# Docker/Singularity Containers

#### Authors: Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts, Hiranyamaya Dash

####

#### Vignette updated: Nov-04-2025

# Contents

# 1 DockerHub

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

## 1.1 Installation

## 1.2 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

### 1.2.1 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.

## 1.3 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

## 1.4 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.

# 2 Session Info

    utils::sessionInfo()

    ## R Under development (unstable) (2025-10-20 r88955)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.3 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so
    ## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_GB              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: America/New_York
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] EpiCompare_1.15.0 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] XML_3.99-0.19
    ##   [9] lifecycle_1.0.4
    ##  [10] httr2_1.2.1
    ##  [11] lattice_0.22-7
    ##  [12] magrittr_2.0.4
    ##  [13] plotly_4.11.0
    ##  [14] sass_0.4.10
    ##  [15] rmarkdown_2.30
    ##  [16] jquerylib_0.1.4
    ##  [17] yaml_2.3.10
    ##  [18] plotrix_3.8-4
    ##  [19] ggtangle_0.0.7
    ##  [20] cowplot_1.2.0
    ##  [21] DBI_1.2.3
    ##  [22] RColorBrewer_1.1-3
    ##  [23] lubridate_1.9.4
    ##  [24] abind_1.4-8
    ##  [25] GenomicRanges_1.63.0
    ##  [26] purrr_1.2.0
    ##  [27] R.utils_2.13.0
    ##  [28] BiocGenerics_0.57.0
    ##  [29] RCurl_1.98-1.17
    ##  [30] yulab.utils_0.2.1
    ##  [31] rappdirs_0.3.3
    ##  [32] gdtools_0.4.4
    ##  [33] IRanges_2.45.0
    ##  [34] S4Vectors_0.49.0
    ##  [35] enrichplot_1.31.0
    ##  [36] ggrepel_0.9.6
    ##  [37] tidytree_0.4.6
    ##  [38] ChIPseeker_1.47.1
    ##  [39] codetools_0.2-20
    ##  [40] DelayedArray_0.37.0
    ##  [41] DOSE_4.5.0
    ##  [42] tidyselect_1.2.1
    ##  [43] aplot_0.2.9
    ##  [44] UCSC.utils_1.7.0
    ##  [45] farver_2.1.2
    ##  [46] base64enc_0.1-3
    ##  [47] matrixStats_1.5.0
    ##  [48] stats4_4.6.0
    ##  [49] BiocFileCache_3.1.0
    ##  [50] Seqinfo_1.1.0
    ##  [51] GenomicAlignments_1.47.0
    ##  [52] jsonlite_2.0.0
    ##  [53] systemfonts_1.3.1
    ##  [54] tools_4.6.0
    ##  [55] treeio_1.35.0
    ##  [56] TxDb.Hsapiens.UCSC.hg19.knownGene_3.22.1
    ##  [57] Rcpp_1.1.0
    ##  [58] glue_1.8.0
    ##  [59] SparseArray_1.11.1
    ##  [60] xfun_0.54
    ##  [61] qvalue_2.43.0
    ##  [62] MatrixGenerics_1.23.0
    ##  [63] GenomeInfoDb_1.47.0
    ##  [64] dplyr_1.1.4
    ##  [65] withr_3.0.2
    ##  [66] BiocManager_1.30.26
    ##  [67] fastmap_1.2.0
    ##  [68] boot_1.3-32
    ##  [69] caTools_1.18.3
    ##  [70] digest_0.6.37
    ##  [71] timechange_0.3.0
    ##  [72] R6_2.6.1
    ##  [73] mime_0.13
    ##  [74] gridGraphics_0.5-1
    ##  [75] seqPattern_1.43.0
    ##  [76] GO.db_3.22.0
    ##  [77] gtools_3.9.5
    ##  [78] dichromat_2.0-0.1
    ##  [79] RSQLite_2.4.3
    ##  [80] cigarillo_1.1.0
    ##  [81] R.methodsS3_1.8.2
    ##  [82] tidyr_1.3.1
    ##  [83] generics_0.1.4
    ##  [84] fontLiberation_0.1.0
    ##  [85] data.table_1.17.8
    ##  [86] rtracklayer_1.71.0
    ##  [87] bsplus_0.1.5
    ##  [88] httr_1.4.7
    ##  [89] htmlwidgets_1.6.4
    ##  [90] S4Arrays_1.11.0
    ##  [91] downloadthis_0.5.0
    ##  [92] pkgconfig_2.0.3
    ##  [93] gtable_0.3.6
    ##  [94] blob_1.2.4
    ##  [95] S7_0.2.0
    ##  [96] impute_1.85.0
    ##  [97] XVector_0.51.0
    ##  [98] htmltools_0.5.8.1
    ##  [99] fontBitstreamVera_0.1.1
    ## [100] bookdown_0.45
    ## [101] fgsea_1.37.0
    ## [102] scales_1.4.0
    ## [103] Biobase_2.71.0
    ## [104] png_0.1-8
    ## [105] ggfun_0.2.0
    ## [106] knitr_1.50
    ## [107] tzdb_0.5.0
    ## [108] reshape2_1.4.4
    ## [109] rjson_0.2.23
    ## [110] nlme_3.1-168
    ## [111] curl_7.0.0
    ## [112] cachem_1.1.0
    ## [113] stringr_1.6.0
    ## [114] BiocVersion_3.23.1
    ## [115] KernSmooth_2.23-26
    ## [116] parallel_4.6.0
    ## [117] AnnotationDbi_1.73.0
    ## [118] restfulr_0.0.16
    ## [119] pillar_1.11.1
    ## [120] grid_4.6.0
    ## [121] vctrs_0.6.5
    ## [122] gplots_3.2.0
    ## [123] dbplyr_2.5.1
    ## [124] evaluate_1.0.5
    ## [125] magick_2.9.0
    ## [126] tinytex_0.57
    ## [127] readr_2.1.5
    ## [128] GenomicFeatures_1.63.1
    ## [129] cli_3.6.5
    ## [130] compiler_4.6.0
    ## [131] Rsamtools_2.27.0
    ## [132] rlang_1.1.6
    ## [133] crayon_1.5.3
    ## [134] labeling_0.4.3
    ## [135] plyr_1.8.9
    ## [136] fs_1.6.6
    ## [137] ggiraph_0.9.2
    ## [138] stringi_1.8.7
    ## [139] genomation_1.43.0
    ## [140] viridisLite_0.4.2
    ## [141] gridBase_0.4-7
    ## [142] BiocParallel_1.45.0
    ## [143] Biostrings_2.79.1
    ## [144] lazyeval_0.2.2
    ## [145] GOSemSim_2.37.0
    ## [146] fontquiver_0.2.1
    ## [147] Matrix_1.7-4
    ## [148] BSgenome_1.79.1
    ## [149] hms_1.1.4
    ## [150] patchwork_1.3.2
    ## [151] bit64_4.6.0-1
    ## [152] ggplot2_4.0.0
    ## [153] KEGGREST_1.51.0
    ## [154] SummarizedExperiment_1.41.0
    ## [155] AnnotationHub_4.1.0
    ## [156] igraph_2.2.1
    ## [157] memoise_2.0.1
    ## [158] bslib_0.9.0
    ## [159] ggtree_4.1.1
    ## [160] fastmatch_1.1-6
    ## [161] bit_4.6.0
    ## [162] ape_5.8-1