Installation

templateR 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/templateR

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/templateR

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/templateR

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 Under development (unstable) (2023-11-22 r85609)
## Platform: x86_64-pc-linux-gnu
## 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] templateR_0.99.0
## 
## loaded via a namespace (and not attached):
##  [1] vctrs_0.6.5       cli_3.6.1         knitr_1.45        rlang_1.1.2      
##  [5] xfun_0.41         stringi_1.8.2     purrr_1.0.2       textshaping_0.3.7
##  [9] jsonlite_1.8.8    glue_1.6.2        rprojroot_2.0.4   htmltools_0.5.7  
## [13] ragg_1.2.6        sass_0.4.8        rmarkdown_2.25    evaluate_0.23    
## [17] jquerylib_0.1.4   fastmap_1.1.1     yaml_2.3.7        lifecycle_1.0.4  
## [21] memoise_2.0.1     stringr_1.5.1     compiler_4.4.0    fs_1.6.3         
## [25] systemfonts_1.0.5 digest_0.6.33     R6_2.5.1          magrittr_2.0.3   
## [29] bslib_0.6.1       tools_4.4.0       pkgdown_2.0.7     cachem_1.0.8     
## [33] desc_1.4.2