orthogene 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/orthogene
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 8787:8787 \
neurogenomicslab/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://neurogenomicslab/orthogene
Finally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8787/
Login using the credentials set during the Installation steps.
utils::sessionInfo()
## R version 4.2.2 (2022-10-31)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.0
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] orthogene_1.4.2 BiocStyle_2.26.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.9 ape_5.6-2
## [3] lattice_0.20-45 tidyr_1.2.1
## [5] assertthat_0.2.1 digest_0.6.31
## [7] utf8_1.2.2 R6_2.5.1
## [9] backports_1.4.1 evaluate_0.20
## [11] httr_1.4.4 ggplot2_3.4.0
## [13] pillar_1.8.1 ggfun_0.0.9
## [15] yulab.utils_0.0.6 rlang_1.0.6
## [17] lazyeval_0.2.2 data.table_1.14.6
## [19] car_3.1-1 jquerylib_0.1.4
## [21] Matrix_1.5-3 grr_0.9.5
## [23] rmarkdown_2.20 stringr_1.5.0
## [25] htmlwidgets_1.6.1 munsell_0.5.0
## [27] broom_1.0.2 gprofiler2_0.2.1
## [29] compiler_4.2.2 xfun_0.36
## [31] pkgconfig_2.0.3 gridGraphics_0.5-1
## [33] htmltools_0.5.4 tidyselect_1.2.0
## [35] tibble_3.1.8 bookdown_0.32
## [37] viridisLite_0.4.1 fansi_1.0.3
## [39] dplyr_1.0.10 ggpubr_0.5.0
## [41] grid_4.2.2 nlme_3.1-161
## [43] jsonlite_1.8.4 gtable_0.3.1
## [45] lifecycle_1.0.3 DBI_1.1.3
## [47] magrittr_2.0.3 scales_1.2.1
## [49] tidytree_0.4.2 cli_3.6.0
## [51] stringi_1.7.12 cachem_1.0.6
## [53] carData_3.0-5 ggsignif_0.6.4
## [55] ggtree_3.6.2 bslib_0.4.2
## [57] generics_0.1.3 vctrs_0.5.1
## [59] treeio_1.22.0 tools_4.2.2
## [61] homologene_1.4.68.19.3.27 ggplotify_0.1.0
## [63] glue_1.6.2 purrr_1.0.1
## [65] abind_1.4-5 parallel_4.2.2
## [67] fastmap_1.1.0 yaml_2.3.6
## [69] babelgene_22.9 colorspace_2.0-3
## [71] BiocManager_1.30.19 rstatix_0.7.1
## [73] aplot_0.1.9 plotly_4.10.1
## [75] knitr_1.41 patchwork_1.1.2
## [77] sass_0.4.4