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 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## 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       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] MungeSumstats_1.5.14 BiocStyle_2.25.0    
## 
## loaded via a namespace (and not attached):
##   [1] fs_1.5.2                                   
##   [2] bitops_1.0-7                               
##   [3] matrixStats_0.62.0                         
##   [4] bit64_4.0.5                                
##   [5] filelock_1.0.2                             
##   [6] progress_1.2.2                             
##   [7] httr_1.4.4                                 
##   [8] GenomeInfoDb_1.33.7                        
##   [9] googleAuthR_2.0.0                          
##  [10] GenomicFiles_1.33.1                        
##  [11] tools_4.2.1                                
##  [12] bslib_0.4.0                                
##  [13] utf8_1.2.2                                 
##  [14] R6_2.5.1                                   
##  [15] DBI_1.1.3                                  
##  [16] BiocGenerics_0.43.4                        
##  [17] tidyselect_1.1.2                           
##  [18] prettyunits_1.1.1                          
##  [19] bit_4.0.4                                  
##  [20] curl_4.3.2                                 
##  [21] compiler_4.2.1                             
##  [22] cli_3.4.0                                  
##  [23] Biobase_2.57.1                             
##  [24] xml2_1.3.3                                 
##  [25] DelayedArray_0.23.2                        
##  [26] rtracklayer_1.57.0                         
##  [27] bookdown_0.29                              
##  [28] sass_0.4.2                                 
##  [29] rappdirs_0.3.3                             
##  [30] stringr_1.4.1                              
##  [31] digest_0.6.29                              
##  [32] Rsamtools_2.13.4                           
##  [33] rmarkdown_2.16                             
##  [34] R.utils_2.12.0                             
##  [35] XVector_0.37.1                             
##  [36] BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1
##  [37] pkgconfig_2.0.3                            
##  [38] htmltools_0.5.3                            
##  [39] MatrixGenerics_1.9.1                       
##  [40] highr_0.9                                  
##  [41] dbplyr_2.2.1                               
##  [42] fastmap_1.1.0                              
##  [43] BSgenome_1.65.2                            
##  [44] rlang_1.0.5                                
##  [45] RSQLite_2.2.17                             
##  [46] jquerylib_0.1.4                            
##  [47] BiocIO_1.7.1                               
##  [48] generics_0.1.3                             
##  [49] jsonlite_1.8.0                             
##  [50] BiocParallel_1.31.12                       
##  [51] dplyr_1.0.10                               
##  [52] R.oo_1.25.0                                
##  [53] VariantAnnotation_1.43.3                   
##  [54] RCurl_1.98-1.8                             
##  [55] magrittr_2.0.3                             
##  [56] GenomeInfoDbData_1.2.8                     
##  [57] Matrix_1.5-1                               
##  [58] Rcpp_1.0.9                                 
##  [59] S4Vectors_0.35.4                           
##  [60] fansi_1.0.3                                
##  [61] lifecycle_1.0.2                            
##  [62] R.methodsS3_1.8.2                          
##  [63] stringi_1.7.8                              
##  [64] yaml_2.3.5                                 
##  [65] SummarizedExperiment_1.27.3                
##  [66] zlibbioc_1.43.0                            
##  [67] BiocFileCache_2.5.0                        
##  [68] grid_4.2.1                                 
##  [69] blob_1.2.3                                 
##  [70] parallel_4.2.1                             
##  [71] crayon_1.5.1                               
##  [72] lattice_0.20-45                            
##  [73] Biostrings_2.65.6                          
##  [74] GenomicFeatures_1.49.7                     
##  [75] hms_1.1.2                                  
##  [76] KEGGREST_1.37.3                            
##  [77] knitr_1.40                                 
##  [78] pillar_1.8.1                               
##  [79] GenomicRanges_1.49.1                       
##  [80] rjson_0.2.21                               
##  [81] SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.22   
##  [82] codetools_0.2-18                           
##  [83] biomaRt_2.53.2                             
##  [84] stats4_4.2.1                               
##  [85] XML_3.99-0.10                              
##  [86] glue_1.6.2                                 
##  [87] evaluate_0.16                              
##  [88] data.table_1.14.2                          
##  [89] BiocManager_1.30.18                        
##  [90] png_0.1-7                                  
##  [91] vctrs_0.4.1                                
##  [92] purrr_0.3.4                                
##  [93] assertthat_0.2.1                           
##  [94] cachem_1.0.6                               
##  [95] xfun_0.33                                  
##  [96] restfulr_0.0.15                            
##  [97] gargle_1.2.1                               
##  [98] tibble_3.1.8                               
##  [99] GenomicAlignments_1.33.1                   
## [100] AnnotationDbi_1.59.1                       
## [101] memoise_2.0.1                              
## [102] IRanges_2.31.2                             
## [103] ellipsis_0.3.2