Docker/Singularity Containers
Authors: Brian Schilder, Alan Murphy, Julien Bryois, Hiranyamaya
(Hiru) Dash, Nathan Skene
Authors: Brian Schilder, Alan Murphy, Julien Bryois, Hiranyamaya (Hiru) Dash, Nathan Skene
Vignette updated: Jan-26-2026
Source: Vignette updated: Jan-26-2026
vignettes/docker.Rmd
docker.RmdInstallation
MAGMA.Celltyping is now available via ghcr.io as a containerised environment with Rstudio and all necessary dependencies pre-installed.
Method 1: via Docker
First, install Docker if you have not already.
Create an image of the Docker container in command line:
docker pull ghcr.io/neurogenomics/MAGMA.CelltypingOnce 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/MAGMA.CelltypingNOTES
- Make sure to replace
<your_password>above with whatever you want your password to be.
- Change the paths supplied to the
-vflags for your particular use case. - The
-densures the container will run in “detached” mode, which means it will persist even after you’ve closed your command line session.
- The username will be “rstudio” by default.
- Optionally, you can also install the Docker Desktop to easily manage your containers.
Method 2: via Singularity
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/MAGMA.CelltypingFor troubleshooting, see the Singularity documentation.
Usage
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.
Session Info
utils::sessionInfo()## R Under development (unstable) (2026-01-25 r89330)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 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-r0.3.26.so; LAPACK version 3.12.0
##
## 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] MAGMA.Celltyping_2.0.16 BiocStyle_2.39.0
##
## loaded via a namespace (and not attached):
## [1] splines_4.6.0 BiocIO_1.21.0
## [3] bitops_1.0-9 ggplotify_0.1.3
## [5] filelock_1.0.3 tibble_3.3.1
## [7] R.oo_1.27.1 XML_3.99-0.20
## [9] lifecycle_1.0.5 httr2_1.2.2
## [11] Rdpack_2.6.5 rstatix_0.7.3
## [13] lattice_0.22-7 MASS_7.3-65
## [15] backports_1.5.0 magrittr_2.0.4
## [17] limma_3.67.0 plotly_4.12.0
## [19] sass_0.4.10 rmarkdown_2.30
## [21] jquerylib_0.1.4 yaml_2.3.12
## [23] otel_0.2.0 HGNChelper_0.8.15
## [25] minqa_1.2.8 DBI_1.2.3
## [27] RColorBrewer_1.1-3 abind_1.4-8
## [29] GenomicRanges_1.63.1 purrr_1.2.1
## [31] R.utils_2.13.0 BiocGenerics_0.57.0
## [33] RCurl_1.98-1.17 yulab.utils_0.2.3
## [35] VariantAnnotation_1.57.1 rappdirs_0.3.4
## [37] gdtools_0.4.4 IRanges_2.45.0
## [39] S4Vectors_0.49.0 tidytree_0.4.7
## [41] pkgdown_2.2.0 codetools_0.2-20
## [43] DelayedArray_0.37.0 tidyselect_1.2.1
## [45] aplot_0.2.9 UCSC.utils_1.7.1
## [47] farver_2.1.2 lme4_1.1-38
## [49] matrixStats_1.5.0 stats4_4.6.0
## [51] BiocFileCache_3.1.0 Seqinfo_1.1.0
## [53] GenomicAlignments_1.47.0 jsonlite_2.0.0
## [55] Formula_1.2-5 systemfonts_1.3.1
## [57] tools_4.6.0 treeio_1.35.0
## [59] ragg_1.5.0 Rcpp_1.1.1
## [61] glue_1.8.0 SparseArray_1.11.10
## [63] xfun_0.56 MatrixGenerics_1.23.0
## [65] GenomeInfoDb_1.47.2 RNOmni_1.0.1.2
## [67] dplyr_1.1.4 BiocManager_1.30.27
## [69] fastmap_1.2.0 boot_1.3-32
## [71] digest_0.6.39 R6_2.6.1
## [73] gridGraphics_0.5-1 textshaping_1.0.4
## [75] RSQLite_2.4.5 cigarillo_1.1.0
## [77] R.methodsS3_1.8.2 tidyr_1.3.2
## [79] generics_0.1.4 fontLiberation_0.1.0
## [81] data.table_1.18.0 rtracklayer_1.71.3
## [83] httr_1.4.7 htmlwidgets_1.6.4
## [85] S4Arrays_1.11.1 pkgconfig_2.0.3
## [87] gtable_0.3.6 blob_1.3.0
## [89] S7_0.2.1 SingleCellExperiment_1.33.0
## [91] XVector_0.51.0 htmltools_0.5.9
## [93] fontBitstreamVera_0.1.1 carData_3.0-5
## [95] bookdown_0.46 scales_1.4.0
## [97] Biobase_2.71.0 png_0.1-8
## [99] reformulas_0.4.3.1 ggfun_0.2.0
## [101] ggdendro_0.2.0 knitr_1.51
## [103] reshape2_1.4.5 rjson_0.2.23
## [105] nloptr_2.2.1 nlme_3.1-168
## [107] curl_7.0.0 cachem_1.1.0
## [109] stringr_1.6.0 BiocVersion_3.23.1
## [111] parallel_4.6.0 AnnotationDbi_1.73.0
## [113] restfulr_0.0.16 desc_1.4.3
## [115] pillar_1.11.1 grid_4.6.0
## [117] vctrs_0.7.1 ggpubr_0.6.2
## [119] car_3.1-3 dbplyr_2.5.1
## [121] evaluate_1.0.5 orthogene_1.17.2
## [123] GenomicFeatures_1.63.1 cli_3.6.5
## [125] compiler_4.6.0 Rsamtools_2.27.0
## [127] rlang_1.1.7 crayon_1.5.3
## [129] ggsignif_0.6.4 gprofiler2_0.2.4
## [131] EWCE_1.19.0 ieugwasr_1.1.0
## [133] plyr_1.8.9 fs_1.6.6
## [135] ggiraph_0.9.3 stringi_1.8.7
## [137] viridisLite_0.4.2 ewceData_1.19.0
## [139] BiocParallel_1.45.0 babelgene_22.9
## [141] Biostrings_2.79.4 lazyeval_0.2.2
## [143] gh_1.5.0 homologene_1.4.68.19.3.27
## [145] fontquiver_0.2.1 Matrix_1.7-4
## [147] ExperimentHub_3.1.0 MungeSumstats_1.19.5
## [149] BSgenome_1.79.1 patchwork_1.3.2
## [151] bit64_4.6.0-1 ggplot2_4.0.1
## [153] KEGGREST_1.51.1 statmod_1.5.1
## [155] SummarizedExperiment_1.41.0 AnnotationHub_4.1.0
## [157] rbibutils_2.4.1 broom_1.0.11
## [159] memoise_2.0.1 bslib_0.10.0
## [161] ggtree_4.1.1 bit_4.6.0
## [163] splitstackshape_1.4.8 ape_5.8-1