Docker/Singularity Containers
Authors: Brian Schilder, Jack Humphrey, Towfique Raj
Authors: Brian Schilder, Jack Humphrey, Towfique Raj
Vignette updated: Mar-16-2026
Source: Vignette updated: Mar-16-2026
vignettes/docker.Rmd
docker.RmdDockerHub
echolocator is now available via DockerHub as a containerised environment with Rstudio and all necessary dependencies pre-installed.
Method 1: via Docker
First, install Docker if you have not already.
Create an image of the Docker container in command line:
docker pull bschilder/echolocatorOnce 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 \
bschilder/echolocatorNOTES
- Make sure to replace
<your_password>above with whatever you want your password to be.
- Change the paths supplied to the
-vflags for your particular use case. - The
-densures 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://bschilder/echolocatorUsage
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 4.5.1 (2025-06-13)
## Platform: aarch64-apple-darwin20
## Running under: macOS Tahoe 26.3.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] echolocatoR_2.0.5 BiocStyle_2.38.0
##
## loaded via a namespace (and not attached):
## [1] splines_4.5.1 aws.s3_0.3.22
## [3] BiocIO_1.20.0 bitops_1.0-9
## [5] filelock_1.0.3 tibble_3.3.1
## [7] R.oo_1.27.1 cellranger_1.1.0
## [9] basilisk.utils_1.22.0 graph_1.88.1
## [11] rpart_4.1.24 XML_3.99-0.22
## [13] lifecycle_1.0.5 mixsqp_0.3-54
## [15] pals_1.10 OrganismDbi_1.52.0
## [17] ensembldb_2.34.0 lattice_0.22-9
## [19] MASS_7.3-65 backports_1.5.0
## [21] magrittr_2.0.4 Hmisc_5.2-5
## [23] openxlsx_4.2.8.1 sass_0.4.10
## [25] rmarkdown_2.30 jquerylib_0.1.4
## [27] yaml_2.3.12 otel_0.2.0
## [29] zip_2.3.3 reticulate_1.45.0
## [31] ggbio_1.58.0 gld_2.6.8
## [33] mapproj_1.2.12 DBI_1.3.0
## [35] RColorBrewer_1.1-3 maps_3.4.3
## [37] abind_1.4-8 expm_1.0-0
## [39] GenomicRanges_1.62.1 purrr_1.2.1
## [41] R.utils_2.13.0 AnnotationFilter_1.34.0
## [43] biovizBase_1.58.0 BiocGenerics_0.56.0
## [45] RCurl_1.98-1.17 nnet_7.3-20
## [47] VariantAnnotation_1.56.0 IRanges_2.44.0
## [49] S4Vectors_0.48.0 echofinemap_1.0.0
## [51] echoLD_0.99.12 catalogueR_2.0.1
## [53] irlba_2.3.7 pkgdown_2.2.0
## [55] echodata_1.0.0 piggyback_0.1.5
## [57] codetools_0.2-20 DelayedArray_0.36.0
## [59] DT_0.34.0 xml2_1.5.2
## [61] tidyselect_1.2.1 UCSC.utils_1.6.1
## [63] farver_2.1.2 viridis_0.6.5
## [65] matrixStats_1.5.0 stats4_4.5.1
## [67] base64enc_0.1-6 Seqinfo_1.0.0
## [69] echotabix_1.0.0 GenomicAlignments_1.46.0
## [71] jsonlite_2.0.0 e1071_1.7-17
## [73] Formula_1.2-5 survival_3.8-6
## [75] systemfonts_1.3.2 ggnewscale_0.5.2
## [77] tools_4.5.1 ragg_1.5.1
## [79] DescTools_0.99.60 Rcpp_1.1.1
## [81] glue_1.8.0 gridExtra_2.3
## [83] SparseArray_1.10.9 xfun_0.56
## [85] MatrixGenerics_1.22.0 GenomeInfoDb_1.46.2
## [87] dplyr_1.2.0 withr_3.0.2
## [89] BiocManager_1.30.27 fastmap_1.2.0
## [91] basilisk_1.22.0 boot_1.3-32
## [93] digest_0.6.39 R6_2.6.1
## [95] colorspace_2.1-2 textshaping_1.0.5
## [97] dichromat_2.0-0.1 RSQLite_2.4.6
## [99] cigarillo_1.0.0 R.methodsS3_1.8.2
## [101] utf8_1.2.6 tidyr_1.3.2
## [103] generics_0.1.4 data.table_1.18.2.1
## [105] rtracklayer_1.70.1 class_7.3-23
## [107] httr_1.4.8 htmlwidgets_1.6.4
## [109] S4Arrays_1.10.1 pkgconfig_2.0.3
## [111] gtable_0.3.6 Exact_3.3
## [113] blob_1.3.0 S7_0.2.1
## [115] XVector_0.50.0 echoconda_1.0.0
## [117] htmltools_0.5.9 susieR_0.14.2
## [119] bookdown_0.46 RBGL_1.86.0
## [121] ProtGenerics_1.42.0 scales_1.4.0
## [123] Biobase_2.70.0 lmom_3.2
## [125] png_0.1-8 knitr_1.51
## [127] rstudioapi_0.18.0 reshape2_1.4.5
## [129] tzdb_0.5.0 rjson_0.2.23
## [131] checkmate_2.3.4 curl_7.0.0
## [133] proxy_0.4-29 cachem_1.1.0
## [135] stringr_1.6.0 rootSolve_1.8.2.4
## [137] parallel_4.5.1 foreign_0.8-91
## [139] AnnotationDbi_1.72.0 restfulr_0.0.16
## [141] desc_1.4.3 pillar_1.11.1
## [143] grid_4.5.1 reshape_0.8.10
## [145] vctrs_0.7.1 cluster_2.1.8.2
## [147] htmlTable_2.4.3 evaluate_1.0.5
## [149] readr_2.2.0 GenomicFeatures_1.62.0
## [151] mvtnorm_1.3-3 cli_3.6.5
## [153] compiler_4.5.1 Rsamtools_2.26.0
## [155] rlang_1.1.7 crayon_1.5.3
## [157] aws.signature_0.6.0 plyr_1.8.9
## [159] forcats_1.0.1 fs_1.6.7
## [161] stringi_1.8.7 coloc_5.2.3
## [163] echoannot_1.0.1 viridisLite_0.4.3
## [165] BiocParallel_1.44.0 Biostrings_2.78.0
## [167] lazyeval_0.2.2 Matrix_1.7-4
## [169] downloadR_1.0.0 echoplot_0.99.9
## [171] dir.expiry_1.18.0 BSgenome_1.78.0
## [173] hms_1.1.4 patchwork_1.3.2
## [175] bit64_4.6.0-1 ggplot2_4.0.2
## [177] KEGGREST_1.50.0 SummarizedExperiment_1.40.0
## [179] haven_2.5.5 memoise_2.0.1
## [181] snpStats_1.60.0 bslib_0.10.0
## [183] bit_4.6.0 readxl_1.4.5