DockerHub

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

Installation

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 8900:8787 \
  neurogenomicslab/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://neurogenomicslab/rworkflows

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 4.3.1 (2023-06-16)
## 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_0.99.14 BiocStyle_2.29.2  
## 
## loaded via a namespace (and not attached):
##  [1] yulab.utils_0.0.9   sass_0.4.7          utf8_1.2.3         
##  [4] generics_0.1.3      renv_1.0.3          stringi_1.7.12     
##  [7] digest_0.6.33       magrittr_2.0.3      evaluate_0.21      
## [10] grid_4.3.1          RColorBrewer_1.1-3  bookdown_0.35      
## [13] fastmap_1.1.1       rprojroot_2.0.3     jsonlite_1.8.7     
## [16] BiocManager_1.30.22 purrr_1.0.2         fansi_1.0.4        
## [19] scales_1.2.1        textshaping_0.3.6   jquerylib_0.1.4    
## [22] cli_3.6.1           rlang_1.1.1         badger_0.2.3       
## [25] munsell_0.5.0       cachem_1.0.8        yaml_2.3.7         
## [28] tools_4.3.1         memoise_2.0.1       dplyr_1.1.3        
## [31] colorspace_2.1-0    ggplot2_3.4.3       here_1.0.1         
## [34] vctrs_0.6.3         R6_2.5.1            lifecycle_1.0.3    
## [37] stringr_1.5.0       fs_1.6.3            ragg_1.2.5         
## [40] pkgconfig_2.0.3     desc_1.4.2          pkgdown_2.0.7      
## [43] bslib_0.5.1         pillar_1.9.0        gtable_0.3.4       
## [46] glue_1.6.2          data.table_1.14.8   systemfonts_1.0.4  
## [49] xfun_0.40           tibble_3.2.1        rvcheck_0.2.1      
## [52] tidyselect_1.2.0    knitr_1.44          htmltools_0.5.6    
## [55] rmarkdown_2.25      dlstats_0.1.7       compiler_4.3.1