackathon hackseq18 package-management package-manager python3 r

Last synced: 1 day ago
JSON representation

beRi "beri environments for R installations" is an R environment, R installation, and R package management system for R

• Host: GitHub
• URL: https://github.com/datasnakes/beRi
• Owner: datasnakes
• License: mit
• Created: 2018-04-19T21:51:25.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2019-10-28T23:09:56.000Z (over 5 years ago)
• Last Synced: 2025-04-15T07:08:38.933Z (17 days ago)
• Topics: biohackathon, cli, environment, hackathon, hackseq18, package-management, package-manager, python3, r
• Language: Python
• Homepage: https://datasnakes.github.io/get-beri/
• Size: 45.9 KB
• Stars: 14
• Watchers: 5
• Forks: 0
• Open Issues: 8
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        


Are you a  bioinformatician who desires to manage R environments, install R, and install R packages using the command-line? Help develop beRi!


# beRi  [![Gitter chat](https://badges.gitter.im/CRANbeRi/Lobby.svg)](https://gitter.im/CRANbeRi/Lobby)

beRi "beri environments for R installations" is an R environment, R installation, and R package management system for R. 

The project was initially conceptualized by [Robert Gilmore](https://github.com/grabear). Gilmore proposed the project to [hackseq18](https://www.hackseq.com/) where it was developed over 3 days by a great team of [developers](#hackseq18-team-members). It ultimately went on to win hackseq18.








## What is beRi?

beRi is a suite of Python packages composed of the following components: (1) [renv](https://github.com/datasnakes/renv), a virtual environment manager for R; [rinse](https://github.com/datasnakes/rinse), an R installation and R version manager; and (3) [rut](https://github.com/datasnakes/rut), an R utility tool for installing packages, managing native R configuration files, and setting up local CRAN-like repositories. These packages will be developed in separate repositories as standalone command-line interfaces (CLIs). [beRi](https://github.com/datasnakes/beRi) will also be developed in a separate repository but will depend on the other three packages.

## Why beRi?

View our [isc proposal](https://github.com/datasnakes/beri-isc-proposal) to the R Consortium for beRi and learn more about why beRi is needed and how we plan to integrate it.

## Dependencies

*  R - [remotes](https://github.com/r-lib/remotes), [packrat](https://github.com/rstudio/packrat), [jetpack](https://github.com/datasnakes/jetpack), [checkpoint](https://github.com/RevolutionAnalytics/checkpoint)

   

* Python (3.6) - [click](https://github.com/pallets/click), [poetry](https://github.com/sdispater/poetry), [PyYaml](http://pyyaml.org/wiki/PyYAMLDocumentation)

## hackseq18 team members

* [Robert Gilmore](https://github.com/grabear) · **hackseq18 Team Lead & Project Manager**

* [Kristen Bystrom](https://github.com/ksbystrom)

* [Bruno Grande](https://github.com/scientificbruno) · **Lead Maintainer**

* [Shaurita Hutchins](https://github.com/sdhutchins) · **Lead Maintainer**

* [Michelle Lee](https://github.com/bitttyyyy)

* [Santina Lin](https://github.com/santina) · **Lead Maintainer**

* [Zhi Yuh Ou Yang](https://github.com/ZhiYuh)

* [Hamid Younesy](https://github.com/hyounesy)

## References

In order to create something valuable to the R community including RStudio and rOpenSci, it is critical that we develop something that has credibility and creates reproducible environments. Below are some useful links and packages that have acted as a guide for helping to create this package:

  * https://cran.r-project.org/web/packages/startup/vignettes/startup-intro.html

  * https://www.osc.edu/resources/getting_started/howto/howto_install_local_r_packages

  * https://csgillespie.github.io/efficientR/r-startup.html

  * https://www.r-bloggers.com/how-to-pimp-your-rprofile/

  * https://github.com/HenrikBengtsson/startup

  * https://github.com/jdblischak/workflowr

  * https://rstudio.github.io/reticulate/

  * https://rpy2.github.io/doc/latest/html/index.html

  * https://github.com/talgalili/installr