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) (2026-01-22 r89323)
## 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=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] piggyback_0.1.5 DBI_1.2.3
## [3] bitops_1.0-9 httr2_1.2.2
## [5] rlang_1.1.7 magrittr_2.0.4
## [7] otel_0.2.0 matrixStats_1.5.0
## [9] compiler_4.6.0 RSQLite_2.4.5
## [11] dir.expiry_1.19.0 png_0.1-8
## [13] systemfonts_1.3.1 vctrs_0.7.1
## [15] rvest_1.0.5 stringr_1.6.0
## [17] pkgconfig_2.0.3 crayon_1.5.3
## [19] fastmap_1.2.0 dbplyr_2.5.1
## [21] XVector_0.51.0 Rsamtools_2.27.0
## [23] rmarkdown_2.30 tzdb_0.5.0
## [25] UCSC.utils_1.7.1 ragg_1.5.0
## [27] purrr_1.2.1 bit_4.6.0
## [29] xfun_0.56 cachem_1.1.0
## [31] cigarillo_1.1.0 GenomeInfoDb_1.47.2
## [33] jsonlite_2.0.0 blob_1.3.0
## [35] DelayedArray_0.37.0 BiocParallel_1.45.0
## [37] echoconda_0.99.10 parallel_4.6.0
## [39] R6_2.6.1 bslib_0.9.0
## [41] stringi_1.8.7 rtracklayer_1.71.3
## [43] limma_3.67.0 reticulate_1.44.1
## [45] GenomicRanges_1.63.1 jquerylib_0.1.4
## [47] Rcpp_1.1.1 Seqinfo_1.1.0
## [49] bookdown_0.46 SummarizedExperiment_1.41.0
## [51] knitr_1.51 R.utils_2.13.0
## [53] readr_2.1.6 IRanges_2.45.0
## [55] rentrez_1.2.4 Matrix_1.7-4
## [57] tidyselect_1.2.1 abind_1.4-8
## [59] yaml_2.3.12 codetools_0.2-20
## [61] curl_7.0.0 regioneR_1.43.0
## [63] lattice_0.22-7 tibble_3.3.1
## [65] Biobase_2.71.0 basilisk.utils_1.23.1
## [67] KEGGREST_1.51.1 evaluate_1.0.5
## [69] desc_1.4.3 BiocFileCache_3.1.0
## [71] zip_2.3.3 xml2_1.5.2
## [73] ExperimentHub_3.1.0 Biostrings_2.79.4
## [75] pillar_1.11.1 BiocManager_1.30.27
## [77] filelock_1.0.3 MatrixGenerics_1.23.0
## [79] DT_0.34.0 stats4_4.6.0
## [81] generics_0.1.4 RCurl_1.98-1.17
## [83] BiocVersion_3.23.1 S4Vectors_0.49.0
## [85] hms_1.1.4 glue_1.8.0
## [87] tools_4.6.0 BiocIO_1.21.0
## [89] AnnotationHub_4.1.0 data.table_1.18.0
## [91] GenomicAlignments_1.47.0 BSgenome_1.79.1
## [93] openxlsx_4.2.8.1 GEOquery_2.79.0
## [95] fs_1.6.6 XML_3.99-0.20
## [97] grid_4.6.0 tidyr_1.3.2
## [99] echodata_0.99.17 AnnotationDbi_1.73.0
## [101] basilisk_1.23.0 restfulr_0.0.16
## [103] cli_3.6.5 rappdirs_0.3.4
## [105] textshaping_1.0.4 S4Arrays_1.11.1
## [107] dplyr_1.1.4 R.methodsS3_1.8.2
## [109] sass_0.4.10 digest_0.6.39
## [111] BiocGenerics_0.57.0 SparseArray_1.11.10
## [113] rjson_0.2.23 htmlwidgets_1.6.4
## [115] memoise_2.0.1 htmltools_0.5.9
## [117] pkgdown_2.2.0 R.oo_1.27.1
## [119] lifecycle_1.0.5 httr_1.4.7
## [121] MACSr_1.13.2 statmod_1.5.1
## [123] bit64_4.6.0-1