vignettes/docker.Rmd
docker.RmdMSTExplorer 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/MSTExplorerOnce 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/MSTExplorer<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/MSTExplorerFor 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] MSTExplorer_1.0.6
##
## loaded via a namespace (and not attached):
## [1] later_1.4.1 bitops_1.0-9
## [3] ggplotify_0.1.2 GeneOverlap_1.43.0
## [5] filelock_1.0.3 tibble_3.2.1
## [7] lifecycle_1.0.4 httr2_1.0.7
## [9] KGExplorer_0.99.03 rstatix_0.7.2
## [11] HPOExplorer_1.0.3 doParallel_1.0.17
## [13] lattice_0.22-6 pals_1.9
## [15] backports_1.5.0 magrittr_2.0.3
## [17] limma_3.63.2 plotly_4.10.4
## [19] sass_0.4.9 rmarkdown_2.29
## [21] jquerylib_0.1.4 yaml_2.3.10
## [23] httpuv_1.6.15 HGNChelper_0.8.15
## [25] mapproj_1.2.11 DBI_1.2.3
## [27] RColorBrewer_1.1-3 maps_3.4.2.1
## [29] abind_1.4-8 zlibbioc_1.53.0
## [31] GenomicRanges_1.59.1 rvest_1.0.4
## [33] purrr_1.0.2 BiocGenerics_0.53.3
## [35] yulab.utils_0.1.8 rappdirs_0.3.3
## [37] circlize_0.4.16 GenomeInfoDbData_1.2.13
## [39] IRanges_2.41.2 S4Vectors_0.45.2
## [41] rols_3.3.0 tidytree_0.4.6
## [43] piggyback_0.1.5 pkgdown_2.1.1
## [45] codetools_0.2-20 DelayedArray_0.33.3
## [47] xml2_1.3.6 tidyselect_1.2.1
## [49] shape_1.4.6.1 aplot_0.2.4
## [51] UCSC.utils_1.3.0 farver_2.1.2
## [53] matrixStats_1.4.1 stats4_4.5.0
## [55] BiocFileCache_2.15.0 jsonlite_1.8.9
## [57] GetoptLong_1.0.5 tidygraph_1.3.1
## [59] Formula_1.2-5 iterators_1.0.14
## [61] systemfonts_1.1.0 foreach_1.5.2
## [63] tools_4.5.0 treeio_1.31.0
## [65] ragg_1.3.3 Rcpp_1.0.13-1
## [67] glue_1.8.0 SparseArray_1.7.2
## [69] xfun_0.49 MatrixGenerics_1.19.0
## [71] GenomeInfoDb_1.43.2 RNOmni_1.0.1.2
## [73] dplyr_1.1.4 BiocManager_1.30.25
## [75] fastmap_1.2.0 caTools_1.18.3
## [77] digest_0.6.37 R6_2.5.1
## [79] mime_0.12 gridGraphics_0.5-1
## [81] textshaping_0.4.1 colorspace_2.1-1
## [83] gtools_3.9.5 dichromat_2.0-0.1
## [85] RSQLite_2.3.9 tidyr_1.3.1
## [87] generics_0.1.3 data.table_1.16.4
## [89] httr_1.4.7 htmlwidgets_1.6.4
## [91] S4Arrays_1.7.1 scatterplot3d_0.3-44
## [93] pkgconfig_2.0.3 gtable_0.3.6
## [95] blob_1.2.4 ComplexHeatmap_2.23.0
## [97] SingleCellExperiment_1.29.1 XVector_0.47.0
## [99] htmltools_0.5.8.1 carData_3.0-5
## [101] clue_0.3-66 scales_1.3.0
## [103] Biobase_2.67.0 png_0.1-8
## [105] ggfun_0.1.8 knitr_1.49
## [107] reshape2_1.4.4 rjson_0.2.23
## [109] nlme_3.1-166 curl_6.0.1
## [111] cachem_1.1.0 GlobalOptions_0.1.2
## [113] Polychrome_1.5.1 stringr_1.5.1
## [115] BiocVersion_3.21.1 KernSmooth_2.23-24
## [117] parallel_4.5.0 AnnotationDbi_1.69.0
## [119] desc_1.4.3 pillar_1.10.0
## [121] grid_4.5.0 vctrs_0.6.5
## [123] gplots_3.2.0 promises_1.3.2
## [125] ggpubr_0.6.0 car_3.1-3
## [127] dbplyr_2.5.0 xtable_1.8-4
## [129] cluster_2.1.8 evaluate_1.0.1
## [131] orthogene_1.13.0 cli_3.6.3
## [133] compiler_4.5.0 rlang_1.1.4
## [135] crayon_1.5.3 grr_0.9.5
## [137] simona_1.5.0 ggsignif_0.6.4
## [139] gprofiler2_0.2.3 plyr_1.8.9
## [141] EWCE_1.15.0 fs_1.6.5
## [143] stringi_1.8.4 viridisLite_0.4.2
## [145] ewceData_1.15.0 BiocParallel_1.41.0
## [147] babelgene_22.9 munsell_0.5.1
## [149] Biostrings_2.75.3 lazyeval_0.2.2
## [151] homologene_1.4.68.19.3.27 Matrix_1.7-1
## [153] ExperimentHub_2.15.0 patchwork_1.3.0
## [155] bit64_4.5.2 ggplot2_3.5.1
## [157] statmod_1.5.0 KEGGREST_1.47.0
## [159] shiny_1.10.0 SummarizedExperiment_1.37.0
## [161] AnnotationHub_3.15.0 igraph_2.1.2
## [163] broom_1.0.7 memoise_2.0.1
## [165] bslib_0.8.0 ggtree_3.15.0
## [167] bit_4.5.0.1 splitstackshape_1.4.8
## [169] ape_5.8-1