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 4.2.0 RC (2022-04-19 r82224)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 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_1.2.0  BiocStyle_2.24.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.8.3              ape_5.6-2                
##  [3] lattice_0.20-45           tidyr_1.2.0              
##  [5] assertthat_0.2.1          digest_0.6.29            
##  [7] utf8_1.2.2                R6_2.5.1                 
##  [9] backports_1.4.1           evaluate_0.15            
## [11] httr_1.4.2                ggplot2_3.3.5            
## [13] pillar_1.7.0              ggfun_0.0.6              
## [15] yulab.utils_0.0.4         rlang_1.0.2              
## [17] lazyeval_0.2.2            data.table_1.14.2        
## [19] car_3.0-12                jquerylib_0.1.4          
## [21] Matrix_1.4-1              rmarkdown_2.14           
## [23] stringr_1.4.0             htmlwidgets_1.5.4        
## [25] munsell_0.5.0             broom_0.8.0              
## [27] gprofiler2_0.2.1          compiler_4.2.0           
## [29] xfun_0.30                 pkgconfig_2.0.3          
## [31] gridGraphics_0.5-1        htmltools_0.5.2          
## [33] tidyselect_1.1.2          tibble_3.1.6             
## [35] bookdown_0.26             viridisLite_0.4.0        
## [37] fansi_1.0.3               crayon_1.5.1             
## [39] dplyr_1.0.8               ggpubr_0.4.0             
## [41] grid_4.2.0                nlme_3.1-157             
## [43] jsonlite_1.8.0            gtable_0.3.0             
## [45] lifecycle_1.0.1           DBI_1.1.2                
## [47] magrittr_2.0.3            scales_1.2.0             
## [49] tidytree_0.3.9            cli_3.3.0                
## [51] stringi_1.7.6             carData_3.0-5            
## [53] ggsignif_0.6.3            ggtree_3.4.0             
## [55] bslib_0.3.1               ellipsis_0.3.2           
## [57] generics_0.1.2            vctrs_0.4.1              
## [59] treeio_1.20.0             tools_4.2.0              
## [61] homologene_1.4.68.19.3.27 ggplotify_0.1.0          
## [63] glue_1.6.2                purrr_0.3.4              
## [65] abind_1.4-5               parallel_4.2.0           
## [67] fastmap_1.1.0             yaml_2.3.5               
## [69] babelgene_22.3            colorspace_2.0-3         
## [71] BiocManager_1.30.17       rstatix_0.7.0            
## [73] aplot_0.1.3               plotly_4.10.0            
## [75] knitr_1.38                patchwork_1.1.1          
## [77] sass_0.4.1