vignettes/docker.Rmd
docker.Rmdorthogene 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/orthogeneOnce 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/orthogene<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/orthogeneFor 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 version 4.3.2 (2023-10-31)
## 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] orthogene_1.9.1 BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.4 babelgene_22.9
## [3] xfun_0.41 bslib_0.6.1
## [5] ggplot2_3.4.4 htmlwidgets_1.6.4
## [7] rstatix_0.7.2 lattice_0.22-5
## [9] vctrs_0.6.5 tools_4.3.2
## [11] generics_0.1.3 yulab.utils_0.1.1
## [13] parallel_4.3.2 tibble_3.2.1
## [15] fansi_1.0.6 pkgconfig_2.0.3
## [17] Matrix_1.6-1.1 ggplotify_0.1.2
## [19] data.table_1.14.10 homologene_1.4.68.19.3.27
## [21] desc_1.4.3 lifecycle_1.0.4
## [23] compiler_4.3.2 stringr_1.5.1
## [25] treeio_1.26.0 textshaping_0.3.7
## [27] munsell_0.5.0 carData_3.0-5
## [29] ggtree_3.10.0 gprofiler2_0.2.2
## [31] ggfun_0.1.3 htmltools_0.5.7
## [33] sass_0.4.8 yaml_2.3.8
## [35] lazyeval_0.2.2 plotly_4.10.3
## [37] pillar_1.9.0 pkgdown_2.0.7
## [39] car_3.1-2 ggpubr_0.6.0
## [41] jquerylib_0.1.4 tidyr_1.3.0
## [43] cachem_1.0.8 grr_0.9.5
## [45] abind_1.4-5 nlme_3.1-163
## [47] tidyselect_1.2.0 aplot_0.2.2
## [49] digest_0.6.33 stringi_1.8.3
## [51] dplyr_1.1.4 purrr_1.0.2
## [53] bookdown_0.37 fastmap_1.1.1
## [55] grid_4.3.2 colorspace_2.1-0
## [57] cli_3.6.2 magrittr_2.0.3
## [59] patchwork_1.1.3 utf8_1.2.4
## [61] broom_1.0.5 ape_5.7-1
## [63] scales_1.3.0 backports_1.4.1
## [65] httr_1.4.7 rmarkdown_2.25
## [67] ggsignif_0.6.4 ragg_1.2.6
## [69] memoise_2.0.1 evaluate_0.23
## [71] knitr_1.45 viridisLite_0.4.2
## [73] gridGraphics_0.5-1 rlang_1.1.2
## [75] Rcpp_1.0.11 glue_1.6.2
## [77] tidytree_0.4.6 BiocManager_1.30.22
## [79] jsonlite_1.8.8 R6_2.5.1
## [81] systemfonts_1.0.5 fs_1.6.3