# 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 24.04.4 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-r0.3.26.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_1.14.0 BiocStyle_2.38.0
    ##
    ## loaded via a namespace (and not attached):
    ##   [1] splines_4.5.2
    ##   [2] BiocIO_1.20.0
    ##   [3] bitops_1.0-9
    ##   [4] ggplotify_0.1.3
    ##   [5] filelock_1.0.3
    ##   [6] tibble_3.3.1
    ##   [7] R.oo_1.27.1
    ##   [8] polyclip_1.10-7
    ##   [9] XML_3.99-0.22
    ##  [10] lifecycle_1.0.5
    ##  [11] httr2_1.2.2
    ##  [12] lattice_0.22-9
    ##  [13] MASS_7.3-65
    ##  [14] magrittr_2.0.4
    ##  [15] plotly_4.12.0
    ##  [16] sass_0.4.10
    ##  [17] rmarkdown_2.30
    ##  [18] jquerylib_0.1.4
    ##  [19] yaml_2.3.12
    ##  [20] plotrix_3.8-14
    ##  [21] otel_0.2.0
    ##  [22] ggtangle_0.1.1
    ##  [23] cowplot_1.2.0
    ##  [24] DBI_1.3.0
    ##  [25] buildtools_1.0.0
    ##  [26] RColorBrewer_1.1-3
    ##  [27] lubridate_1.9.5
    ##  [28] abind_1.4-8
    ##  [29] GenomicRanges_1.62.1
    ##  [30] purrr_1.2.1
    ##  [31] R.utils_2.13.0
    ##  [32] BiocGenerics_0.56.0
    ##  [33] RCurl_1.98-1.17
    ##  [34] yulab.utils_0.2.4
    ##  [35] tweenr_2.0.3
    ##  [36] rappdirs_0.3.4
    ##  [37] gdtools_0.5.0
    ##  [38] IRanges_2.44.0
    ##  [39] S4Vectors_0.48.0
    ##  [40] enrichplot_1.30.5
    ##  [41] ggrepel_0.9.7
    ##  [42] tidytree_0.4.7
    ##  [43] maketools_1.3.2
    ##  [44] ChIPseeker_1.46.1
    ##  [45] codetools_0.2-20
    ##  [46] DelayedArray_0.36.0
    ##  [47] DOSE_4.4.0
    ##  [48] ggforce_0.5.0
    ##  [49] tidyselect_1.2.1
    ##  [50] aplot_0.2.9
    ##  [51] UCSC.utils_1.6.1
    ##  [52] farver_2.1.2
    ##  [53] base64enc_0.1-6
    ##  [54] matrixStats_1.5.0
    ##  [55] stats4_4.5.2
    ##  [56] BiocFileCache_3.0.0
    ##  [57] Seqinfo_1.0.0
    ##  [58] GenomicAlignments_1.46.0
    ##  [59] jsonlite_2.0.0
    ##  [60] systemfonts_1.3.2
    ##  [61] tools_4.5.2
    ##  [62] ggnewscale_0.5.2
    ##  [63] treeio_1.34.0
    ##  [64] TxDb.Hsapiens.UCSC.hg19.knownGene_3.22.1
    ##  [65] Rcpp_1.1.1
    ##  [66] glue_1.8.0
    ##  [67] SparseArray_1.10.9
    ##  [68] xfun_0.56
    ##  [69] qvalue_2.42.0
    ##  [70] MatrixGenerics_1.22.0
    ##  [71] GenomeInfoDb_1.46.2
    ##  [72] dplyr_1.2.0
    ##  [73] withr_3.0.2
    ##  [74] BiocManager_1.30.27
    ##  [75] fastmap_1.2.0
    ##  [76] boot_1.3-32
    ##  [77] caTools_1.18.3
    ##  [78] digest_0.6.39
    ##  [79] mime_0.13
