vignettes/docker.Rmd
docker.Rmdpeakyfinders 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/peakyfindersOnce 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/peakyfinders<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/peakyfindersFinally, 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) (2026-03-12 r89607)
## 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=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] PeakyFinders_0.99.4 BiocStyle_2.39.0
##
## loaded via a namespace (and not attached):
## [1] DBI_1.3.0 bitops_1.0-9
## [3] httr2_1.2.2 rlang_1.1.7
## [5] magrittr_2.0.4 otel_0.2.0
## [7] matrixStats_1.5.0 compiler_4.6.0
## [9] RSQLite_2.4.6 dir.expiry_1.19.0
## [11] png_0.1-8 systemfonts_1.3.2
## [13] vctrs_0.7.1 stringr_1.6.0
## [15] rvest_1.0.5 pkgconfig_2.0.3
## [17] crayon_1.5.3 fastmap_1.2.0
## [19] dbplyr_2.5.2 XVector_0.51.0
## [21] Rsamtools_2.27.1 rmarkdown_2.30
## [23] tzdb_0.5.0 UCSC.utils_1.7.1
## [25] ragg_1.5.1 purrr_1.2.1
## [27] bit_4.6.0 xfun_0.56
## [29] cachem_1.1.0 cigarillo_1.1.0
## [31] GenomeInfoDb_1.47.2 jsonlite_2.0.0
## [33] blob_1.3.0 DelayedArray_0.37.0
## [35] BiocParallel_1.45.0 parallel_4.6.0
## [37] R6_2.6.1 stringi_1.8.7
## [39] bslib_0.10.0 limma_3.67.0
## [41] reticulate_1.45.0 rtracklayer_1.71.3
## [43] GenomicRanges_1.63.1 jquerylib_0.1.4
## [45] Rcpp_1.1.1 Seqinfo_1.1.0
## [47] bookdown_0.46 SummarizedExperiment_1.41.1
## [49] knitr_1.51 R.utils_2.13.0
## [51] readr_2.2.0 IRanges_2.45.0
## [53] rentrez_1.2.4 Matrix_1.7-4
## [55] tidyselect_1.2.1 abind_1.4-8
## [57] yaml_2.3.12 codetools_0.2-20
## [59] curl_7.0.0 lattice_0.22-9
## [61] tibble_3.3.1 regioneR_1.43.0
## [63] Biobase_2.71.0 KEGGREST_1.51.1
## [65] evaluate_1.0.5 desc_1.4.3
## [67] BiocFileCache_3.1.0 xml2_1.5.2
## [69] ExperimentHub_3.1.0 Biostrings_2.79.5
## [71] pillar_1.11.1 BiocManager_1.30.27
## [73] filelock_1.0.3 MatrixGenerics_1.23.0
## [75] stats4_4.6.0 generics_0.1.4
## [77] RCurl_1.98-1.17 BiocVersion_3.23.1
## [79] S4Vectors_0.49.0 hms_1.1.4
## [81] glue_1.8.0 tools_4.6.0
## [83] AnnotationHub_4.1.0 BiocIO_1.21.0
## [85] data.table_1.18.2.1 GenomicAlignments_1.47.0
## [87] BSgenome_1.79.1 GEOquery_2.79.0
## [89] fs_1.6.7 XML_3.99-0.22
## [91] grid_4.6.0 tidyr_1.3.2
## [93] AnnotationDbi_1.73.0 basilisk_1.23.0
## [95] restfulr_0.0.16 cli_3.6.5
## [97] rappdirs_0.3.4 textshaping_1.0.5
## [99] S4Arrays_1.11.1 dplyr_1.2.0
## [101] R.methodsS3_1.8.2 sass_0.4.10
## [103] digest_0.6.39 BiocGenerics_0.57.0
## [105] SparseArray_1.11.11 rjson_0.2.23
## [107] htmlwidgets_1.6.4 memoise_2.0.1
## [109] htmltools_0.5.9 pkgdown_2.2.0
## [111] R.oo_1.27.1 lifecycle_1.0.5
## [113] httr_1.4.8 MACSr_1.13.2
## [115] statmod_1.5.1 bit64_4.6.0-1