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 version 4.2.0 (2022-04-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 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/liblapack.so.3
##
## 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
##
## attached base packages:
## [1] base
##
## other attached packages:
## [1] PeakyFinders_0.99.0 BiocStyle_2.25.0
##
## loaded via a namespace (and not attached):
## [1] rjson_0.2.21 ellipsis_0.3.2
## [3] rprojroot_2.0.3 XVector_0.37.0
## [5] GenomicRanges_1.49.0 fs_1.5.2
## [7] stats_4.2.0 bit64_4.0.5
## [9] interactiveDisplayBase_1.35.0 AnnotationDbi_1.59.1
## [11] fansi_1.0.3 xml2_1.3.3
## [13] R.methodsS3_1.8.1 cachem_1.0.6
## [15] knitr_1.39 jsonlite_1.8.0
## [17] Rsamtools_2.13.3 dbplyr_2.1.1
## [19] png_0.1-7 R.oo_1.24.0
## [21] shiny_1.7.1 BiocManager_1.30.18
## [23] readr_2.1.2 compiler_4.2.0
## [25] httr_1.4.3 basilisk_1.9.0
## [27] assertthat_0.2.1 Matrix_1.4-1
## [29] fastmap_1.1.0 limma_3.53.2
## [31] cli_3.3.0 later_1.3.0
## [33] htmltools_0.5.2 tools_4.2.0
## [35] glue_1.6.2 GenomeInfoDbData_1.2.8
## [37] dplyr_1.0.9 grDevices_4.2.0
## [39] rappdirs_0.3.3 Rcpp_1.0.8.3
## [41] Biobase_2.57.1 jquerylib_0.1.4
## [43] pkgdown_2.0.3.9000 vctrs_0.4.1
## [45] Biostrings_2.65.0 ExperimentHub_2.5.0
## [47] rtracklayer_1.57.0 xfun_0.31
## [49] stringr_1.4.0 mime_0.12
## [51] lifecycle_1.0.1 restfulr_0.0.13
## [53] XML_3.99-0.9 AnnotationHub_3.5.0
## [55] zlibbioc_1.43.0 basilisk.utils_1.9.0
## [57] BSgenome_1.65.1 MatrixGenerics_1.9.0
## [59] ragg_1.2.2 graphics_4.2.0
## [61] hms_1.1.1 promises_1.2.0.1
## [63] SummarizedExperiment_1.27.1 parallel_4.2.0
## [65] GEOquery_2.65.2 utils_4.2.0
## [67] yaml_2.3.5 curl_4.3.2
## [69] memoise_2.0.1 reticulate_1.25
## [71] sass_0.4.1 datasets_4.2.0
## [73] stringi_1.7.6 RSQLite_2.2.14
## [75] BiocVersion_3.16.0 S4Vectors_0.35.0
## [77] BiocIO_1.7.1 desc_1.4.1
## [79] BiocGenerics_0.43.0 filelock_1.0.2
## [81] BiocParallel_1.31.6 GenomeInfoDb_1.33.3
## [83] rlang_1.0.2 pkgconfig_2.0.3
## [85] systemfonts_1.0.4 bitops_1.0-7
## [87] matrixStats_0.62.0 evaluate_0.15
## [89] lattice_0.20-45 purrr_0.3.4
## [91] GenomicAlignments_1.33.0 bit_4.0.4
## [93] tidyselect_1.1.2 magrittr_2.0.3
## [95] bookdown_0.26 R6_2.5.1
## [97] IRanges_2.31.0 generics_0.1.2
## [99] DelayedArray_0.23.0 DBI_1.1.2
## [101] MACSr_1.5.0 pillar_1.7.0
## [103] KEGGREST_1.37.0 RCurl_1.98-1.6
## [105] tibble_3.1.7 dir.expiry_1.5.0
## [107] crayon_1.5.1 utf8_1.2.2
## [109] BiocFileCache_2.5.0 tzdb_0.3.0
## [111] rmarkdown_2.14 grid_4.2.0
## [113] data.table_1.14.2 blob_1.2.3
## [115] methods_4.2.0 digest_0.6.29
## [117] xtable_1.8-4 tidyr_1.2.0
## [119] httpuv_1.6.5 regioneR_1.29.0
## [121] R.utils_2.11.0 textshaping_0.3.6
## [123] stats4_4.2.0 bslib_0.3.1