Contents

1 DockerHub

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

1.1 Installation

1.2 Method 1: via Docker

First, install Docker if you have not already.

Create an image of the Docker container in command line:

docker pull neurogenomicslab/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 8787:8787 \
  neurogenomicslab/rworkflows

1.2.1 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.

1.3 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://neurogenomicslab/rworkflows

1.4 Usage

Finally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8787/

Login using the credentials set during the Installation steps.

2 Session Info

utils::sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur ... 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] rworkflows_0.99.5 data.table_1.14.6 BiocStyle_2.26.0 
## 
## loaded via a namespace (and not attached):
##  [1] bslib_0.4.2         compiler_4.2.1      pillar_1.8.1       
##  [4] BiocManager_1.30.19 RColorBrewer_1.1-3  jquerylib_0.1.4    
##  [7] yulab.utils_0.0.6   tools_4.2.1         digest_0.6.31      
## [10] jsonlite_1.8.4      evaluate_0.19       lifecycle_1.0.3    
## [13] tibble_3.1.8        gtable_0.3.1        pkgconfig_2.0.3    
## [16] rlang_1.0.6         DBI_1.1.3           cli_3.5.0          
## [19] rvcheck_0.2.1       yaml_2.3.6          xfun_0.36          
## [22] fastmap_1.1.0       dplyr_1.0.10        stringr_1.5.0      
## [25] knitr_1.41          desc_1.4.2          generics_0.1.3     
## [28] vctrs_0.5.1         sass_0.4.4          dlstats_0.1.6      
## [31] rprojroot_2.0.3     tidyselect_1.2.0    grid_4.2.1         
## [34] here_1.0.1          glue_1.6.2          R6_2.5.1           
## [37] fansi_1.0.3         rmarkdown_2.19      bookdown_0.31      
## [40] ggplot2_3.4.0       badger_0.2.2        magrittr_2.0.3     
## [43] scales_1.2.1        htmltools_0.5.4     assertthat_0.2.1   
## [46] colorspace_2.0-3    utf8_1.2.2          stringi_1.7.8      
## [49] munsell_0.5.0       cachem_1.0.6