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 version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 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-r0.3.20.so; LAPACK version 3.10.0
##
## 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_1.0.2
##
## loaded via a namespace (and not attached):
## [1] grr_0.9.5 httr2_1.0.1
## [3] rlang_1.1.3 magrittr_2.0.3
## [5] clue_0.3-65 GetoptLong_1.0.5
## [7] matrixStats_1.3.0 compiler_4.4.0
## [9] png_0.1-8 systemfonts_1.1.0
## [11] vctrs_0.6.5 maps_3.4.2
## [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_1.5.2
## [19] fastmap_1.2.0 backports_1.4.1
## [21] utf8_1.2.4 promises_1.3.0
## [23] rmarkdown_2.27 ragg_1.3.2
## [25] purrr_1.0.2 xfun_0.44
## [27] cachem_1.1.0 pals_1.9
## [29] aplot_0.2.2 jsonlite_1.8.8
## [31] later_1.3.2 BiocParallel_1.39.0
## [33] cluster_2.1.6 broom_1.0.6
## [35] parallel_4.4.0 R6_2.5.1
## [37] rols_3.1.0 stringi_1.8.4
## [39] RColorBrewer_1.1-3 bslib_0.7.0
## [41] car_3.1-2 jquerylib_0.1.4
## [43] Rcpp_1.0.12 iterators_1.0.14
## [45] knitr_1.46 IRanges_2.39.0
## [47] httpuv_1.6.15 igraph_2.0.3
## [49] Matrix_1.7-0 tidyselect_1.2.1
## [51] dichromat_2.0-0.1 abind_1.4-5
## [53] yaml_2.3.8 doParallel_1.0.17
## [55] codetools_0.2-20 lattice_0.22-6
## [57] tibble_3.2.1 shiny_1.8.1.1
## [59] Biobase_2.65.0 treeio_1.29.0
## [61] evaluate_0.23 gridGraphics_0.5-1
## [63] desc_1.4.3 xml2_1.3.6
## [65] circlize_0.4.16 pillar_1.9.0
## [67] ggtree_3.13.0 ggpubr_0.6.0
## [69] carData_3.0-5 stats4_4.4.0
## [71] foreach_1.5.2 ggfun_0.1.4
## [73] plotly_4.10.4 generics_0.1.3
## [75] S4Vectors_0.43.0 ggplot2_3.5.1
## [77] munsell_0.5.1 scales_1.3.0
## [79] tidytree_0.4.6 xtable_1.8-4
## [81] glue_1.7.0 orthogene_1.11.0
## [83] mapproj_1.2.11 scatterplot3d_0.3-44
## [85] lazyeval_0.2.2 tools_4.4.0
## [87] data.table_1.15.4 KGExplorer_0.99.01
## [89] ggsignif_0.6.4 babelgene_22.9
## [91] fs_1.6.4 tidygraph_1.3.1
## [93] grid_4.4.0 tidyr_1.3.1
## [95] ape_5.8 colorspace_2.1-0
## [97] nlme_3.1-164 patchwork_1.2.0
## [99] homologene_1.4.68.19.3.27 cli_3.6.2
## [101] rappdirs_0.3.3 Polychrome_1.5.1
## [103] textshaping_0.3.7 fansi_1.0.6
## [105] viridisLite_0.4.2 ComplexHeatmap_2.21.0
## [107] dplyr_1.1.4 gtable_0.3.5
## [109] rstatix_0.7.2 yulab.utils_0.1.4
## [111] sass_0.4.9 digest_0.6.35
## [113] BiocGenerics_0.51.0 ggplotify_0.1.2
## [115] rjson_0.2.21 htmlwidgets_1.6.4
## [117] memoise_2.0.1 htmltools_0.5.8.1
## [119] pkgdown_2.0.9 simona_1.3.0
## [121] lifecycle_1.0.4 httr_1.4.7
## [123] mime_0.12 GlobalOptions_0.1.2