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 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.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: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] MungeSumstats_1.12.0 BiocStyle_2.32.0    
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.2.1            dplyr_1.1.4                
##  [3] blob_1.2.4                  R.utils_2.12.3             
##  [5] Biostrings_2.72.0           bitops_1.0-7               
##  [7] fastmap_1.1.1               RCurl_1.98-1.14            
##  [9] VariantAnnotation_1.50.0    GenomicAlignments_1.40.0   
## [11] XML_3.99-0.16.1             digest_0.6.35              
## [13] lifecycle_1.0.4             KEGGREST_1.44.0            
## [15] RSQLite_2.3.6               magrittr_2.0.3             
## [17] googleAuthR_2.0.1           compiler_4.4.0             
## [19] rlang_1.1.3                 sass_0.4.9                 
## [21] tools_4.4.0                 utf8_1.2.4                 
## [23] yaml_2.3.8                  data.table_1.15.4          
## [25] rtracklayer_1.64.0          knitr_1.46                 
## [27] S4Arrays_1.4.0              bit_4.0.5                  
## [29] curl_5.2.1                  DelayedArray_0.30.0        
## [31] abind_1.4-5                 BiocParallel_1.38.0        
## [33] BiocGenerics_0.50.0         R.oo_1.26.0                
## [35] grid_4.4.0                  stats4_4.4.0               
## [37] fansi_1.0.6                 SummarizedExperiment_1.34.0
## [39] cli_3.6.2                   rmarkdown_2.26             
## [41] crayon_1.5.2                generics_0.1.3             
## [43] httr_1.4.7                  rjson_0.2.21               
## [45] DBI_1.2.2                   cachem_1.0.8               
## [47] stringr_1.5.1               zlibbioc_1.50.0            
## [49] assertthat_0.2.1            parallel_4.4.0             
## [51] AnnotationDbi_1.66.0        BiocManager_1.30.22        
## [53] XVector_0.44.0              restfulr_0.0.15            
## [55] matrixStats_1.3.0           vctrs_0.6.5                
## [57] Matrix_1.7-0                jsonlite_1.8.8             
## [59] bookdown_0.39               IRanges_2.38.0             
## [61] S4Vectors_0.42.0            bit64_4.0.5                
## [63] GenomicFeatures_1.56.0      jquerylib_0.1.4            
## [65] glue_1.7.0                  codetools_0.2-20           
## [67] stringi_1.8.3               GenomeInfoDb_1.40.0        
## [69] BiocIO_1.14.0               GenomicRanges_1.56.0       
## [71] UCSC.utils_1.0.0            tibble_3.2.1               
## [73] pillar_1.9.0                htmltools_0.5.8.1          
## [75] GenomeInfoDbData_1.2.12     BSgenome_1.72.0            
## [77] R6_2.5.1                    evaluate_0.23              
## [79] lattice_0.22-6              Biobase_2.64.0             
## [81] R.methodsS3_1.8.2           png_0.1-8                  
## [83] Rsamtools_2.20.0            gargle_1.5.2               
## [85] memoise_2.0.1               bslib_0.7.0                
## [87] SparseArray_1.4.0           xfun_0.43                  
## [89] fs_1.6.4                    MatrixGenerics_1.16.0      
## [91] pkgconfig_2.0.3