Contents

1 DockerHub

mungesumstats is now available via DockerHub as a containerised environment with Rstudio and all necessary dependencies pre-installed.

1.1 Installation

1.2 Method 1: via Docker

First, install Docker if you have not already.

Create an image of the Docker container in command line:

docker pull neurogenomicslab/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 8787:8787 \
  neurogenomicslab/mungesumstats

1.2.1 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.

1.3 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://neurogenomicslab/mungesumstats

1.4 Usage

Finally, 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.

2 Session Info

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:   /home/biocbuild/bbs-3.18-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_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] XVector_0.42.0       GenomicRanges_1.54.0 S4Vectors_0.40.1    
## [4] IRanges_2.36.0       MungeSumstats_1.10.1 BiocStyle_2.30.0    
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.2.0                           
##  [2] dplyr_1.1.3                                
##  [3] blob_1.2.4                                 
##  [4] filelock_1.0.2                             
##  [5] R.utils_2.12.2                             
##  [6] Biostrings_2.70.1                          
##  [7] bitops_1.0-7                               
##  [8] fastmap_1.1.1                              
##  [9] RCurl_1.98-1.12                            
## [10] BiocFileCache_2.10.1                       
## [11] VariantAnnotation_1.48.0                   
## [12] GenomicAlignments_1.38.0                   
## [13] XML_3.99-0.14                              
## [14] digest_0.6.33                              
## [15] lifecycle_1.0.3                            
## [16] KEGGREST_1.42.0                            
## [17] RSQLite_2.3.1                              
## [18] googleAuthR_2.0.1                          
## [19] magrittr_2.0.3                             
## [20] compiler_4.3.1                             
## [21] rlang_1.1.1                                
## [22] sass_0.4.7                                 
## [23] progress_1.2.2                             
## [24] tools_4.3.1                                
## [25] utf8_1.2.4                                 
## [26] yaml_2.3.7                                 
## [27] data.table_1.14.8                          
## [28] rtracklayer_1.62.0                         
## [29] knitr_1.44                                 
## [30] prettyunits_1.2.0                          
## [31] S4Arrays_1.2.0                             
## [32] curl_5.1.0                                 
## [33] bit_4.0.5                                  
## [34] DelayedArray_0.28.0                        
## [35] xml2_1.3.5                                 
## [36] abind_1.4-5                                
## [37] BiocParallel_1.36.0                        
## [38] BiocGenerics_0.48.0                        
## [39] R.oo_1.25.0                                
## [40] grid_4.3.1                                 
## [41] stats4_4.3.1                               
## [42] fansi_1.0.5                                
## [43] biomaRt_2.58.0                             
## [44] SummarizedExperiment_1.32.0                
## [45] cli_3.6.1                                  
## [46] rmarkdown_2.25                             
## [47] crayon_1.5.2                               
## [48] generics_0.1.3                             
## [49] BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1
## [50] httr_1.4.7                                 
## [51] rjson_0.2.21                               
## [52] DBI_1.1.3                                  
## [53] cachem_1.0.8                               
## [54] stringr_1.5.0                              
## [55] zlibbioc_1.48.0                            
## [56] assertthat_0.2.1                           
## [57] parallel_4.3.1                             
## [58] AnnotationDbi_1.64.0                       
## [59] BiocManager_1.30.22                        
## [60] restfulr_0.0.15                            
## [61] matrixStats_1.0.0                          
## [62] vctrs_0.6.4                                
## [63] Matrix_1.6-1.1                             
## [64] jsonlite_1.8.7                             
## [65] bookdown_0.36                              
## [66] hms_1.1.3                                  
## [67] bit64_4.0.5                                
## [68] GenomicFiles_1.38.0                        
## [69] GenomicFeatures_1.54.0                     
## [70] jquerylib_0.1.4                            
## [71] glue_1.6.2                                 
## [72] codetools_0.2-19                           
## [73] stringi_1.7.12                             
## [74] GenomeInfoDb_1.38.0                        
## [75] BiocIO_1.12.0                              
## [76] tibble_3.2.1                               
## [77] pillar_1.9.0                               
## [78] SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24   
## [79] rappdirs_0.3.3                             
## [80] htmltools_0.5.6.1                          
## [81] GenomeInfoDbData_1.2.11                    
## [82] BSgenome_1.70.0                            
## [83] R6_2.5.1                                   
## [84] dbplyr_2.4.0                               
## [85] evaluate_0.22                              
## [86] lattice_0.22-5                             
## [87] Biobase_2.62.0                             
## [88] R.methodsS3_1.8.2                          
## [89] png_0.1-8                                  
## [90] Rsamtools_2.18.0                           
## [91] gargle_1.5.2                               
## [92] memoise_2.0.1                              
## [93] bslib_0.5.1                                
## [94] SparseArray_1.2.0                          
## [95] xfun_0.40                                  
## [96] fs_1.6.3                                   
## [97] MatrixGenerics_1.14.0                      
## [98] pkgconfig_2.0.3