Making simple Bioconductor containers • SimpleBiocContainer

Introduction

SimpleBiocContainer provides a simple, user-friendly way for users to create R/Bioconductor containers with the convenient packages, datasets and R scripts, as well as to share those containers with the community through Docker Hub or the GitHub container registry.

Note that you must have installed Docker on your system to be able to execute SimpleBiocContainer functions. You can download and install Docker Desktop here.

Functions

SimpleBiocContainer contains the following functions:

makeSimpleBiocContainer(), which creates a container directory and the respective files;
buildPushDocker(), which builds the created container and pushes it to Docker Hub.

Packages to include in the container are either the currently attached packages (default) or specified by users. The files mentioned for makeSimpleBiocContainer() include datasets and scripts users may find useful to have in the container.

Quick start

We have one or multiple packages that we want to add to the container and character vectors with data and scripts file names to be included. We can create our container and name it "my_container" as follows:

file.create("data.rda")

[1] TRUE

file.create("script.R")

[1] TRUE

library(SimpleBiocContainer)
container_path <- makeSimpleBiocContainer(
  package = "MsCoreUtils",
  container = "my_container",
  data = "data.rda",
  script = "script.R")

Creating the container directory 🪐.

Creating the Dockerfile 🔔.

Adding data.rda 📂

Adding script.R 📂

Done 👍.

container_path

[1] "/home/runner/work/SimpleBiocContainer/SimpleBiocContainer/vignettes/my_container"

The code chunk above then creates our container, stores it in the working directory, and stores the path to the container directory in container_path. If package is not specified, makeSimpleBiocContainer() will store all the packages that are loaded in the current session.

After running makeSimpleBiocConductor(), we can build our container and push it to Docker Hub as shown below:

buildPushDocker(
  container = container_path,
  dockerUsername = "docker_username") # replace by the intended Docker username

The argument ghUsername (NULL by default) allows us to push the container to GitHub as well, being enough to feed it with a character object that contains the username we intend to push the container to.

Session information

sessionInfo()

R version 4.6.1 (2026-06-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

time zone: UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] SimpleBiocContainer_0.2.1

loaded via a namespace (and not attached):
 [1] BiocManager_1.30.27 compiler_4.6.1      fastmap_1.2.0
 [4] cli_3.6.6           tools_4.6.1         htmltools_0.5.9
 [7] otel_0.2.0          yaml_2.3.12         rmarkdown_2.31
[10] knitr_1.51          jsonlite_2.0.0      xfun_0.60
[13] digest_0.6.39       rlang_1.3.0         evaluate_1.0.5