vignettes/docker.Rmd
docker.RmdHPOExplorer 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/HPOExplorerOnce 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/HPOExplorer<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/HPOExplorerFor 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) (2025-11-30 r89082)
## 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] HPOExplorer_1.0.6
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 jsonlite_2.0.0
## [3] shape_1.4.6.1 magrittr_2.0.4
## [5] farver_2.1.2 rmarkdown_2.30
## [7] GlobalOptions_0.1.3 fs_1.6.6
## [9] ragg_1.5.0 vctrs_0.6.5
## [11] ggtree_4.1.1 rstatix_0.7.3
## [13] htmltools_0.5.8.1 broom_1.0.10
## [15] Formula_1.2-5 gridGraphics_0.5-1
## [17] sass_0.4.10 bslib_0.9.0
## [19] htmlwidgets_1.6.4 desc_1.4.3
## [21] httr2_1.2.1 plotly_4.11.0
## [23] cachem_1.1.0 igraph_2.2.1
## [25] mime_0.13 lifecycle_1.0.4
## [27] iterators_1.0.14 pkgconfig_2.0.3
## [29] Matrix_1.7-4 R6_2.6.1
## [31] fastmap_1.2.0 shiny_1.11.1
## [33] clue_0.3-66 digest_0.6.39
## [35] aplot_0.2.9 colorspace_2.1-2
## [37] patchwork_1.3.2 S4Vectors_0.49.0
## [39] grr_0.9.5 textshaping_1.0.4
## [41] ggpubr_0.6.2 httr_1.4.7
## [43] KGExplorer_0.99.10 abind_1.4-8
## [45] compiler_4.6.0 fontquiver_0.2.1
## [47] doParallel_1.0.17 S7_0.2.1
## [49] backports_1.5.0 BiocParallel_1.45.0
## [51] orthogene_1.17.0 carData_3.0-5
## [53] homologene_1.4.68.19.3.27 maps_3.4.3
## [55] ggsignif_0.6.4 rappdirs_0.3.3
## [57] rjson_0.2.23 scatterplot3d_0.3-44
## [59] tools_4.6.0 otel_0.2.0
## [61] ape_5.8-1 httpuv_1.6.16
## [63] glue_1.8.0 rols_2.99.5
## [65] nlme_3.1-168 promises_1.5.0
## [67] grid_4.6.0 cluster_2.1.8.1
## [69] generics_0.1.4 gtable_0.3.6
## [71] tidyr_1.3.1 data.table_1.17.8
## [73] tidygraph_1.3.1 xml2_1.5.1
## [75] car_3.1-3 BiocGenerics_0.57.0
## [77] foreach_1.5.2 pillar_1.11.1
## [79] stringr_1.6.0 yulab.utils_0.2.2
## [81] babelgene_22.9 pals_1.10
## [83] later_1.4.4 circlize_0.4.16
## [85] dplyr_1.1.4 treeio_1.35.0
## [87] lattice_0.22-7 tidyselect_1.2.1
## [89] fontLiberation_0.1.0 ComplexHeatmap_2.27.0
## [91] knitr_1.50 fontBitstreamVera_0.1.1
## [93] IRanges_2.45.0 stats4_4.6.0
## [95] xfun_0.54 Biobase_2.71.0
## [97] matrixStats_1.5.0 stringi_1.8.7
## [99] lazyeval_0.2.2 ggfun_0.2.0
## [101] yaml_2.3.11 evaluate_1.0.5
## [103] codetools_0.2-20 gdtools_0.4.4
## [105] tibble_3.3.0 ggplotify_0.1.3
## [107] Polychrome_1.5.4 cli_3.6.5
## [109] xtable_1.8-4 systemfonts_1.3.1
## [111] jquerylib_0.1.4 dichromat_2.0-0.1
## [113] Rcpp_1.1.0 mapproj_1.2.12
## [115] gprofiler2_0.2.4 png_0.1-8
## [117] parallel_4.6.0 simona_1.9.0
## [119] pkgdown_2.2.0 ggplot2_4.0.1
## [121] viridisLite_0.4.2 tidytree_0.4.6
## [123] ggiraph_0.9.2 scales_1.4.0
## [125] purrr_1.2.0 crayon_1.5.3
## [127] GetoptLong_1.1.0 rlang_1.1.6
## [129] fastmatch_1.1-6 rvest_1.0.5