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 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## 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_1.8.0  BiocStyle_2.30.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.4              babelgene_22.9           
##  [3] xfun_0.40                 bslib_0.5.1              
##  [5] ggplot2_3.4.4             htmlwidgets_1.6.2        
##  [7] rstatix_0.7.2             lattice_0.22-5           
##  [9] vctrs_0.6.4               tools_4.3.1              
## [11] generics_0.1.3            yulab.utils_0.1.0        
## [13] parallel_4.3.1            tibble_3.2.1             
## [15] fansi_1.0.5               pkgconfig_2.0.3          
## [17] Matrix_1.6-1.1            data.table_1.14.8        
## [19] homologene_1.4.68.19.3.27 ggplotify_0.1.2          
## [21] lifecycle_1.0.3           compiler_4.3.1           
## [23] treeio_1.26.0             munsell_0.5.0            
## [25] carData_3.0-5             ggtree_3.10.0            
## [27] ggfun_0.1.3               gprofiler2_0.2.2         
## [29] htmltools_0.5.6.1         sass_0.4.7               
## [31] yaml_2.3.7                lazyeval_0.2.2           
## [33] plotly_4.10.3             pillar_1.9.0             
## [35] car_3.1-2                 ggpubr_0.6.0             
## [37] jquerylib_0.1.4           tidyr_1.3.0              
## [39] cachem_1.0.8              grr_0.9.5                
## [41] abind_1.4-5               nlme_3.1-163             
## [43] tidyselect_1.2.0          aplot_0.2.2              
## [45] digest_0.6.33             dplyr_1.1.3              
## [47] purrr_1.0.2               bookdown_0.36            
## [49] fastmap_1.1.1             grid_4.3.1               
## [51] colorspace_2.1-0          cli_3.6.1                
## [53] magrittr_2.0.3            patchwork_1.1.3          
## [55] utf8_1.2.4                broom_1.0.5              
## [57] ape_5.7-1                 scales_1.2.1             
## [59] backports_1.4.1           httr_1.4.7               
## [61] rmarkdown_2.25            ggsignif_0.6.4           
## [63] memoise_2.0.1             evaluate_0.22            
## [65] knitr_1.44                viridisLite_0.4.2        
## [67] gridGraphics_0.5-1        rlang_1.1.1              
## [69] Rcpp_1.0.11               glue_1.6.2               
## [71] tidytree_0.4.5            BiocManager_1.30.22      
## [73] jsonlite_1.8.7            R6_2.5.1                 
## [75] fs_1.6.3