vignettes/docker.Rmd
docker.Rmdecholocator 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 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/echolocator<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://bschilder/echolocatorFinally, 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) (2023-01-11 r83598)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 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-r0.3.20.so; LAPACK version 3.10.0
##
## 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] echolocatoR_2.0.3 BiocStyle_2.27.0
##
## loaded via a namespace (and not attached):
## [1] ProtGenerics_1.31.0 fs_1.5.2
## [3] matrixStats_0.63.0 bitops_1.0-7
## [5] httr_1.4.4 RColorBrewer_1.1-3
## [7] Rgraphviz_2.43.0 tools_4.3.0
## [9] backports_1.4.1 utf8_1.2.2
## [11] R6_2.5.1 DT_0.27
## [13] lazyeval_0.2.2 prettyunits_1.1.1
## [15] GGally_2.1.2 gridExtra_2.3
## [17] cli_3.6.0 Biobase_2.59.0
## [19] textshaping_0.3.6 ggbio_1.47.0
## [21] sass_0.4.4 mvtnorm_1.1-3
## [23] readr_2.1.3 proxy_0.4-27
## [25] pkgdown_2.0.7 mixsqp_0.3-48
## [27] Rsamtools_2.15.1 systemfonts_1.0.4
## [29] foreign_0.8-84 R.utils_2.12.2
## [31] dichromat_2.0-0.1 maps_3.4.1
## [33] BSgenome_1.67.3 readxl_1.4.1
## [35] susieR_0.12.27 pals_1.7
## [37] rstudioapi_0.14 RSQLite_2.2.20
## [39] httpcode_0.3.0 generics_0.1.3
## [41] BiocIO_1.9.1 echoconda_0.99.9
## [43] dplyr_1.0.10 zip_2.2.2
## [45] Matrix_1.5-3 interp_1.1-3
## [47] fansi_1.0.3 DescTools_0.99.47
## [49] S4Vectors_0.37.3 catalogueR_1.0.1
## [51] R.methodsS3_1.8.2 lifecycle_1.0.3
## [53] yaml_2.3.6 SummarizedExperiment_1.29.1
## [55] BiocFileCache_2.7.1 echoplot_0.99.6
## [57] grid_4.3.0 blob_1.2.3
## [59] crayon_1.5.2 dir.expiry_1.7.0
## [61] lattice_0.20-45 GenomicFeatures_1.51.2
## [63] mapproj_1.2.11 KEGGREST_1.39.0
## [65] pillar_1.8.1 knitr_1.41
## [67] GenomicRanges_1.51.4 rjson_0.2.21
## [69] osfr_0.2.9 boot_1.3-28.1
## [71] gld_2.6.6 codetools_0.2-18
## [73] glue_1.6.2 data.table_1.14.6
## [75] coloc_5.1.0.1 vctrs_0.5.1
## [77] png_0.1-8 XGR_1.1.8
## [79] cellranger_1.1.0 gtable_0.3.1
## [81] assertthat_0.2.1 cachem_1.0.6
## [83] dnet_1.1.7 xfun_0.36
## [85] openxlsx_4.2.5.1 survival_3.5-0
## [87] ellipsis_0.3.2 nlme_3.1-161
## [89] bit64_4.0.5 progress_1.2.2
## [91] filelock_1.0.2 GenomeInfoDb_1.35.12
## [93] rprojroot_2.0.3 bslib_0.4.2
## [95] irlba_2.3.5.1 rpart_4.1.19
## [97] colorspace_2.0-3 BiocGenerics_0.45.0
## [99] DBI_1.1.3 Hmisc_4.7-2
## [101] nnet_7.3-18 Exact_3.2
## [103] tidyselect_1.2.0 bit_4.0.5
## [105] compiler_4.3.0 curl_5.0.0
## [107] graph_1.77.1 htmlTable_2.4.1
## [109] expm_0.999-7 basilisk.utils_1.11.1
## [111] xml2_1.3.3 desc_1.4.2
## [113] DelayedArray_0.25.0 bookdown_0.32
## [115] rtracklayer_1.59.1 checkmate_2.1.0
## [117] scales_1.2.1 hexbin_1.28.2
## [119] echoLD_0.99.9 RBGL_1.75.0
## [121] RCircos_1.2.2 rappdirs_0.3.3
## [123] stringr_1.5.0 supraHex_1.37.0
## [125] digest_0.6.31 piggyback_0.1.4
## [127] rmarkdown_2.20 basilisk_1.11.2
## [129] XVector_0.39.0 htmltools_0.5.4
## [131] pkgconfig_2.0.3 jpeg_0.1-10
## [133] base64enc_0.1-3 MatrixGenerics_1.11.0
## [135] echodata_0.99.16 ensembldb_2.23.1
## [137] dbplyr_2.3.0 fastmap_1.1.0
## [139] rlang_1.0.6 htmlwidgets_1.6.1
## [141] echofinemap_0.99.5 jquerylib_0.1.4
## [143] jsonlite_1.8.4 BiocParallel_1.33.9
## [145] R.oo_1.25.0 VariantAnnotation_1.45.0
## [147] RCurl_1.98-1.9 magrittr_2.0.3
## [149] Formula_1.2-4 GenomeInfoDbData_1.2.9
## [151] ggnetwork_0.5.10 patchwork_1.1.2
## [153] munsell_0.5.0 Rcpp_1.0.9
## [155] ggnewscale_0.4.8 ape_5.6-2
## [157] viridis_0.6.2 reticulate_1.27
## [159] stringi_1.7.12 rootSolve_1.8.2.3
## [161] zlibbioc_1.45.0 MASS_7.3-58.1
## [163] plyr_1.8.8 parallel_4.3.0
## [165] ggrepel_0.9.2 snpStats_1.49.0
## [167] lmom_2.9 deldir_1.0-6
## [169] echoannot_0.99.10 Biostrings_2.67.0
## [171] splines_4.3.0 hms_1.1.2
## [173] igraph_1.3.5 reshape2_1.4.4
## [175] biomaRt_2.55.0 stats4_4.3.0
## [177] crul_1.3 XML_3.99-0.13
## [179] evaluate_0.20 latticeExtra_0.6-30
## [181] biovizBase_1.47.0 BiocManager_1.30.19
## [183] tzdb_0.3.0 tidyr_1.2.1
## [185] purrr_1.0.1 reshape_0.8.9
## [187] ggplot2_3.4.0 echotabix_0.99.9
## [189] restfulr_0.0.15 AnnotationFilter_1.23.0
## [191] e1071_1.7-12 downloadR_0.99.6
## [193] viridisLite_0.4.1 class_7.3-20.1
## [195] ragg_1.2.5 OrganismDbi_1.41.0
## [197] tibble_3.1.8 memoise_2.0.1
## [199] AnnotationDbi_1.61.0 GenomicAlignments_1.35.0
## [201] IRanges_2.33.0 cluster_2.1.4