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 version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 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-r0.3.20.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_2.29.1
##
## loaded via a namespace (and not attached):
## [1] jsonlite_1.8.7 magrittr_2.0.3
## [3] rmarkdown_2.24 fs_1.6.3
## [5] BiocIO_1.11.0 zlibbioc_1.47.0
## [7] ragg_1.2.5 vctrs_0.6.3
## [9] memoise_2.0.1 Rsamtools_2.17.0
## [11] RCurl_1.98-1.12 htmltools_0.5.6
## [13] S4Arrays_1.1.6 CNEr_1.37.0
## [15] SparseArray_1.1.12 sass_0.4.7
## [17] pracma_2.4.2 bslib_0.5.1
## [19] htmlwidgets_1.6.2 desc_1.4.2
## [21] plyr_1.8.8 plotly_4.10.2
## [23] cachem_1.0.8 GenomicAlignments_1.37.0
## [25] igraph_1.5.1 mime_0.12
## [27] lifecycle_1.0.3 pkgconfig_2.0.3
## [29] Matrix_1.6-1 R6_2.5.1
## [31] fastmap_1.1.1 GenomeInfoDbData_1.2.10
## [33] MatrixGenerics_1.13.1 shiny_1.7.5
## [35] digest_0.6.33 gchromVAR_0.3.2
## [37] colorspace_2.1-0 TFMPvalue_0.0.9
## [39] AnnotationDbi_1.63.2 S4Vectors_0.39.1
## [41] rprojroot_2.0.3 irlba_2.3.5.1
## [43] textshaping_0.3.6 GenomicRanges_1.53.1
## [45] RSQLite_2.3.1 seqLogo_1.67.0
## [47] fansi_1.0.4 httr_1.4.7
## [49] abind_1.4-5 compiler_4.3.1
## [51] bit64_4.0.5 BiocParallel_1.35.4
## [53] DBI_1.1.3 R.utils_2.12.2
## [55] poweRlaw_0.70.6 DelayedArray_0.27.10
## [57] rjson_0.2.21 gtools_3.9.4
## [59] caTools_1.18.2 tools_4.3.1
## [61] httpuv_1.6.11 R.oo_1.25.0
## [63] glue_1.6.2 restfulr_0.0.15
## [65] promises_1.2.1 grid_4.3.1
## [67] reshape2_1.4.4 TFBSTools_1.39.0
## [69] generics_0.1.3 gtable_0.3.4
## [71] BSgenome_1.69.0 tzdb_0.4.0
## [73] R.methodsS3_1.8.2 tidyr_1.3.0
## [75] data.table_1.14.8 hms_1.1.3
## [77] utf8_1.2.3 XVector_0.41.1
## [79] BiocGenerics_0.47.0 RANN_2.6.1
## [81] pillar_1.9.0 stringr_1.5.0
## [83] later_1.3.1 dplyr_1.1.2
## [85] lattice_0.21-8 rtracklayer_1.61.1
## [87] bit_4.0.5 chromVAR_1.23.0
## [89] annotate_1.79.0 tidyselect_1.2.0
## [91] DirichletMultinomial_1.43.0 GO.db_3.17.0
## [93] Biostrings_2.69.2 miniUI_0.1.1.1
## [95] knitr_1.43 bookdown_0.35
## [97] IRanges_2.35.2 SummarizedExperiment_1.31.1
## [99] stats4_4.3.1 xfun_0.40
## [101] Biobase_2.61.0 matrixStats_1.0.0
## [103] DT_0.29 stringi_1.7.12
## [105] lazyeval_0.2.2 yaml_2.3.7
## [107] evaluate_0.21 codetools_0.2-19
## [109] tibble_3.2.1 BiocManager_1.30.22
## [111] cli_3.6.1 xtable_1.8-4
## [113] systemfonts_1.0.4 munsell_0.5.0
## [115] jquerylib_0.1.4 Rcpp_1.0.11
## [117] GenomeInfoDb_1.37.3 png_0.1-8
## [119] XML_3.99-0.14 parallel_4.3.1
## [121] ellipsis_0.3.2 pkgdown_2.0.7
## [123] ggplot2_3.4.3 readr_2.1.4
## [125] blob_1.2.4 bitops_1.0-7
## [127] viridisLite_0.4.2 scales_1.2.1
## [129] purrr_1.0.2 crayon_1.5.2
## [131] rlang_1.1.1 KEGGREST_1.41.0