Contents

1 Installation

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

1.1 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

1.1.1 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.

1.2 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.

2 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.

3 Session Info

utils::sessionInfo()
## R version 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Sonoma 14.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.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_1.14.8 rworkflows_1.0.0  BiocStyle_2.29.2 
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.4        jsonlite_1.8.7      renv_1.0.3         
##  [4] dplyr_1.1.3         compiler_4.3.1      BiocManager_1.30.22
##  [7] tidyselect_1.2.0    jquerylib_0.1.4     rvcheck_0.2.1      
## [10] scales_1.2.1        yaml_2.3.7          fastmap_1.1.1      
## [13] here_1.0.1          ggplot2_3.4.4       R6_2.5.1           
## [16] generics_0.1.3      knitr_1.44          yulab.utils_0.1.0  
## [19] tibble_3.2.1        bookdown_0.36       desc_1.4.2         
## [22] dlstats_0.1.7       rprojroot_2.0.3     munsell_0.5.0      
## [25] bslib_0.5.1         pillar_1.9.0        RColorBrewer_1.1-3 
## [28] rlang_1.1.1         utf8_1.2.4          cachem_1.0.8       
## [31] badger_0.2.3        xfun_0.40           fs_1.6.3           
## [34] sass_0.4.7          memoise_2.0.1.9000  cli_3.6.1          
## [37] magrittr_2.0.3      digest_0.6.33       grid_4.3.1         
## [40] lifecycle_1.0.3     vctrs_0.6.4         evaluate_0.22      
## [43] glue_1.6.2          fansi_1.0.5         colorspace_2.1-0   
## [46] rmarkdown_2.25      tools_4.3.1         pkgconfig_2.0.3    
## [49] htmltools_0.5.6.1