Contents

1 DockerHub

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 neurogenomicslab/orthogene

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/orthogene

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/orthogene

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 4.2.2 (2022-10-31)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.0
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] orthogene_1.4.2  BiocStyle_2.26.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.9                ape_5.6-2                
##  [3] lattice_0.20-45           tidyr_1.2.1              
##  [5] assertthat_0.2.1          digest_0.6.31            
##  [7] utf8_1.2.2                R6_2.5.1                 
##  [9] backports_1.4.1           evaluate_0.20            
## [11] httr_1.4.4                ggplot2_3.4.0            
## [13] pillar_1.8.1              ggfun_0.0.9              
## [15] yulab.utils_0.0.6         rlang_1.0.6              
## [17] lazyeval_0.2.2            data.table_1.14.6        
## [19] car_3.1-1                 jquerylib_0.1.4          
## [21] Matrix_1.5-3              grr_0.9.5                
## [23] rmarkdown_2.20            stringr_1.5.0            
## [25] htmlwidgets_1.6.1         munsell_0.5.0            
## [27] broom_1.0.2               gprofiler2_0.2.1         
## [29] compiler_4.2.2            xfun_0.36                
## [31] pkgconfig_2.0.3           gridGraphics_0.5-1       
## [33] htmltools_0.5.4           tidyselect_1.2.0         
## [35] tibble_3.1.8              bookdown_0.32            
## [37] viridisLite_0.4.1         fansi_1.0.3              
## [39] dplyr_1.0.10              ggpubr_0.5.0             
## [41] grid_4.2.2                nlme_3.1-161             
## [43] jsonlite_1.8.4            gtable_0.3.1             
## [45] lifecycle_1.0.3           DBI_1.1.3                
## [47] magrittr_2.0.3            scales_1.2.1             
## [49] tidytree_0.4.2            cli_3.6.0                
## [51] stringi_1.7.12            cachem_1.0.6             
## [53] carData_3.0-5             ggsignif_0.6.4           
## [55] ggtree_3.6.2              bslib_0.4.2              
## [57] generics_0.1.3            vctrs_0.5.1              
## [59] treeio_1.22.0             tools_4.2.2              
## [61] homologene_1.4.68.19.3.27 ggplotify_0.1.0          
## [63] glue_1.6.2                purrr_1.0.1              
## [65] abind_1.4-5               parallel_4.2.2           
## [67] fastmap_1.1.0             yaml_2.3.6               
## [69] babelgene_22.9            colorspace_2.0-3         
## [71] BiocManager_1.30.19       rstatix_0.7.1            
## [73] aplot_0.1.9               plotly_4.10.1            
## [75] knitr_1.41                patchwork_1.1.2          
## [77] sass_0.4.4