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https://github.com/ltrr-arizona-edu/vice-rstudio

The CyVerse VICE customized RStudio Docker images in a monorepo.
https://github.com/ltrr-arizona-edu/vice-rstudio

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The CyVerse VICE customized RStudio Docker images in a monorepo.

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README 

        
# VICE-RStudio



The [Rocker Project](https://www.rocker-project.org) provides Docker images for

running statistical software based on [R](https://www.r-project.org/) within

standardized container environments, including containers with the popular IDE

for R, [RStudio](https://rstudio.com/products/rstudio/#rstudio-server).

[CyVerse](https://www.cyverse.org/) provides tools for large-scale data analysis

to the academic life science community, including

[VICE](https://learning.cyverse.org/projects/vice/en/latest/), which runs

interactive containerized applications. The Rocker RStudio images need some

minor additioms before they will work in VICE, so the VICE-RStudio images extend

the Rocker images with these changes.



## Variants



The [upstream Rocker images](https://hub.docker.com/r/rocker/r-ver) come from a

series intended to produce reproducible data analysis results. Different

variants in this series have different amounts of system software and R packages

included, and the variants included here range from a basic RStudio installation

(here `base`, `rstudio` upstream), to a variant with a very popular set of R

packages and a development environment pre-installed (`tidyverse`), to a variant

with a full-scale publication package included (`verse`), and finally to a

variant that includes a selected subset of the R-based software for geospatial

analysis (`geospatial`).



## Tags



Rocker uses tags differently from the most common convention for tagged Docker

images. It's usual for tags to refer to a snapshot of the development of

software at some particular time, immutably freezing the state it was in then

(often corresponding to a particular tag or commit in a Git repository, and

follwing the the conventions of semantic versioning). Tags in the versioned

series of Rocker images refer instead to the particular release of R software

they use. R is indeed frozen to a very specific version, but other aspects of

the container (such as OS security patches) can change through time. The intent

is to hold the statistical software environment as constant as possible to

ensure reproducible results, but allow the supporting software to change in

response to current circumstances. Rocker's approach continues to be relevant to

the VICE-RStudio images. If there s some change to the VICE environmant (such as

an update to the iRODS software) it's important that all tagged images (not just

the most recent) adapt to the change: someone may need to re-run an analysis

that's defined using an older version of R. Because these tags refer to mutable

images, there may be problems with image caching under some circumstances: for

example a CI/CD system may not realize that the cached copy of the image it is

holding isn't the most recent available, so in some circumstances it might be

necessary to use explicit sha256 hashes rather than tags to refer to these

images.



## Updating



Because all variants and tags may need re-built for an update, the Git

repository for VICE-RStudio steals an idea from the repositories behind some of

the official Docker images on Docker Hub, such as the

[PHP](https://github.com/docker-library/php) repository. It is structured as a

two-level branching hierarchy (here with the tags nested withon the variants,

the reverse of the PHP example); a top-level script, `update.sh` re-generates

the Dockerfiles that define the image builds for each combination of a variant

and a tag, analogous to the

[update.sh](https://github.com/docker-library/php/blob/master/update.sh) in the

official Docker PHP example. So although for convenience everything in the

repository is under version control, in practice many of the contents are

automatically generated artefacts. The individual tag subdirectories are

completely ephemeral, destroyed and re-created on each update. The variant

subdirectories and top-level directory survive, and can hold various

customizations, but the updating script re-generates the variant README.md files

from a template. The script itself uses only a minimal set of POSIX-compliant

features, and can run in a tiny environment, such as a Busybox container (it

does not require anything included in the VICE-Rstudio images).