vignettes/docker.Rmd
docker.Rmddevoptera 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/RajLabMSSM/devopteraOnce 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/RajLabMSSM/devoptera<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/RajLabMSSM/devopteraFor 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) (2024-03-28 r86224)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 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] devoptera_0.99.1
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 dplyr_1.1.4 blob_1.2.4
## [4] filelock_1.0.3 R.utils_2.12.3 bitops_1.0-7
## [7] fastmap_1.1.1 RCurl_1.98-1.14 BiocFileCache_2.11.2
## [10] promises_1.2.1 XML_3.99-0.16.1 digest_0.6.35
## [13] mime_0.12 lifecycle_1.0.4 ellipsis_0.3.2
## [16] RSQLite_2.3.6 magrittr_2.0.3 compiler_4.5.0
## [19] rlang_1.1.3 sass_0.4.9 tools_4.5.0
## [22] utf8_1.2.4 yaml_2.3.8 data.table_1.15.4
## [25] knitr_1.45 htmlwidgets_1.6.4 bit_4.0.5
## [28] pkgbuild_1.4.4 curl_5.2.1 here_1.0.1
## [31] pkgload_1.3.4 miniUI_0.1.1.1 purrr_1.0.2
## [34] BiocGenerics_0.49.1 desc_1.4.3 R.oo_1.26.0
## [37] stats4_4.5.0 fansi_1.0.6 urlchecker_1.0.1
## [40] profvis_0.3.8 xtable_1.8-4 cli_3.6.2
## [43] rmarkdown_2.26 ragg_1.3.0 generics_0.1.3
## [46] remotes_2.5.0.9000 stringdist_0.9.12 rstudioapi_0.16.0
## [49] httr_1.4.7 sessioninfo_1.2.2 BiocBaseUtils_1.5.1
## [52] RUnit_0.4.33 DBI_1.2.2 cachem_1.0.8
## [55] stringr_1.5.1 parallel_4.5.0 BiocManager_1.30.22
## [58] vctrs_0.6.5 devtools_2.4.5 jsonlite_1.8.8
## [61] bit64_4.0.5 RBGL_1.79.0 systemfonts_1.0.6
## [64] jquerylib_0.1.4 glue_1.7.0 pkgdown_2.0.7
## [67] codetools_0.2-19 stringi_1.8.3 later_1.3.2
## [70] BiocCheck_1.39.27 tibble_3.2.1 pillar_1.9.0
## [73] rappdirs_0.3.3 htmltools_0.5.8 graph_1.81.0
## [76] R6_2.5.1 dbplyr_2.5.0 httr2_1.0.0
## [79] textshaping_0.3.7 rprojroot_2.0.4 evaluate_0.23
## [82] shiny_1.8.1 Biobase_2.63.1 R.methodsS3_1.8.2
## [85] memoise_2.0.1 httpuv_1.6.15 bslib_0.7.0
## [88] Rcpp_1.0.12 xfun_0.43 usethis_2.2.3
## [91] fs_1.6.3 biocViews_1.71.1 pkgconfig_2.0.3