vignettes/docker.Rmd
docker.Rmd
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 4.3.1 (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] rworkflows_0.99.14 BiocStyle_2.29.2
##
## loaded via a namespace (and not attached):
## [1] yulab.utils_0.0.9 sass_0.4.7 utf8_1.2.3
## [4] generics_0.1.3 renv_1.0.3 stringi_1.7.12
## [7] digest_0.6.33 magrittr_2.0.3 evaluate_0.21
## [10] grid_4.3.1 RColorBrewer_1.1-3 bookdown_0.35
## [13] fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.7
## [16] BiocManager_1.30.22 purrr_1.0.2 fansi_1.0.4
## [19] scales_1.2.1 textshaping_0.3.6 jquerylib_0.1.4
## [22] cli_3.6.1 rlang_1.1.1 badger_0.2.3
## [25] munsell_0.5.0 cachem_1.0.8 yaml_2.3.7
## [28] tools_4.3.1 memoise_2.0.1 dplyr_1.1.3
## [31] colorspace_2.1-0 ggplot2_3.4.3 here_1.0.1
## [34] vctrs_0.6.3 R6_2.5.1 lifecycle_1.0.3
## [37] stringr_1.5.0 fs_1.6.3 ragg_1.2.5
## [40] pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7
## [43] bslib_0.5.1 pillar_1.9.0 gtable_0.3.4
## [46] glue_1.6.2 data.table_1.14.8 systemfonts_1.0.4
## [49] xfun_0.40 tibble_3.2.1 rvcheck_0.2.1
## [52] tidyselect_1.2.0 knitr_1.44 htmltools_0.5.6
## [55] rmarkdown_2.25 dlstats_0.1.7 compiler_4.3.1