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 Under development (unstable) (2026-01-03 r89269)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 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_1.17.2 BiocStyle_2.39.0
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.6 babelgene_22.9
## [3] xfun_0.55 bslib_0.9.0
## [5] ggplot2_4.0.1 htmlwidgets_1.6.4
## [7] rstatix_0.7.3 lattice_0.22-7
## [9] vctrs_0.6.5 tools_4.6.0
## [11] generics_0.1.4 yulab.utils_0.2.3
## [13] parallel_4.6.0 tibble_3.3.0
## [15] pkgconfig_2.0.3 Matrix_1.7-4
## [17] ggplotify_0.1.3 data.table_1.18.0
## [19] homologene_1.4.68.19.3.27 RColorBrewer_1.1-3
## [21] S7_0.2.1 desc_1.4.3
## [23] lifecycle_1.0.4 compiler_4.6.0
## [25] farver_2.1.2 treeio_1.35.0
## [27] textshaping_1.0.4 carData_3.0-5
## [29] ggtree_4.1.1 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_0.2.2 plotly_4.11.0
## [39] Formula_1.2-5 pillar_1.11.1
## [41] pkgdown_2.2.0 car_3.1-3
## [43] ggpubr_0.6.2 jquerylib_0.1.4
## [45] tidyr_1.3.2 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_1.1.4 purrr_1.2.0
## [55] bookdown_0.46 fastmap_1.2.0
## [57] grid_4.6.0 cli_3.6.5
## [59] magrittr_2.0.4 patchwork_1.3.2
## [61] broom_1.0.11 ape_5.8-1
## [63] gdtools_0.4.4 scales_1.4.0
## [65] backports_1.5.0 rappdirs_0.3.3
## [67] httr_1.4.7 rmarkdown_2.30
## [69] otel_0.2.0 ggsignif_0.6.4
## [71] ragg_1.5.0 evaluate_1.0.5
## [73] knitr_1.51 viridisLite_0.4.2
## [75] gridGraphics_0.5-1 rlang_1.1.6
## [77] ggiraph_0.9.2 Rcpp_1.1.0.8.1
## [79] glue_1.8.0 tidytree_0.4.6
## [81] BiocManager_1.30.27 jsonlite_2.0.0
## [83] R6_2.6.1 systemfonts_1.3.1
## [85] fs_1.6.6