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 4.5.1 (2025-06-13)
## 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_1.15.02 BiocStyle_2.37.1
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.6 babelgene_22.9
## [3] xfun_0.53 bslib_0.9.0
## [5] ggplot2_4.0.0 htmlwidgets_1.6.4
## [7] rstatix_0.7.2 lattice_0.22-7
## [9] vctrs_0.6.5 tools_4.5.1
## [11] generics_0.1.4 yulab.utils_0.2.1
## [13] parallel_4.5.1 tibble_3.3.0
## [15] pkgconfig_2.0.3 Matrix_1.7-4
## [17] data.table_1.17.8 homologene_1.4.68.19.3.27
## [19] ggplotify_0.1.3 RColorBrewer_1.1-3
## [21] S7_0.2.0 desc_1.4.3
## [23] uuid_1.2-1 lifecycle_1.0.4
## [25] compiler_4.5.1 farver_2.1.2
## [27] treeio_1.33.0 textshaping_1.0.3
## [29] carData_3.0-5 ggtree_3.99.0
## [31] gprofiler2_0.2.3 ggfun_0.2.0
## [33] htmltools_0.5.8.1 sass_0.4.10
## [35] yaml_2.3.10 lazyeval_0.2.2
## [37] plotly_4.11.0 Formula_1.2-5
## [39] pillar_1.11.1 pkgdown_2.1.3
## [41] car_3.1-3 ggpubr_0.6.1
## [43] jquerylib_0.1.4 tidyr_1.3.1
## [45] cachem_1.1.0 grr_0.9.5
## [47] abind_1.4-8 nlme_3.1-168
## [49] tidyselect_1.2.1 aplot_0.2.9
## [51] digest_0.6.37 dplyr_1.1.4
## [53] purrr_1.1.0 bookdown_0.44
## [55] fastmap_1.2.0 grid_4.5.1
## [57] cli_3.6.5 magrittr_2.0.4
## [59] patchwork_1.3.2 broom_1.0.10
## [61] ape_5.8-1 scales_1.4.0
## [63] backports_1.5.0 rappdirs_0.3.3
## [65] httr_1.4.7 rmarkdown_2.29
## [67] ggsignif_0.6.4 ragg_1.5.0
## [69] evaluate_1.0.5 knitr_1.50
## [71] viridisLite_0.4.2 gridGraphics_0.5-1
## [73] rlang_1.1.6 ggiraph_0.9.1
## [75] Rcpp_1.1.0 glue_1.8.0
## [77] tidytree_0.4.6 BiocManager_1.30.26
## [79] jsonlite_2.0.0 R6_2.6.1
## [81] systemfonts_1.2.3 fs_1.6.6