vignettes/docker.Rmd
docker.Rmdscavenge 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/scavengeOnce 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/scavenge<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/scavengeFinally, 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) (2023-02-16 r83857)
## 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] SCAVENGE_1.0.2 BiocStyle_2.27.1
##
## loaded via a namespace (and not attached):
## [1] jsonlite_1.8.4 magrittr_2.0.3
## [3] rmarkdown_2.20 fs_1.6.1
## [5] BiocIO_1.9.2 zlibbioc_1.45.0
## [7] ragg_1.2.5 vctrs_0.5.2
## [9] memoise_2.0.1 Rsamtools_2.15.1
## [11] RCurl_1.98-1.10 htmltools_0.5.4
## [13] CNEr_1.35.0 sass_0.4.5
## [15] pracma_2.4.2 bslib_0.4.2
## [17] htmlwidgets_1.6.1 desc_1.4.2
## [19] plyr_1.8.8 plotly_4.10.1
## [21] cachem_1.0.6 GenomicAlignments_1.35.0
## [23] igraph_1.4.0 mime_0.12
## [25] lifecycle_1.0.3 pkgconfig_2.0.3
## [27] Matrix_1.5-3 R6_2.5.1
## [29] fastmap_1.1.0 GenomeInfoDbData_1.2.9
## [31] MatrixGenerics_1.11.0 shiny_1.7.4
## [33] digest_0.6.31 gchromVAR_0.3.2
## [35] colorspace_2.1-0 TFMPvalue_0.0.9
## [37] AnnotationDbi_1.61.0 S4Vectors_0.37.3
## [39] rprojroot_2.0.3 irlba_2.3.5.1
## [41] textshaping_0.3.6 GenomicRanges_1.51.4
## [43] RSQLite_2.3.0 seqLogo_1.65.0
## [45] fansi_1.0.4 httr_1.4.4
## [47] compiler_4.3.0 bit64_4.0.5
## [49] BiocParallel_1.33.9 DBI_1.1.3
## [51] R.utils_2.12.2 poweRlaw_0.70.6
## [53] DelayedArray_0.25.0 rjson_0.2.21
## [55] gtools_3.9.4 caTools_1.18.2
## [57] tools_4.3.0 httpuv_1.6.9
## [59] R.oo_1.25.0 glue_1.6.2
## [61] restfulr_0.0.15 promises_1.2.0.1
## [63] grid_4.3.0 reshape2_1.4.4
## [65] TFBSTools_1.37.0 generics_0.1.3
## [67] gtable_0.3.1 BSgenome_1.67.4
## [69] tzdb_0.3.0 R.methodsS3_1.8.2
## [71] tidyr_1.3.0 data.table_1.14.8
## [73] hms_1.1.2 utf8_1.2.3
## [75] XVector_0.39.0 BiocGenerics_0.45.0
## [77] RANN_2.6.1 pillar_1.8.1
## [79] stringr_1.5.0 later_1.3.0
## [81] dplyr_1.1.0 lattice_0.20-45
## [83] rtracklayer_1.59.1 bit_4.0.5
## [85] chromVAR_1.21.0 annotate_1.77.0
## [87] tidyselect_1.2.0 DirichletMultinomial_1.41.0
## [89] GO.db_3.16.0 Biostrings_2.67.0
## [91] miniUI_0.1.1.1 knitr_1.42
## [93] bookdown_0.32 IRanges_2.33.0
## [95] SummarizedExperiment_1.29.1 stats4_4.3.0
## [97] xfun_0.37 Biobase_2.59.0
## [99] matrixStats_0.63.0 DT_0.27
## [101] stringi_1.7.12 lazyeval_0.2.2
## [103] yaml_2.3.7 evaluate_0.20
## [105] codetools_0.2-19 tibble_3.1.8
## [107] BiocManager_1.30.19 cli_3.6.0
## [109] xtable_1.8-4 systemfonts_1.0.4
## [111] munsell_0.5.0 jquerylib_0.1.4
## [113] Rcpp_1.0.10 GenomeInfoDb_1.35.15
## [115] png_0.1-8 XML_3.99-0.13
## [117] parallel_4.3.0 ellipsis_0.3.2
## [119] pkgdown_2.0.7 ggplot2_3.4.1
## [121] readr_2.1.4 blob_1.2.3
## [123] bitops_1.0-7 viridisLite_0.4.1
## [125] scales_1.2.1 purrr_1.0.1
## [127] crayon_1.5.2 rlang_1.0.6
## [129] KEGGREST_1.39.0