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.
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
your R session
if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("BiocDockerManager")
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
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
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out of date.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" )
Please read the package vignette for more help.
Martin Morgan (@mtmorgan) and Kayla Morell (@Kayla-Morrell).
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