    ##  [80] timechange_0.4.0
    ##  [81] R6_2.6.1
    ##  [82] gridGraphics_0.5-1
    ##  [83] seqPattern_1.42.0
    ##  [84] GO.db_3.22.0
    ##  [85] gtools_3.9.5
    ##  [86] RSQLite_2.4.6
    ##  [87] cigarillo_1.0.0
    ##  [88] R.methodsS3_1.8.2
    ##  [89] tidyr_1.3.2
    ##  [90] generics_0.1.4
    ##  [91] fontLiberation_0.1.0
    ##  [92] data.table_1.18.2.1
    ##  [93] bsplus_0.1.5
    ##  [94] rtracklayer_1.70.1
    ##  [95] httr_1.4.8
    ##  [96] htmlwidgets_1.6.4
    ##  [97] S4Arrays_1.10.1
    ##  [98] scatterpie_0.2.6
    ##  [99] downloadthis_0.5.0
    ## [100] pkgconfig_2.0.3
    ## [101] gtable_0.3.6
    ## [102] blob_1.3.0
    ## [103] impute_1.84.0
    ## [104] S7_0.2.1
    ## [105] XVector_0.50.0
    ## [106] sys_3.4.3
    ## [107] htmltools_0.5.9
    ## [108] fontBitstreamVera_0.1.1
    ## [109] fgsea_1.36.2
    ## [110] scales_1.4.0
    ## [111] Biobase_2.70.0
    ## [112] png_0.1-8
    ## [113] ggfun_0.2.0
    ## [114] knitr_1.51
    ## [115] tzdb_0.5.0
    ## [116] reshape2_1.4.5
    ## [117] rjson_0.2.23
    ## [118] nlme_3.1-168
    ## [119] curl_7.0.0
    ## [120] cachem_1.1.0
    ## [121] stringr_1.6.0
    ## [122] BiocVersion_3.22.0
    ## [123] KernSmooth_2.23-26
    ## [124] parallel_4.5.2
    ## [125] AnnotationDbi_1.72.0
    ## [126] restfulr_0.0.16
    ## [127] pillar_1.11.1
    ## [128] grid_4.5.2
    ## [129] vctrs_0.7.1
    ## [130] gplots_3.3.0
    ## [131] tidydr_0.0.6
    ## [132] dbplyr_2.5.2
    ## [133] cluster_2.1.8.2
    ## [134] evaluate_1.0.5
    ## [135] readr_2.2.0
    ## [136] GenomicFeatures_1.62.0
    ## [137] cli_3.6.5
    ## [138] compiler_4.5.2
    ## [139] Rsamtools_2.26.0
    ## [140] rlang_1.1.7
    ## [141] crayon_1.5.3
    ## [142] labeling_0.4.3
    ## [143] plyr_1.8.9
    ## [144] fs_1.6.7
    ## [145] ggiraph_0.9.6
    ## [146] stringi_1.8.7
    ## [147] viridisLite_0.4.3
    ## [148] genomation_1.42.0
    ## [149] gridBase_0.4-7
    ## [150] BiocParallel_1.44.0
    ## [151] Biostrings_2.78.0
    ## [152] lazyeval_0.2.2
    ## [153] GOSemSim_2.36.0
    ## [154] fontquiver_0.2.1
    ## [155] Matrix_1.7-4
    ## [156] BSgenome_1.78.0
    ## [157] hms_1.1.4
    ## [158] patchwork_1.3.2
    ## [159] bit64_4.6.0-1
    ## [160] ggplot2_4.0.2
    ## [161] KEGGREST_1.50.0
    ## [162] SummarizedExperiment_1.40.0
    ## [163] AnnotationHub_4.0.0
    ## [164] igraph_2.2.2
    ## [165] memoise_2.0.1
    ## [166] bslib_0.10.0
    ## [167] ggtree_4.0.4
    ## [168] fastmatch_1.1-8
    ## [169] bit_4.6.0
    ## [170] ape_5.8-1