vignettes/docker.Rmd
docker.RmdMAGMA.Celltyping 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/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.Celltyping<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/MAGMA.CelltypingFor 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) (2025-02-15 r87726)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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_2.0.15 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] splines_4.5.0 BiocIO_1.17.1
## [3] bitops_1.0-9 ggplotify_0.1.2
## [5] filelock_1.0.3 tibble_3.2.1
## [7] R.oo_1.27.0 XML_3.99-0.18
## [9] lifecycle_1.0.4 Rdpack_2.6.2
## [11] rstatix_0.7.2 lattice_0.22-6
## [13] MASS_7.3-64 backports_1.5.0
## [15] magrittr_2.0.3 limma_3.63.4
## [17] plotly_4.10.4 sass_0.4.9
## [19] rmarkdown_2.29 jquerylib_0.1.4
## [21] yaml_2.3.10 HGNChelper_0.8.15
## [23] DBI_1.2.3 minqa_1.2.8
## [25] abind_1.4-8 GenomicRanges_1.59.1
## [27] purrr_1.0.4 R.utils_2.13.0
## [29] BiocGenerics_0.53.6 RCurl_1.98-1.16
## [31] yulab.utils_0.2.0 VariantAnnotation_1.53.1
## [33] rappdirs_0.3.3 GenomeInfoDbData_1.2.13
## [35] IRanges_2.41.3 S4Vectors_0.45.4
## [37] tidytree_0.4.6 pkgdown_2.1.1
## [39] codetools_0.2-20 DelayedArray_0.33.6
## [41] tidyselect_1.2.1 aplot_0.2.4
## [43] UCSC.utils_1.3.1 farver_2.1.2
## [45] lme4_1.1-36 matrixStats_1.5.0
## [47] stats4_4.5.0 BiocFileCache_2.15.1
## [49] GenomicAlignments_1.43.0 jsonlite_1.9.0
## [51] Formula_1.2-5 systemfonts_1.2.1
## [53] tools_4.5.0 treeio_1.31.0
## [55] ragg_1.3.3 Rcpp_1.0.14
## [57] glue_1.8.0 SparseArray_1.7.6
## [59] xfun_0.51 MatrixGenerics_1.19.1
## [61] GenomeInfoDb_1.43.4 RNOmni_1.0.1.2
## [63] dplyr_1.1.4 BiocManager_1.30.25
## [65] fastmap_1.2.0 boot_1.3-31
## [67] digest_0.6.37 R6_2.6.1
## [69] gridGraphics_0.5-1 textshaping_1.0.0
## [71] colorspace_2.1-1 RSQLite_2.3.9
## [73] R.methodsS3_1.8.2 tidyr_1.3.1
## [75] generics_0.1.3 data.table_1.17.0
## [77] rtracklayer_1.67.1 httr_1.4.7
## [79] htmlwidgets_1.6.4 S4Arrays_1.7.3
## [81] pkgconfig_2.0.3 gtable_0.3.6
## [83] blob_1.2.4 SingleCellExperiment_1.29.1
## [85] XVector_0.47.2 htmltools_0.5.8.1
## [87] carData_3.0-5 bookdown_0.42
## [89] scales_1.3.0 Biobase_2.67.0
## [91] png_0.1-8 reformulas_0.4.0
## [93] ggfun_0.1.8 ggdendro_0.2.0
## [95] knitr_1.49 reshape2_1.4.4
## [97] rjson_0.2.23 nlme_3.1-167
## [99] curl_6.2.1 nloptr_2.1.1
## [101] cachem_1.1.0 stringr_1.5.1
## [103] BiocVersion_3.21.1 parallel_4.5.0
## [105] AnnotationDbi_1.69.0 restfulr_0.0.15
## [107] desc_1.4.3 pillar_1.10.1
## [109] grid_4.5.0 vctrs_0.6.5
## [111] ggpubr_0.6.0 car_3.1-3
## [113] dbplyr_2.5.0 evaluate_1.0.3
## [115] orthogene_1.13.0 GenomicFeatures_1.59.1
## [117] cli_3.6.4 compiler_4.5.0
## [119] Rsamtools_2.23.1 rlang_1.1.5
## [121] crayon_1.5.3 grr_0.9.5
## [123] ggsignif_0.6.4 gprofiler2_0.2.3
## [125] EWCE_1.15.1 ieugwasr_1.0.1
## [127] plyr_1.8.9 fs_1.6.5
## [129] stringi_1.8.4 viridisLite_0.4.2
## [131] ewceData_1.15.0 BiocParallel_1.41.2
## [133] babelgene_22.9 munsell_0.5.1
## [135] Biostrings_2.75.4 lazyeval_0.2.2
## [137] gh_1.4.1 homologene_1.4.68.19.3.27
## [139] Matrix_1.7-2 ExperimentHub_2.15.0
## [141] MungeSumstats_1.15.12 BSgenome_1.75.1
## [143] patchwork_1.3.0 bit64_4.6.0-1
## [145] ggplot2_3.5.1 KEGGREST_1.47.0
## [147] statmod_1.5.0 SummarizedExperiment_1.37.0
## [149] AnnotationHub_3.15.0 rbibutils_2.3
## [151] broom_1.0.7 memoise_2.0.1
## [153] bslib_0.9.0 ggtree_3.15.0
## [155] bit_4.5.0.1 splitstackshape_1.4.8
## [157] ape_5.8-1