vignettes/docker.Rmd
docker.Rmdepicompare is now available via DockerHub 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 neurogenomicslab/epicompareOnce 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 8787:8787 \
neurogenomicslab/epicompare<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://neurogenomicslab/epicompareFinally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8787/
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] EpiCompare_1.15.2 BiocStyle_2.39.0
##
## loaded via a namespace (and not attached):
## [1] splines_4.6.0
## [2] BiocIO_1.21.0
## [3] bitops_1.0-9
## [4] ggplotify_0.1.3
## [5] filelock_1.0.3
## [6] tibble_3.3.0
## [7] R.oo_1.27.1
## [8] polyclip_1.10-7
## [9] XML_3.99-0.20
## [10] lifecycle_1.0.4
## [11] httr2_1.2.1
## [12] lattice_0.22-7
## [13] MASS_7.3-65
## [14] magrittr_2.0.4
## [15] plotly_4.11.0
## [16] sass_0.4.10
## [17] rmarkdown_2.30
## [18] jquerylib_0.1.4
## [19] yaml_2.3.11
## [20] plotrix_3.8-13
## [21] ggtangle_0.0.9
## [22] cowplot_1.2.0
## [23] DBI_1.2.3
## [24] RColorBrewer_1.1-3
## [25] abind_1.4-8
## [26] GenomicRanges_1.63.0
## [27] purrr_1.2.0
## [28] R.utils_2.13.0
## [29] BiocGenerics_0.57.0
## [30] RCurl_1.98-1.17
## [31] yulab.utils_0.2.2
## [32] tweenr_2.0.3
## [33] rappdirs_0.3.3
## [34] gdtools_0.4.4
## [35] IRanges_2.45.0
## [36] S4Vectors_0.49.0
## [37] enrichplot_1.31.2
## [38] ggrepel_0.9.6
## [39] tidytree_0.4.6
## [40] pkgdown_2.2.0
## [41] ChIPseeker_1.47.1
## [42] codetools_0.2-20
## [43] DelayedArray_0.37.0
## [44] DOSE_4.5.0
## [45] ggforce_0.5.0
## [46] tidyselect_1.2.1
## [47] aplot_0.2.9
## [48] UCSC.utils_1.7.0
## [49] farver_2.1.2
## [50] matrixStats_1.5.0
## [51] stats4_4.6.0
## [52] BiocFileCache_3.1.0
## [53] Seqinfo_1.1.0
## [54] GenomicAlignments_1.47.0
## [55] jsonlite_2.0.0
## [56] systemfonts_1.3.1
## [57] tools_4.6.0
## [58] ggnewscale_0.5.2
## [59] treeio_1.35.0
## [60] TxDb.Hsapiens.UCSC.hg19.knownGene_3.22.1
## [61] ragg_1.5.0
## [62] Rcpp_1.1.0
## [63] glue_1.8.0
## [64] SparseArray_1.11.6
## [65] xfun_0.54
## [66] qvalue_2.43.0
## [67] MatrixGenerics_1.23.0
## [68] GenomeInfoDb_1.47.1
## [69] dplyr_1.1.4
## [70] withr_3.0.2
## [71] BiocManager_1.30.27
## [72] fastmap_1.2.0
## [73] boot_1.3-32
## [74] caTools_1.18.3
## [75] digest_0.6.39
## [76] R6_2.6.1
## [77] gridGraphics_0.5-1
## [78] seqPattern_1.43.0
## [79] textshaping_1.0.4
## [80] GO.db_3.22.0
## [81] gtools_3.9.5
## [82] RSQLite_2.4.5
## [83] cigarillo_1.1.0
## [84] R.methodsS3_1.8.2
## [85] tidyr_1.3.1
## [86] generics_0.1.4
## [87] fontLiberation_0.1.0
## [88] data.table_1.17.8
## [89] rtracklayer_1.71.0
## [90] httr_1.4.7
## [91] htmlwidgets_1.6.4
## [92] S4Arrays_1.11.1
## [93] scatterpie_0.2.6
## [94] downloadthis_0.5.0
## [95] pkgconfig_2.0.3
## [96] gtable_0.3.6
## [97] blob_1.2.4
## [98] impute_1.85.0
## [99] S7_0.2.1
## [100] XVector_0.51.0
## [101] htmltools_0.5.8.1
## [102] fontBitstreamVera_0.1.1
## [103] bookdown_0.45
## [104] fgsea_1.37.0
## [105] scales_1.4.0
## [106] Biobase_2.71.0
## [107] png_0.1-8
## [108] ggfun_0.2.0
## [109] knitr_1.50
## [110] tzdb_0.5.0
## [111] reshape2_1.4.5
## [112] rjson_0.2.23
## [113] nlme_3.1-168
## [114] curl_7.0.0
## [115] cachem_1.1.0
## [116] stringr_1.6.0
## [117] BiocVersion_3.23.1
## [118] KernSmooth_2.23-26
## [119] parallel_4.6.0
## [120] AnnotationDbi_1.73.0
## [121] restfulr_0.0.16
## [122] desc_1.4.3
## [123] pillar_1.11.1
## [124] grid_4.6.0
## [125] vctrs_0.6.5
## [126] gplots_3.3.0
## [127] tidydr_0.0.6
## [128] dbplyr_2.5.1
## [129] cluster_2.1.8.1
## [130] evaluate_1.0.5
## [131] readr_2.1.6
## [132] GenomicFeatures_1.63.1
## [133] cli_3.6.5
## [134] compiler_4.6.0
## [135] Rsamtools_2.27.0
## [136] rlang_1.1.6
## [137] crayon_1.5.3
## [138] plyr_1.8.9
## [139] fs_1.6.6
## [140] ggiraph_0.9.2
## [141] stringi_1.8.7
## [142] viridisLite_0.4.2
## [143] genomation_1.43.0
## [144] gridBase_0.4-7
## [145] BiocParallel_1.45.0
## [146] Biostrings_2.79.2
## [147] lazyeval_0.2.2
## [148] GOSemSim_2.37.0
## [149] fontquiver_0.2.1
## [150] Matrix_1.7-4
## [151] BSgenome_1.79.1
## [152] hms_1.1.4
## [153] patchwork_1.3.2
## [154] bit64_4.6.0-1
## [155] ggplot2_4.0.1
## [156] KEGGREST_1.51.1
## [157] SummarizedExperiment_1.41.0
## [158] AnnotationHub_4.1.0
## [159] igraph_2.2.1
## [160] memoise_2.0.1
## [161] bslib_0.9.0
## [162] ggtree_4.1.1
## [163] fastmatch_1.1-6
## [164] bit_4.6.0
## [165] ape_5.8-1