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 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-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_1.0.2  BiocStyle_2.22.0
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.1.2          xfun_0.30                
##  [3] bslib_0.3.1               purrr_0.3.4              
##  [5] lattice_0.20-45           carData_3.0-5            
##  [7] gprofiler2_0.2.1          colorspace_2.0-3         
##  [9] vctrs_0.4.0               generics_0.1.2           
## [11] viridisLite_0.4.0         htmltools_0.5.2          
## [13] yaml_2.3.5                plotly_4.10.0            
## [15] utf8_1.2.2                rlang_1.0.2              
## [17] jquerylib_0.1.4           pillar_1.7.0             
## [19] ggpubr_0.4.0              glue_1.6.2               
## [21] DBI_1.1.2                 GenomeInfoDbData_1.2.7   
## [23] lifecycle_1.0.1           stringr_1.4.0            
## [25] munsell_0.5.0             ggsignif_0.6.3           
## [27] gtable_0.3.0              htmlwidgets_1.5.4        
## [29] evaluate_0.15             knitr_1.38               
## [31] fastmap_1.1.0             parallel_4.1.3           
## [33] fansi_1.0.3               broom_0.7.12             
## [35] backports_1.4.1           scales_1.1.1             
## [37] BiocManager_1.30.16       jsonlite_1.8.0           
## [39] abind_1.4-5               babelgene_22.3           
## [41] ggplot2_3.3.5             digest_0.6.29            
## [43] stringi_1.7.6             bookdown_0.25            
## [45] rstatix_0.7.0             dplyr_1.0.8              
## [47] grid_4.1.3                cli_3.2.0                
## [49] tools_4.1.3               magrittr_2.0.3           
## [51] sass_0.4.1                patchwork_1.1.1          
## [53] lazyeval_0.2.2            tibble_3.1.6             
## [55] car_3.0-12                tidyr_1.2.0              
## [57] crayon_1.5.1              pkgconfig_2.0.3          
## [59] ellipsis_0.3.2            Matrix_1.4-1             
## [61] homologene_1.4.68.19.3.27 data.table_1.14.2        
## [63] httr_1.4.2                assertthat_0.2.1         
## [65] rmarkdown_2.13            R6_2.5.1                 
## [67] compiler_4.1.3