nturaga / biocdockermanager

Bioconductor package to manage docker images

BiocDockerManager - An R Package to manage Bioconductor Docker Images

The BiocDockerManager package was designed to work analogous to BiocManager but for docker images. Use the BiocDockerManager package manage docker images provided by the Bioconductor project. The package provides convenient ways to install images, update images, confirm validity and find which Bioconductor based docker images are available.

Install

Preliminary Step 0: Install Docker Desktop on your local machine, and sign in https://docs.docker.com/get-docker/

Install the package BiocManager, then install BiocDockerManager in your R session

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("BiocDockerManager")

Example Workflow

We hope to provide functionality which is useful to R and Bioconductor Docker users in the form of an R package.

The typical workflow would look like the following:

First, you check the available() images. Then you install() a required image say bioconductor/bioconductor_docker:devel.

## 1. Check available images
BiocDockerManager::available()

## 2. Install a new image
BiocDockerManager::install(
	repository = "bioconductor/bioconductor_docker",
	tag = "devel"
)

Once some time has passed and if you are not sure if you image is up to date, you have to check if the image is valid().

Then, install() an update if the validity check returns that it is out of date. Check the version() of the latest image to make sure you understand the consequences of updating.

## 3. Check if image is valid
BiocDockerManager::valid(
	"bioconductor/bioconductor_docker",
	tag = "devel"
)

## 4. Download update to image
BiocDockerManager::install(
	"bioconductor/bioconductor_docker",
	tag = "devel"
)

## 5. Check version
BiocDockerManager::version(
	"bioconductor/bioconductor_docker",
	tag = "devel"
)

Help

Please read the package vignette for more help.

Acknowledgements

Martin Morgan (@mtmorgan) and Kayla Morell (@Kayla-Morrell).