rworkflows 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/rworkflows
Once 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 8900:8787 \
neurogenomicslab/rworkflows
<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/rworkflows
Finally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8900/
Login using the credentials set during the Installation steps.
utils::sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur ... 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
##
## locale:
## [1] C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] rworkflows_0.99.12 data.table_1.14.8 BiocStyle_2.26.0
##
## loaded via a namespace (and not attached):
## [1] Biobase_2.58.0 httr_1.4.6 sass_0.4.6
## [4] bit64_4.0.5 jsonlite_1.8.4 here_1.0.1
## [7] bslib_0.4.2 BiocManager_1.30.20 rvcheck_0.2.1
## [10] stats4_4.2.1 BiocFileCache_2.6.1 yulab.utils_0.0.6
## [13] RBGL_1.74.0 BiocPkgTools_1.16.1 blob_1.2.4
## [16] renv_0.17.3 yaml_2.3.7 pillar_1.9.0
## [19] RSQLite_2.3.1 glue_1.6.2 RUnit_0.4.32
## [22] digest_0.6.31 RColorBrewer_1.1-3 rvest_1.0.3
## [25] colorspace_2.1-0 htmltools_0.5.5 XML_3.99-0.14
## [28] pkgconfig_2.0.3 httpcode_0.3.0 bookdown_0.34
## [31] scales_1.2.1 whisker_0.4.1 tzdb_0.4.0
## [34] tibble_3.2.1 biocViews_1.66.3 generics_0.1.3
## [37] ggplot2_3.4.2 DT_0.28 cachem_1.0.8
## [40] BiocGenerics_0.44.0 cli_3.6.1 magrittr_2.0.3
## [43] memoise_2.0.1 evaluate_0.21 badger_0.2.3
## [46] fansi_1.0.4 xml2_1.3.4 graph_1.76.0
## [49] tools_4.2.1 gh_1.4.0 hms_1.1.3
## [52] lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0
## [55] compiler_4.2.1 jquerylib_0.1.4 rlang_1.1.1
## [58] grid_4.2.1 RCurl_1.98-1.12 rappdirs_0.3.3
## [61] htmlwidgets_1.6.2 igraph_1.5.0.1 bitops_1.0-7
## [64] rmarkdown_2.22 rorcid_0.7.0 gtable_0.3.3
## [67] DBI_1.1.3 curl_5.0.0 fauxpas_0.5.2
## [70] R6_2.5.1 knitr_1.43 dplyr_1.1.2
## [73] fastmap_1.1.1 bit_4.0.5 utf8_1.2.3
## [76] rprojroot_2.0.3 filelock_1.0.2 dlstats_0.1.7
## [79] readr_2.1.4 desc_1.4.2 stringi_1.7.12
## [82] crul_1.4.0 vctrs_0.6.2 dbplyr_2.3.2
## [85] tidyselect_1.2.0 xfun_0.39