Docker/Singularity Containers

Authors: Brian Schilder

Vignette updated: Mar-16-2026

Installation

devoptera 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/RajLabMSSM/devoptera

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/RajLabMSSM/devoptera

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/RajLabMSSM/devoptera

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) (2026-03-12 r89607)
## 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=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.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] devoptera_1.0.0
## 
## loaded via a namespace (and not attached):
##  [1] stringdist_0.9.17    xfun_0.56            bslib_0.10.0        
##  [4] httr2_1.2.2          remotes_2.5.0.9000   devtools_2.4.6      
##  [7] htmlwidgets_1.6.4    Biobase_2.71.0       vctrs_0.7.1         
## [10] tools_4.6.0          bitops_1.0-9         generics_0.1.4      
## [13] stats4_4.6.0         RUnit_0.4.33.1       curl_7.0.0          
## [16] parallel_4.6.0       tibble_3.3.1         RSQLite_2.4.6       
## [19] blob_1.3.0           R.oo_1.27.1          pkgconfig_2.0.3     
## [22] BiocCheck_1.47.18    BiocBaseUtils_1.13.0 data.table_1.18.2.1 
## [25] dbplyr_2.5.2         desc_1.4.3           graph_1.89.1        
## [28] lifecycle_1.0.5      compiler_4.6.0       textshaping_1.0.5   
## [31] biocViews_1.79.3     codetools_0.2-20     usethis_3.2.1       
## [34] htmltools_0.5.9      sass_0.4.10          RCurl_1.98-1.17     
## [37] yaml_2.3.12          pillar_1.11.1        pkgdown_2.2.0       
## [40] jquerylib_0.1.4      ellipsis_0.3.2       R.utils_2.13.0      
## [43] cachem_1.1.0         sessioninfo_1.2.3    tidyselect_1.2.1    
## [46] digest_0.6.39        purrr_1.2.1          dplyr_1.2.0         
## [49] rprojroot_2.1.1      fastmap_1.2.0        here_1.0.2          
## [52] cli_3.6.5            magrittr_2.0.4       pkgbuild_1.4.8      
## [55] RBGL_1.87.0          XML_3.99-0.22        filelock_1.0.3      
## [58] rappdirs_0.3.4       bit64_4.6.0-1        rmarkdown_2.30      
## [61] bit_4.6.0            otel_0.2.0           ragg_1.5.1          
## [64] R.methodsS3_1.8.2    memoise_2.0.1        evaluate_1.0.5      
## [67] knitr_1.51           BiocFileCache_3.1.0  rlang_1.1.7         
## [70] glue_1.8.0           DBI_1.3.0            BiocManager_1.30.27 
## [73] BiocGenerics_0.57.0  pkgload_1.5.0        rstudioapi_0.18.0   
## [76] jsonlite_2.0.0       R6_2.6.1             systemfonts_1.3.2   
## [79] fs_1.6.7