# Docker/Singularity Containers

# Installation

orthogene is now available via ghcr.io as a containerised environment with Rstudio and all necessary dependencies pre-installed.

## Method 1: via Docker

First, install Docker if you have not already.

Create an image of the Docker container in command line:

    docker pull ghcr.io/neurogenomics/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 8900:8787 \
      ghcr.io/neurogenomics/orthogene

### 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.

## 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://ghcr.io/neurogenomics/orthogene

For troubleshooting, see the Singularity documentation.

# Usage

Finally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8900/

Login using the credentials set during the Installation steps.

# Session Info

    utils::sessionInfo()

    ## R version 4.5.2 (2025-10-31)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
    ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_US.UTF-8        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: Etc/UTC
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] orthogene_1.17.2 BiocStyle_2.39.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] gtable_0.3.6              babelgene_22.9
    ##  [3] xfun_0.56                 bslib_0.10.0
    ##  [5] ggplot2_4.0.2             htmlwidgets_1.6.4
    ##  [7] rstatix_0.7.3             lattice_0.22-9
    ##  [9] vctrs_0.7.1               tools_4.5.2
    ## [11] generics_0.1.4            yulab.utils_0.2.4
    ## [13] parallel_4.5.2            tibble_3.3.1
    ## [15] pkgconfig_2.0.3           Matrix_1.7-4
    ## [17] data.table_1.18.2.1       homologene_1.4.68.19.3.27
    ## [19] ggplotify_0.1.3           RColorBrewer_1.1-3
    ## [21] S7_0.2.1                  lifecycle_1.0.5
    ## [23] compiler_4.5.2            farver_2.1.2
    ## [25] treeio_1.35.0             carData_3.0-6
    ## [27] ggtree_4.1.1              gprofiler2_0.2.4
    ## [29] fontLiberation_0.1.0      fontquiver_0.2.1
    ## [31] ggfun_0.2.0               htmltools_0.5.9
    ## [33] sys_3.4.3                 buildtools_1.0.0
    ## [35] sass_0.4.10               yaml_2.3.12
    ## [37] lazyeval_0.2.2            plotly_4.12.0
    ## [39] Formula_1.2-5             pillar_1.11.1
    ## [41] car_3.1-5                 ggpubr_0.6.3
    ## [43] jquerylib_0.1.4           tidyr_1.3.2
    ## [45] MASS_7.3-65               cachem_1.1.0
    ## [47] abind_1.4-8               fontBitstreamVera_0.1.1
    ## [49] nlme_3.1-168              tidyselect_1.2.1
    ## [51] aplot_0.2.9               digest_0.6.39
    ## [53] dplyr_1.2.0               purrr_1.2.1
    ## [55] maketools_1.3.2           fastmap_1.2.0
    ## [57] grid_4.5.2                cli_3.6.5
    ## [59] magrittr_2.0.4            patchwork_1.3.2
    ## [61] broom_1.0.12              ape_5.8-1
    ## [63] gdtools_0.5.0             scales_1.4.0
    ## [65] backports_1.5.0           rappdirs_0.3.4
    ## [67] httr_1.4.8                rmarkdown_2.30
    ## [69] otel_0.2.0                ggsignif_0.6.4
    ## [71] evaluate_1.0.5            knitr_1.51
    ## [73] viridisLite_0.4.3         gridGraphics_0.5-1
    ## [75] rlang_1.1.7               ggiraph_0.9.6
    ## [77] Rcpp_1.1.1                glue_1.8.0
    ## [79] tidytree_0.4.7            BiocManager_1.30.27
    ## [81] jsonlite_2.0.0            R6_2.6.1
    ## [83] systemfonts_1.3.2         fs_1.6.7