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 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 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] orthogene_1.2.1  BiocStyle_2.24.0
## 
## 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_0.6.29            
##  [7] utf8_1.2.2                R6_2.5.1                 
##  [9] backports_1.4.1           evaluate_0.16            
## [11] httr_1.4.4                ggplot2_3.3.6            
## [13] pillar_1.8.1              ggfun_0.0.7              
## [15] yulab.utils_0.0.5         rlang_1.0.6              
## [17] lazyeval_0.2.2            data.table_1.14.2        
## [19] car_3.1-0                 jquerylib_0.1.4          
## [21] Matrix_1.5-1              rmarkdown_2.16           
## [23] stringr_1.4.1             htmlwidgets_1.5.4        
## [25] munsell_0.5.0             broom_1.0.1              
## [27] gprofiler2_0.2.1          compiler_4.2.1           
## [29] xfun_0.33                 pkgconfig_2.0.3          
## [31] gridGraphics_0.5-1        htmltools_0.5.3          
## [33] tidyselect_1.1.2          tibble_3.1.8             
## [35] bookdown_0.29             viridisLite_0.4.1        
## [37] fansi_1.0.3               dplyr_1.0.10             
## [39] ggpubr_0.4.0              grid_4.2.1               
## [41] nlme_3.1-159              jsonlite_1.8.2           
## [43] gtable_0.3.1              lifecycle_1.0.2          
## [45] DBI_1.1.3                 magrittr_2.0.3           
## [47] scales_1.2.1              tidytree_0.4.1           
## [49] cli_3.4.1                 stringi_1.7.8            
## [51] cachem_1.0.6              carData_3.0-5            
## [53] ggsignif_0.6.3            ggtree_3.4.4             
## [55] bslib_0.4.0               generics_0.1.3           
## [57] vctrs_0.4.2               treeio_1.20.2            
## [59] tools_4.2.1               homologene_1.4.68.19.3.27
## [61] ggplotify_0.1.0           glue_1.6.2               
## [63] purrr_0.3.4               abind_1.4-5              
## [65] parallel_4.2.1            fastmap_1.1.0            
## [67] yaml_2.3.5                babelgene_22.9           
## [69] colorspace_2.0-3          BiocManager_1.30.18      
## [71] rstatix_0.7.0             aplot_0.1.7              
## [73] plotly_4.10.0             knitr_1.40               
## [75] patchwork_1.1.2           sass_0.4.2