Docker/Singularity Containers


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


Vignette updated: Jan-08-2026

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 version 4.5.1 (2025-06-13)
## Platform: aarch64-apple-darwin20
## Running under: macOS Tahoe 26.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/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: America/Mexico_City
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] data.table_1.18.0 rworkflows_1.0.8 
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6        jsonlite_2.0.0      renv_1.1.5         
##  [4] dplyr_1.1.4         compiler_4.5.1      BiocManager_1.30.27
##  [7] tidyselect_1.2.1    dichromat_2.0-0.1   jquerylib_0.1.4    
## [10] rvcheck_0.2.1       scales_1.4.0        yaml_2.3.12        
## [13] fastmap_1.2.0       here_1.0.2          ggplot2_4.0.1      
## [16] R6_2.6.1            generics_0.1.4      knitr_1.51         
## [19] yulab.utils_0.2.3   tibble_3.3.0        desc_1.4.3         
## [22] dlstats_0.1.7       rprojroot_2.1.1     bslib_0.9.0        
## [25] pillar_1.11.1       RColorBrewer_1.1-3  rlang_1.1.6        
## [28] cachem_1.1.0        badger_0.2.5        xfun_0.55          
## [31] fs_1.6.6            sass_0.4.10         S7_0.2.1           
## [34] otel_0.2.0          cli_3.6.5           magrittr_2.0.4     
## [37] digest_0.6.39       grid_4.5.1          rstudioapi_0.17.1  
## [40] rappdirs_0.3.3      lifecycle_1.0.4     vctrs_0.6.5        
## [43] evaluate_1.0.5      glue_1.8.0          farver_2.1.2       
## [46] rmarkdown_2.30      tools_4.5.1         pkgconfig_2.0.3    
## [49] htmltools_0.5.9