vignettes/docker.Rmd
docker.Rmdorthogene is now available via ghcr.io as a containerised environment with Rstudio and all necessary dependencies pre-installed.
First, install Docker if you have not already.
Create an image of the Docker container in command line:
docker pull ghcr.io/neurogenomics/orthogeneOnce 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<your_password> above with
whatever you want your password to be.-v flags for your
particular use case.-d ensures the container will run in “detached”
mode, which means it will persist even after you’ve closed your command
line session.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/orthogeneFor troubleshooting, see the Singularity documentation.
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.
utils::sessionInfo()## R version 4.6.0 (2026-04-24)
## 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=en_US.UTF-8
## [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: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] orthogene_1.19.3 BiocStyle_2.40.0
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.6 babelgene_22.9
## [3] xfun_0.57 bslib_0.10.0
## [5] ggplot2_4.0.3 htmlwidgets_1.6.4
## [7] rstatix_0.7.3 lattice_0.22-9
## [9] vctrs_0.7.3 tools_4.6.0
## [11] generics_0.1.4 yulab.utils_0.2.4
## [13] parallel_4.6.0 tibble_3.3.1
## [15] pkgconfig_2.0.3 Matrix_1.7-5
## [17] ggplotify_0.1.3 data.table_1.18.2.1
## [19] homologene_1.4.68.19.3.27 RColorBrewer_1.1-3
## [21] S7_0.2.2 desc_1.4.3
## [23] lifecycle_1.0.5 compiler_4.6.0
## [25] farver_2.1.2 treeio_1.36.0
## [27] textshaping_1.0.5 carData_3.0-6
## [29] ggtree_4.2.0 gprofiler2_0.2.4
## [31] fontLiberation_0.1.0 fontquiver_0.2.1
## [33] ggfun_0.2.0 htmltools_0.5.9
## [35] sass_0.4.10 yaml_2.3.12
## [37] lazyeval_0.2.3 plotly_4.12.0
## [39] Formula_1.2-5 pillar_1.11.1
## [41] pkgdown_2.2.0 car_3.1-5
## [43] ggpubr_0.6.3 jquerylib_0.1.4
## [45] tidyr_1.3.2 MASS_7.3-65
## [47] cachem_1.1.0 abind_1.4-8
## [49] fontBitstreamVera_0.1.1 nlme_3.1-169
## [51] tidyselect_1.2.1 aplot_0.2.9
## [53] digest_0.6.39 dplyr_1.2.1
## [55] purrr_1.2.2 bookdown_0.46
## [57] fastmap_1.2.0 grid_4.6.0
## [59] cli_3.6.6 magrittr_2.0.5
## [61] patchwork_1.3.2 broom_1.0.12
## [63] ape_5.8-1 gdtools_0.5.0
## [65] scales_1.4.0 backports_1.5.1
## [67] rappdirs_0.3.4 httr_1.4.8
## [69] rmarkdown_2.31 otel_0.2.0
## [71] ggsignif_0.6.4 ragg_1.5.2
## [73] evaluate_1.0.5 knitr_1.51
## [75] viridisLite_0.4.3 gridGraphics_0.5-1
## [77] rlang_1.2.0 ggiraph_0.9.6
## [79] Rcpp_1.1.1-1.1 glue_1.8.1
## [81] tidytree_0.4.7 BiocManager_1.30.27
## [83] jsonlite_2.0.0 R6_2.6.1
## [85] systemfonts_1.3.2 fs_2.1.0