vignettes/docker.Rmd
docker.Rmdmagma.celltyping 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/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 8787:8787 \
neurogenomicslab/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://neurogenomicslab/magma.celltypingFinally, 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 4.3.1 (2023-06-16)
## 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] MAGMA.Celltyping_2.0.11 BiocStyle_2.29.1
##
## loaded via a namespace (and not attached):
## [1] splines_4.3.1 later_1.3.1
## [3] BiocIO_1.11.0 bitops_1.0-7
## [5] ggplotify_0.1.2 filelock_1.0.2
## [7] tibble_3.2.1 R.oo_1.25.0
## [9] XML_3.99-0.14 lifecycle_1.0.3
## [11] rstatix_0.7.2 rprojroot_2.0.3
## [13] MASS_7.3-60 lattice_0.21-8
## [15] backports_1.4.1 magrittr_2.0.3
## [17] limma_3.57.7 plotly_4.10.2
## [19] sass_0.4.7 rmarkdown_2.24
## [21] jquerylib_0.1.4 yaml_2.3.7
## [23] httpuv_1.6.11 HGNChelper_0.8.1
## [25] minqa_1.2.5 DBI_1.1.3
## [27] abind_1.4-5 zlibbioc_1.47.0
## [29] GenomicRanges_1.53.1 purrr_1.0.2
## [31] R.utils_2.12.2 BiocGenerics_0.47.0
## [33] RCurl_1.98-1.12 yulab.utils_0.0.7
## [35] VariantAnnotation_1.47.1 rappdirs_0.3.3
## [37] GenomeInfoDbData_1.2.10 IRanges_2.35.2
## [39] S4Vectors_0.39.1 tidytree_0.4.5
## [41] pkgdown_2.0.7 codetools_0.2-19
## [43] DelayedArray_0.27.10 xml2_1.3.5
## [45] tidyselect_1.2.0 aplot_0.2.0
## [47] lme4_1.1-34 matrixStats_1.0.0
## [49] stats4_4.3.1 BiocFileCache_2.9.1
## [51] GenomicAlignments_1.37.0 jsonlite_1.8.7
## [53] ellipsis_0.3.2 systemfonts_1.0.4
## [55] tools_4.3.1 progress_1.2.2
## [57] treeio_1.25.3 ragg_1.2.5
## [59] Rcpp_1.0.11 glue_1.6.2
## [61] SparseArray_1.1.11 xfun_0.40
## [63] MatrixGenerics_1.13.1 GenomeInfoDb_1.37.2
## [65] RNOmni_1.0.1 dplyr_1.1.2
## [67] BiocManager_1.30.22 fastmap_1.1.1
## [69] boot_1.3-28.1 fansi_1.0.4
## [71] digest_0.6.33 R6_2.5.1
## [73] mime_0.12 gridGraphics_0.5-1
## [75] textshaping_0.3.6 colorspace_2.1-0
## [77] biomaRt_2.57.1 RSQLite_2.3.1
## [79] R.methodsS3_1.8.2 utf8_1.2.3
## [81] tidyr_1.3.0 generics_0.1.3
## [83] data.table_1.14.8 rtracklayer_1.61.1
## [85] prettyunits_1.1.1 httr_1.4.7
## [87] htmlwidgets_1.6.2 S4Arrays_1.1.5
## [89] pkgconfig_2.0.3 gtable_0.3.3
## [91] blob_1.2.4 SingleCellExperiment_1.23.0
## [93] XVector_0.41.1 htmltools_0.5.6
## [95] carData_3.0-5 bookdown_0.35
## [97] scales_1.2.1 Biobase_2.61.0
## [99] png_0.1-8 ggdendro_0.1.23
## [101] ggfun_0.1.2 knitr_1.43
## [103] reshape2_1.4.4 rjson_0.2.21
## [105] nloptr_2.0.3 nlme_3.1-163
## [107] curl_5.0.2 cachem_1.0.8
## [109] stringr_1.5.0 BiocVersion_3.18.0
## [111] parallel_4.3.1 AnnotationDbi_1.63.2
## [113] restfulr_0.0.15 desc_1.4.2
## [115] pillar_1.9.0 grid_4.3.1
## [117] vctrs_0.6.3 promises_1.2.1
## [119] ggpubr_0.6.0 car_3.1-2
## [121] dbplyr_2.3.3 xtable_1.8-4
## [123] evaluate_0.21 orthogene_1.7.0
## [125] GenomicFeatures_1.53.1 cli_3.6.1
## [127] compiler_4.3.1 Rsamtools_2.17.0
## [129] rlang_1.1.1 crayon_1.5.2
## [131] grr_0.9.5 ggsignif_0.6.4
## [133] gprofiler2_0.2.2 EWCE_1.9.2
## [135] plyr_1.8.8 fs_1.6.3
## [137] stringi_1.7.12 viridisLite_0.4.2
## [139] ewceData_1.9.0 BiocParallel_1.35.4
## [141] assertthat_0.2.1 babelgene_22.9
## [143] munsell_0.5.0 Biostrings_2.69.2
## [145] gh_1.4.0 lazyeval_0.2.2
## [147] homologene_1.4.68.19.3.27 Matrix_1.6-1
## [149] ExperimentHub_2.9.1 MungeSumstats_1.9.15
## [151] BSgenome_1.69.0 hms_1.1.3
## [153] patchwork_1.1.3 bit64_4.0.5
## [155] ggplot2_3.4.3 KEGGREST_1.41.0
## [157] statmod_1.5.0 shiny_1.7.5
## [159] SummarizedExperiment_1.31.1 interactiveDisplayBase_1.39.0
## [161] AnnotationHub_3.9.1 googleAuthR_2.0.1
## [163] gargle_1.5.2 broom_1.0.5
## [165] memoise_2.0.1 bslib_0.5.1
## [167] ggtree_3.9.1 bit_4.0.5
## [169] ape_5.7-1