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 4.2.3 (2023-03-15)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-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] orthogene_1.4.2  BiocStyle_2.26.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10               ape_5.7-1                
##  [3] lattice_0.21-8            tidyr_1.3.0              
##  [5] digest_0.6.31             utf8_1.2.3               
##  [7] R6_2.5.1                  backports_1.4.1          
##  [9] evaluate_0.20             httr_1.4.5               
## [11] ggplot2_3.4.2             pillar_1.9.0             
## [13] ggfun_0.0.9               yulab.utils_0.0.6        
## [15] rlang_1.1.0               lazyeval_0.2.2           
## [17] data.table_1.14.8         car_3.1-2                
## [19] jquerylib_0.1.4           Matrix_1.5-4             
## [21] grr_0.9.5                 rmarkdown_2.21           
## [23] htmlwidgets_1.6.2         munsell_0.5.0            
## [25] broom_1.0.4               compiler_4.2.3           
## [27] gprofiler2_0.2.1          xfun_0.38                
## [29] pkgconfig_2.0.3           gridGraphics_0.5-1       
## [31] htmltools_0.5.5           tidyselect_1.2.0         
## [33] tibble_3.2.1              bookdown_0.33            
## [35] viridisLite_0.4.1         fansi_1.0.4              
## [37] dplyr_1.1.1               ggpubr_0.6.0             
## [39] grid_4.2.3                nlme_3.1-162             
## [41] jsonlite_1.8.4            gtable_0.3.3             
## [43] lifecycle_1.0.3           magrittr_2.0.3           
## [45] scales_1.2.1              tidytree_0.4.2           
## [47] cli_3.6.1                 cachem_1.0.7             
## [49] carData_3.0-5             ggsignif_0.6.4           
## [51] ggtree_3.6.2              bslib_0.4.2              
## [53] generics_0.1.3            vctrs_0.6.1              
## [55] tools_4.2.3               treeio_1.22.0            
## [57] homologene_1.4.68.19.3.27 ggplotify_0.1.0          
## [59] glue_1.6.2                purrr_1.0.1              
## [61] abind_1.4-5               parallel_4.2.3           
## [63] fastmap_1.1.1             yaml_2.3.7               
## [65] babelgene_22.9            colorspace_2.1-0         
## [67] BiocManager_1.30.20       rstatix_0.7.2            
## [69] aplot_0.1.10              plotly_4.10.1            
## [71] knitr_1.42                patchwork_1.1.2          
## [73] sass_0.4.5