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 8900:8787 \
  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:8900/

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_0.99.12 data.table_1.14.8  BiocStyle_2.26.0  
## 
## loaded via a namespace (and not attached):
##  [1] Biobase_2.58.0      httr_1.4.6          sass_0.4.6         
##  [4] bit64_4.0.5         jsonlite_1.8.4      here_1.0.1         
##  [7] bslib_0.4.2         BiocManager_1.30.20 rvcheck_0.2.1      
## [10] stats4_4.2.1        BiocFileCache_2.6.1 yulab.utils_0.0.6  
## [13] RBGL_1.74.0         BiocPkgTools_1.16.1 blob_1.2.4         
## [16] renv_0.17.3         yaml_2.3.7          pillar_1.9.0       
## [19] RSQLite_2.3.1       glue_1.6.2          RUnit_0.4.32       
## [22] digest_0.6.31       RColorBrewer_1.1-3  rvest_1.0.3        
## [25] colorspace_2.1-0    htmltools_0.5.5     XML_3.99-0.14      
## [28] pkgconfig_2.0.3     httpcode_0.3.0      bookdown_0.34      
## [31] scales_1.2.1        whisker_0.4.1       tzdb_0.4.0         
## [34] tibble_3.2.1        biocViews_1.66.3    generics_0.1.3     
## [37] ggplot2_3.4.2       DT_0.28             cachem_1.0.8       
## [40] BiocGenerics_0.44.0 cli_3.6.1           magrittr_2.0.3     
## [43] memoise_2.0.1       evaluate_0.21       badger_0.2.3       
## [46] fansi_1.0.4         xml2_1.3.4          graph_1.76.0       
## [49] tools_4.2.1         gh_1.4.0            hms_1.1.3          
## [52] lifecycle_1.0.3     stringr_1.5.0       munsell_0.5.0      
## [55] compiler_4.2.1      jquerylib_0.1.4     rlang_1.1.1        
## [58] grid_4.2.1          RCurl_1.98-1.12     rappdirs_0.3.3     
## [61] htmlwidgets_1.6.2   igraph_1.5.0.1      bitops_1.0-7       
## [64] rmarkdown_2.22      rorcid_0.7.0        gtable_0.3.3       
## [67] DBI_1.1.3           curl_5.0.0          fauxpas_0.5.2      
## [70] R6_2.5.1            knitr_1.43          dplyr_1.1.2        
## [73] fastmap_1.1.1       bit_4.0.5           utf8_1.2.3         
## [76] rprojroot_2.0.3     filelock_1.0.2      dlstats_0.1.7      
## [79] readr_2.1.4         desc_1.4.2          stringi_1.7.12     
## [82] crul_1.4.0          vctrs_0.6.2         dbplyr_2.3.2       
## [85] tidyselect_1.2.0    xfun_0.39