# Docker/Singularity Containers

# DockerHub

epicompare is now available via DockerHub as a containerised environment with Rstudio and all necessary dependencies pre-installed.

## Installation

## Method 1: via Docker

First, install Docker if you have not already.

Create an image of the Docker container in command line:

    docker pull neurogenomicslab/epicompare

Once 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

### NOTES

- Make sure to replace `<your_password>` above with whatever you want your password to be.
- Change the paths supplied to the `-v` flags for your particular use case.
- The `-d` ensures the container will run in “detached” mode, which means it will persist even after you’ve closed your command line session.
- The username will be “rstudio” by default.
- Optionally, you can also install the Docker Desktop to easily manage your containers.

## Method 2: via Singularity

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/epicompare

## Usage

Finally, 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.

# Session Info

    utils::sessionInfo()

    ## R version 4.5.2 (2025-10-31)
    ## 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=C
    ##  [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: Etc/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_4.5.2
    ##   [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] buildtools_1.0.0
    ##  [25] RColorBrewer_1.1-3
    ##  [26] lubridate_1.9.4
    ##  [27] abind_1.4-8
    ##  [28] GenomicRanges_1.63.0
    ##  [29] purrr_1.2.0
    ##  [30] R.utils_2.13.0
    ##  [31] BiocGenerics_0.57.0
    ##  [32] RCurl_1.98-1.17
    ##  [33] yulab.utils_0.2.2
    ##  [34] tweenr_2.0.3
    ##  [35] rappdirs_0.3.3
    ##  [36] gdtools_0.4.4
    ##  [37] IRanges_2.45.0
    ##  [38] S4Vectors_0.49.0
    ##  [39] enrichplot_1.31.2
    ##  [40] ggrepel_0.9.6
    ##  [41] tidytree_0.4.6
    ##  [42] maketools_1.3.2
    ##  [43] ChIPseeker_1.47.1
    ##  [44] codetools_0.2-20
    ##  [45] DelayedArray_0.37.0
    ##  [46] DOSE_4.5.0
    ##  [47] ggforce_0.5.0
    ##  [48] tidyselect_1.2.1
    ##  [49] aplot_0.2.9
    ##  [50] UCSC.utils_1.7.0
    ##  [51] farver_2.1.2
    ##  [52] base64enc_0.1-3
    ##  [53] matrixStats_1.5.0
    ##  [54] stats4_4.5.2
    ##  [55] BiocFileCache_3.1.0
    ##  [56] Seqinfo_1.1.0
    ##  [57] GenomicAlignments_1.47.0
    ##  [58] jsonlite_2.0.0
    ##  [59] systemfonts_1.3.1
    ##  [60] tools_4.5.2
    ##  [61] ggnewscale_0.5.2
    ##  [62] treeio_1.35.0
    ##  [63] TxDb.Hsapiens.UCSC.hg19.knownGene_3.22.1
    ##  [64] Rcpp_1.1.0
    ##  [65] glue_1.8.0
    ##  [66] SparseArray_1.11.7
    ##  [67] xfun_0.54
    ##  [68] qvalue_2.43.0
    ##  [69] MatrixGenerics_1.23.0
    ##  [70] GenomeInfoDb_1.47.1
    ##  [71] dplyr_1.1.4
    ##  [72] withr_3.0.2
    ##  [73] BiocManager_1.30.27
    ##  [74] fastmap_1.2.0
    ##  [75] boot_1.3-32
    ##  [76] caTools_1.18.3
    ##  [77] digest_0.6.39
    ##  [78] mime_0.13
    ##  [79] timechange_0.3.0
    ##  [80] R6_2.6.1
    ##  [81] gridGraphics_0.5-1
    ##  [82] seqPattern_1.43.0
    ##  [83] GO.db_3.22.0
    ##  [84] gtools_3.9.5
    ##  [85] RSQLite_2.4.5
    ##  [86] cigarillo_1.1.0
    ##  [87] R.methodsS3_1.8.2
    ##  [88] tidyr_1.3.1
    ##  [89] generics_0.1.4
    ##  [90] fontLiberation_0.1.0
    ##  [91] data.table_1.17.8
    ##  [92] bsplus_0.1.5
    ##  [93] rtracklayer_1.71.0
    ##  [94] httr_1.4.7
    ##  [95] htmlwidgets_1.6.4
    ##  [96] S4Arrays_1.11.1
    ##  [97] scatterpie_0.2.6
    ##  [98] downloadthis_0.5.0
    ##  [99] pkgconfig_2.0.3
    ## [100] gtable_0.3.6
    ## [101] blob_1.2.4
    ## [102] S7_0.2.1
    ## [103] impute_1.85.0
    ## [104] XVector_0.51.0
    ## [105] sys_3.4.3
    ## [106] htmltools_0.5.8.1
    ## [107] fontBitstreamVera_0.1.1
    ## [108] fgsea_1.37.0
    ## [109] scales_1.4.0
    ## [110] Biobase_2.71.0
    ## [111] png_0.1-8
    ## [112] ggfun_0.2.0
    ## [113] knitr_1.50
    ## [114] tzdb_0.5.0
    ## [115] reshape2_1.4.5
    ## [116] rjson_0.2.23
    ## [117] nlme_3.1-168
    ## [118] curl_7.0.0
    ## [119] cachem_1.1.0
    ## [120] stringr_1.6.0
    ## [121] BiocVersion_3.23.1
    ## [122] KernSmooth_2.23-26
    ## [123] parallel_4.5.2
    ## [124] AnnotationDbi_1.73.0
    ## [125] restfulr_0.0.16
    ## [126] pillar_1.11.1
    ## [127] grid_4.5.2
    ## [128] vctrs_0.6.5
    ## [129] gplots_3.3.0
    ## [130] tidydr_0.0.6
    ## [131] dbplyr_2.5.1
    ## [132] cluster_2.1.8.1
    ## [133] evaluate_1.0.5
    ## [134] readr_2.1.6
    ## [135] GenomicFeatures_1.63.1
    ## [136] cli_3.6.5
    ## [137] compiler_4.5.2
    ## [138] Rsamtools_2.27.0
    ## [139] rlang_1.1.6
    ## [140] crayon_1.5.3
    ## [141] labeling_0.4.3
    ## [142] plyr_1.8.9
    ## [143] fs_1.6.6
    ## [144] ggiraph_0.9.2
    ## [145] stringi_1.8.7
    ## [146] viridisLite_0.4.2
    ## [147] genomation_1.41.1
    ## [148] gridBase_0.4-7
    ## [149] BiocParallel_1.45.0
    ## [150] Biostrings_2.79.2
    ## [151] lazyeval_0.2.2
    ## [152] GOSemSim_2.37.0
    ## [153] fontquiver_0.2.1
    ## [154] Matrix_1.7-4
    ## [155] BSgenome_1.79.1
    ## [156] hms_1.1.4
    ## [157] patchwork_1.3.2
    ## [158] bit64_4.6.0-1
    ## [159] ggplot2_4.0.1
    ## [160] KEGGREST_1.51.1
    ## [161] SummarizedExperiment_1.41.0
    ## [162] AnnotationHub_4.1.0
    ## [163] igraph_2.2.1
    ## [164] memoise_2.0.1
    ## [165] bslib_0.9.0
    ## [166] ggtree_4.1.1
    ## [167] fastmatch_1.1-6
    ## [168] bit_4.6.0
    ## [169] ape_5.8-1