Docker/Singularity Containers


Authors: Brian Schilder, Alan Murphy, Hiranyamaya (Hiru) Dash, Nathan Skene


Vignette updated: Mar-23-2026

Installation

rworkflows is now available via ghcr.io as a containerised environment with Rstudio and all necessary dependencies pre-installed.

Method 1: via Docker

First, install Docker if you have not already.

Create an image of the Docker container in command line:

docker pull ghcr.io/neurogenomics/rworkflows

Once the image has been created, you can launch it with:

docker run \
  -d \
  -e ROOT=true \
  -e PASSWORD="<your_password>" \
  -v ~/Desktop:/Desktop \
  -v /Volumes:/Volumes \
  -p 8900:8787 \
  ghcr.io/neurogenomics/rworkflows

NOTES

  • Make sure to replace <your_password> above with whatever you want your password to be.
  • Change the paths supplied to the -v flags for your particular use case.
  • The -d ensures the container will run in “detached” mode, which means it will persist even after you’ve closed your command line session.
  • The username will be “rstudio” by default.
  • Optionally, you can also install the Docker Desktop to easily manage your containers.

Method 2: via Singularity

If you are using a system that does not allow Docker (as is the case for many institutional computing clusters), you can instead install Docker images via Singularity.

singularity pull docker://ghcr.io/neurogenomics/rworkflows

For troubleshooting, see the Singularity documentation.

Usage

Finally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8900/

Login using the credentials set during the Installation steps.

Session Info

utils::sessionInfo()
## R Under development (unstable) (2026-02-16 r89426)
## Platform: aarch64-apple-darwin23
## Running under: macOS Tahoe 26.3
## 
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: Europe/London
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] data.table_1.18.2.1 rworkflows_1.0.10  
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6        jsonlite_2.0.0      renv_1.1.7         
##  [4] dplyr_1.2.0         compiler_4.6.0      BiocManager_1.30.27
##  [7] tidyselect_1.2.1    jquerylib_0.1.4     rvcheck_0.2.1      
## [10] scales_1.4.0        yaml_2.3.12         fastmap_1.2.0      
## [13] here_1.0.2          ggplot2_4.0.2       R6_2.6.1           
## [16] generics_0.1.4      knitr_1.51          yulab.utils_0.2.4  
## [19] tibble_3.3.1        desc_1.4.3          dlstats_0.1.7      
## [22] rprojroot_2.1.1     bslib_0.10.0        pillar_1.11.1      
## [25] RColorBrewer_1.1-3  rlang_1.1.7         cachem_1.1.0       
## [28] badger_0.2.5        xfun_0.56           fs_1.6.6           
## [31] sass_0.4.10         S7_0.2.1            otel_0.2.0         
## [34] cli_3.6.5           magrittr_2.0.4      digest_0.6.39      
## [37] grid_4.6.0          rstudioapi_0.18.0   rappdirs_0.3.4     
## [40] lifecycle_1.0.5     vctrs_0.7.1         evaluate_1.0.5     
## [43] glue_1.8.0          farver_2.1.2        rmarkdown_2.30     
## [46] tools_4.6.0         pkgconfig_2.0.3     htmltools_0.5.9