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) (2024-12-15 r87442)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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_1.0.4
##
## loaded via a namespace (and not attached):
## [1] grr_0.9.5 httr2_1.0.7
## [3] rlang_1.1.4 magrittr_2.0.3
## [5] clue_0.3-66 GetoptLong_1.0.5
## [7] matrixStats_1.4.1 compiler_4.5.0
## [9] png_0.1-8 systemfonts_1.1.0
## [11] vctrs_0.6.5 maps_3.4.2.1
## [13] gprofiler2_0.2.3 stringr_1.5.1
## [15] rvest_1.0.4 shape_1.4.6.1
## [17] pkgconfig_2.0.3 crayon_1.5.3
## [19] fastmap_1.2.0 backports_1.5.0
## [21] promises_1.3.2 rmarkdown_2.29
## [23] ragg_1.3.3 purrr_1.0.2
## [25] xfun_0.49 cachem_1.1.0
## [27] pals_1.9 aplot_0.2.4
## [29] jsonlite_1.8.9 later_1.4.1
## [31] BiocParallel_1.41.0 cluster_2.1.8
## [33] broom_1.0.7 parallel_4.5.0
## [35] R6_2.5.1 rols_3.3.0
## [37] stringi_1.8.4 RColorBrewer_1.1-3
## [39] bslib_0.8.0 car_3.1-3
## [41] jquerylib_0.1.4 Rcpp_1.0.13-1
## [43] iterators_1.0.14 knitr_1.49
## [45] IRanges_2.41.2 httpuv_1.6.15
## [47] igraph_2.1.2 Matrix_1.7-1
## [49] tidyselect_1.2.1 dichromat_2.0-0.1
## [51] abind_1.4-8 yaml_2.3.10
## [53] doParallel_1.0.17 codetools_0.2-20
## [55] lattice_0.22-6 tibble_3.2.1
## [57] shiny_1.10.0 Biobase_2.67.0
## [59] treeio_1.31.0 evaluate_1.0.1
## [61] gridGraphics_0.5-1 desc_1.4.3
## [63] xml2_1.3.6 circlize_0.4.16
## [65] pillar_1.10.0 ggtree_3.15.0
## [67] ggpubr_0.6.0 carData_3.0-5
## [69] stats4_4.5.0 foreach_1.5.2
## [71] ggfun_0.1.8 plotly_4.10.4
## [73] generics_0.1.3 S4Vectors_0.45.2
## [75] ggplot2_3.5.1 munsell_0.5.1
## [77] scales_1.3.0 tidytree_0.4.6
## [79] xtable_1.8-4 glue_1.8.0
## [81] orthogene_1.13.0 mapproj_1.2.11
## [83] scatterplot3d_0.3-44 lazyeval_0.2.2
## [85] tools_4.5.0 data.table_1.16.4
## [87] KGExplorer_0.99.03 ggsignif_0.6.4
## [89] babelgene_22.9 fs_1.6.5
## [91] tidygraph_1.3.1 grid_4.5.0
## [93] tidyr_1.3.1 ape_5.8-1
## [95] colorspace_2.1-1 nlme_3.1-166
## [97] patchwork_1.3.0 homologene_1.4.68.19.3.27
## [99] Formula_1.2-5 cli_3.6.3
## [101] rappdirs_0.3.3 Polychrome_1.5.1
## [103] textshaping_0.4.1 viridisLite_0.4.2
## [105] ComplexHeatmap_2.23.0 dplyr_1.1.4
## [107] gtable_0.3.6 rstatix_0.7.2
## [109] yulab.utils_0.1.8 sass_0.4.9
## [111] digest_0.6.37 BiocGenerics_0.53.3
## [113] ggplotify_0.1.2 rjson_0.2.23
## [115] htmlwidgets_1.6.4 farver_2.1.2
## [117] htmltools_0.5.8.1 pkgdown_2.1.1
## [119] simona_1.5.0 lifecycle_1.0.4
## [121] httr_1.4.7 mime_0.12
## [123] GlobalOptions_0.1.2