vignettes/docker.Rmd
docker.Rmd
templateR is now available via ghcr.io 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 ghcr.io/neurogenomics/templateR
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 \
ghcr.io/neurogenomics/templateR
<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://ghcr.io/neurogenomics/templateR
For troubleshooting, see the Singularity documentation.
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 Under development (unstable) (2023-11-22 r85609)
## Platform: x86_64-pc-linux-gnu
## 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] templateR_0.99.0
##
## loaded via a namespace (and not attached):
## [1] vctrs_0.6.5 cli_3.6.1 knitr_1.45 rlang_1.1.2
## [5] xfun_0.41 stringi_1.8.2 purrr_1.0.2 textshaping_0.3.7
## [9] jsonlite_1.8.8 glue_1.6.2 rprojroot_2.0.4 htmltools_0.5.7
## [13] ragg_1.2.6 sass_0.4.8 rmarkdown_2.25 evaluate_0.23
## [17] jquerylib_0.1.4 fastmap_1.1.1 yaml_2.3.7 lifecycle_1.0.4
## [21] memoise_2.0.1 stringr_1.5.1 compiler_4.4.0 fs_1.6.3
## [25] systemfonts_1.0.5 digest_0.6.33 R6_2.5.1 magrittr_2.0.3
## [29] bslib_0.6.1 tools_4.4.0 pkgdown_2.0.7 cachem_1.0.8
## [33] desc_1.4.2