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 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 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-r0.3.20.so;  LAPACK version 3.10.0
## 
## 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] rworkflows_1.0.1
## 
## loaded via a namespace (and not attached):
##  [1] yulab.utils_0.1.2   sass_0.4.8          utf8_1.2.4         
##  [4] generics_0.1.3      renv_1.0.3          stringi_1.8.3      
##  [7] digest_0.6.33       magrittr_2.0.3      evaluate_0.23      
## [10] grid_4.3.2          RColorBrewer_1.1-3  fastmap_1.1.1      
## [13] rprojroot_2.0.4     jsonlite_1.8.8      BiocManager_1.30.22
## [16] purrr_1.0.2         fansi_1.0.6         scales_1.3.0       
## [19] textshaping_0.3.7   jquerylib_0.1.4     cli_3.6.2          
## [22] rlang_1.1.2         badger_0.2.3        munsell_0.5.0      
## [25] cachem_1.0.8        yaml_2.3.8          tools_4.3.2        
## [28] memoise_2.0.1       dplyr_1.1.4         colorspace_2.1-0   
## [31] ggplot2_3.4.4       here_1.0.1          vctrs_0.6.5        
## [34] R6_2.5.1            lifecycle_1.0.4     stringr_1.5.1      
## [37] fs_1.6.3            ragg_1.2.6          pkgconfig_2.0.3    
## [40] desc_1.4.3          pkgdown_2.0.7       bslib_0.6.1        
## [43] pillar_1.9.0        gtable_0.3.4        glue_1.6.2         
## [46] data.table_1.14.10  systemfonts_1.0.5   xfun_0.41          
## [49] tibble_3.2.1        rvcheck_0.2.1       tidyselect_1.2.0   
## [52] knitr_1.45          htmltools_0.5.7     rmarkdown_2.25     
## [55] dlstats_0.1.7       compiler_4.3.2