Contents

1 Installation

MungeSumstats is now available via ghcr.io as a containerised environment with Rstudio and all necessary dependencies pre-installed.

1.1 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/MungeSumstats

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 8900:8787 \
  ghcr.io/neurogenomics/MungeSumstats

1.1.1 NOTES

  • Make sure to replace <your_password> above with whatever you want your password to be.
  • Change the paths supplied to the -v flags for your particular use case.
  • The -d ensures 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.

1.2 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/MungeSumstats

For troubleshooting, see the Singularity documentation.

2 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.

3 Session Info

utils::sessionInfo()
## R version 4.5.1 (2025-06-13)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [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: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] MungeSumstats_1.17.2 BiocStyle_2.37.0    
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.2.1                           
##  [2] dplyr_1.1.4                                
##  [3] blob_1.2.4                                 
##  [4] R.utils_2.13.0                             
##  [5] Biostrings_2.77.2                          
##  [6] bitops_1.0-9                               
##  [7] fastmap_1.2.0                              
##  [8] RCurl_1.98-1.17                            
##  [9] VariantAnnotation_1.55.1                   
## [10] GenomicAlignments_1.45.1                   
## [11] XML_3.99-0.18                              
## [12] digest_0.6.37                              
## [13] lifecycle_1.0.4                            
## [14] KEGGREST_1.49.1                            
## [15] RSQLite_2.4.1                              
## [16] magrittr_2.0.3                             
## [17] compiler_4.5.1                             
## [18] rlang_1.1.6                                
## [19] sass_0.4.10                                
## [20] tools_4.5.1                                
## [21] yaml_2.3.10                                
## [22] data.table_1.17.8                          
## [23] rtracklayer_1.69.1                         
## [24] knitr_1.50                                 
## [25] S4Arrays_1.9.1                             
## [26] bit_4.6.0                                  
## [27] curl_6.4.0                                 
## [28] DelayedArray_0.35.2                        
## [29] ieugwasr_1.0.4                             
## [30] abind_1.4-8                                
## [31] BiocParallel_1.43.4                        
## [32] BiocGenerics_0.55.0                        
## [33] R.oo_1.27.1                                
## [34] grid_4.5.1                                 
## [35] stats4_4.5.1                               
## [36] SummarizedExperiment_1.39.1                
## [37] cli_3.6.5                                  
## [38] rmarkdown_2.29                             
## [39] crayon_1.5.3                               
## [40] generics_0.1.4                             
## [41] BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1
## [42] httr_1.4.7                                 
## [43] rjson_0.2.23                               
## [44] DBI_1.2.3                                  
## [45] cachem_1.1.0                               
## [46] stringr_1.5.1                              
## [47] parallel_4.5.1                             
## [48] AnnotationDbi_1.71.0                       
## [49] BiocManager_1.30.26                        
## [50] XVector_0.49.0                             
## [51] restfulr_0.0.16                            
## [52] matrixStats_1.5.0                          
## [53] vctrs_0.6.5                                
## [54] Matrix_1.7-3                               
## [55] jsonlite_2.0.0                             
## [56] bookdown_0.43                              
## [57] IRanges_2.43.0                             
## [58] S4Vectors_0.47.0                           
## [59] bit64_4.6.0-1                              
## [60] GenomicFiles_1.45.0                        
## [61] GenomicFeatures_1.61.4                     
## [62] jquerylib_0.1.4                            
## [63] glue_1.8.0                                 
## [64] codetools_0.2-20                           
## [65] stringi_1.8.7                              
## [66] GenomeInfoDb_1.45.7                        
## [67] BiocIO_1.19.0                              
## [68] GenomicRanges_1.61.1                       
## [69] UCSC.utils_1.5.0                           
## [70] tibble_3.3.0                               
## [71] pillar_1.11.0                              
## [72] SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24   
## [73] htmltools_0.5.8.1                          
## [74] Seqinfo_0.99.1                             
## [75] BSgenome_1.77.1                            
## [76] R6_2.6.1                                   
## [77] evaluate_1.0.4                             
## [78] lattice_0.22-7                             
## [79] Biobase_2.69.0                             
## [80] R.methodsS3_1.8.2                          
## [81] png_0.1-8                                  
## [82] Rsamtools_2.25.1                           
## [83] memoise_2.0.1                              
## [84] bslib_0.9.0                                
## [85] SparseArray_1.9.0                          
## [86] xfun_0.52                                  
## [87] MatrixGenerics_1.21.0                      
## [88] pkgconfig_2.0.3