Contents

1 Docker

orthogene 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 bschilder/orthogene

Once the image has been created, you can launch it with:

docker run \
  -d \
  --rm \
  -e ROOT=true \
  -e PASSWORD=bioc \
  -v ~/Desktop:/Desktop \
  -v /Volumes:/Volumes \
  -p 8788:8787 \
  bschilder/orthogene
  • The -d ensures the container will run in “detached” mode, which means it will persist even after you’ve closed your command line session.
  • Optionally, you can also install the Docker Desktop to easily manage your containers.
  • You can set the password to whatever you like by changing the -e PASSWORD=... flag.
  • The username will be “rstudio” by default.

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://bschilder/orthogene

1.4 Usage

Finally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8788/

Login using the credentials set during the Installation steps.

2 Session Info

utils::sessionInfo()
## R Under development (unstable) (2021-10-19 r81077)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [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       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.23.0
## 
## loaded via a namespace (and not attached):
##  [1] bookdown_0.24       rprojroot_2.0.2     crayon_1.4.1       
##  [4] digest_0.6.28       R6_2.5.1            jsonlite_1.7.2     
##  [7] magrittr_2.0.1      evaluate_0.14       stringi_1.7.5      
## [10] rlang_0.4.12        jquerylib_0.1.4     bslib_0.3.1        
## [13] rmarkdown_2.11      desc_1.4.0          tools_4.2.0        
## [16] stringr_1.4.0       xfun_0.27           yaml_2.2.1         
## [19] fastmap_1.1.0       compiler_4.2.0      BiocManager_1.30.16
## [22] htmltools_0.5.2     knitr_1.36          sass_0.4.0