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 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
## 
## 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       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] orthogene_1.12.0 BiocStyle_2.34.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6              babelgene_22.9           
##  [3] xfun_0.48                 bslib_0.8.0              
##  [5] ggplot2_3.5.1             htmlwidgets_1.6.4        
##  [7] rstatix_0.7.2             lattice_0.22-6           
##  [9] vctrs_0.6.5               tools_4.4.1              
## [11] generics_0.1.3            yulab.utils_0.1.7        
## [13] parallel_4.4.1            tibble_3.2.1             
## [15] fansi_1.0.6               pkgconfig_2.0.3          
## [17] Matrix_1.7-1              data.table_1.16.2        
## [19] homologene_1.4.68.19.3.27 ggplotify_0.1.2          
## [21] lifecycle_1.0.4           compiler_4.4.1           
## [23] farver_2.1.2              treeio_1.30.0            
## [25] munsell_0.5.1             carData_3.0-5            
## [27] ggtree_3.14.0             ggfun_0.1.7              
## [29] gprofiler2_0.2.3          htmltools_0.5.8.1        
## [31] sass_0.4.9                yaml_2.3.10              
## [33] lazyeval_0.2.2            plotly_4.10.4            
## [35] Formula_1.2-5             pillar_1.9.0             
## [37] car_3.1-3                 ggpubr_0.6.0             
## [39] jquerylib_0.1.4           tidyr_1.3.1              
## [41] cachem_1.1.0              grr_0.9.5                
## [43] abind_1.4-8               nlme_3.1-166             
## [45] tidyselect_1.2.1          aplot_0.2.3              
## [47] digest_0.6.37             dplyr_1.1.4              
## [49] purrr_1.0.2               bookdown_0.41            
## [51] fastmap_1.2.0             grid_4.4.1               
## [53] colorspace_2.1-1          cli_3.6.3                
## [55] magrittr_2.0.3            patchwork_1.3.0          
## [57] utf8_1.2.4                broom_1.0.7              
## [59] ape_5.8                   scales_1.3.0             
## [61] backports_1.5.0           httr_1.4.7               
## [63] rmarkdown_2.28            ggsignif_0.6.4           
## [65] evaluate_1.0.1            knitr_1.48               
## [67] viridisLite_0.4.2         gridGraphics_0.5-1       
## [69] rlang_1.1.4               Rcpp_1.0.13              
## [71] glue_1.8.0                tidytree_0.4.6           
## [73] BiocManager_1.30.25       jsonlite_1.8.9           
## [75] R6_2.5.1                  fs_1.6.4