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] MungeSumstats_1.9.17 BiocStyle_2.29.1    
## 
## loaded via a namespace (and not attached):
##   [1] tidyselect_1.2.0                           
##   [2] dplyr_1.1.2                                
##   [3] blob_1.2.4                                 
##   [4] filelock_1.0.2                             
##   [5] R.utils_2.12.2                             
##   [6] Biostrings_2.69.2                          
##   [7] bitops_1.0-7                               
##   [8] fastmap_1.1.1                              
##   [9] RCurl_1.98-1.12                            
##  [10] BiocFileCache_2.9.1                        
##  [11] VariantAnnotation_1.47.1                   
##  [12] GenomicAlignments_1.37.0                   
##  [13] XML_3.99-0.14                              
##  [14] digest_0.6.33                              
##  [15] lifecycle_1.0.3                            
##  [16] KEGGREST_1.41.0                            
##  [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_1.2.3                                 
##  [26] yaml_2.3.7                                 
##  [27] data.table_1.14.8                          
##  [28] rtracklayer_1.61.1                         
##  [29] knitr_1.43                                 
##  [30] prettyunits_1.1.1                          
##  [31] S4Arrays_1.1.5                             
##  [32] curl_5.0.2                                 
##  [33] bit_4.0.5                                  
##  [34] DelayedArray_0.27.10                       
##  [35] xml2_1.3.5                                 
##  [36] abind_1.4-5                                
##  [37] BiocParallel_1.35.4                        
##  [38] BiocGenerics_0.47.0                        
##  [39] R.oo_1.25.0                                
##  [40] grid_4.3.1                                 
##  [41] stats4_4.3.1                               
##  [42] fansi_1.0.4                                
##  [43] biomaRt_2.57.1                             
##  [44] SummarizedExperiment_1.31.1                
##  [45] cli_3.6.1                                  
##  [46] rmarkdown_2.24                             
##  [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_1.47.0                            
##  [56] assertthat_0.2.1                           
##  [57] parallel_4.3.1                             
##  [58] AnnotationDbi_1.63.2                       
##  [59] BiocManager_1.30.22                        
##  [60] XVector_0.41.1                             
##  [61] restfulr_0.0.15                            
##  [62] matrixStats_1.0.0                          
##  [63] vctrs_0.6.3                                
##  [64] Matrix_1.6-1                               
##  [65] jsonlite_1.8.7                             
##  [66] bookdown_0.35                              
##  [67] IRanges_2.35.2                             
##  [68] hms_1.1.3                                  
##  [69] S4Vectors_0.39.1                           
##  [70] bit64_4.0.5                                
##  [71] GenomicFiles_1.37.0                        
##  [72] GenomicFeatures_1.53.1                     
##  [73] jquerylib_0.1.4                            
##  [74] glue_1.6.2                                 
##  [75] codetools_0.2-19                           
##  [76] stringi_1.7.12                             
##  [77] GenomeInfoDb_1.37.2                        
##  [78] BiocIO_1.11.0                              
##  [79] GenomicRanges_1.53.1                       
##  [80] tibble_3.2.1                               
##  [81] pillar_1.9.0                               
##  [82] SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24   
##  [83] rappdirs_0.3.3                             
##  [84] htmltools_0.5.6                            
##  [85] GenomeInfoDbData_1.2.10                    
##  [86] BSgenome_1.69.0                            
##  [87] R6_2.5.1                                   
##  [88] dbplyr_2.3.3                               
##  [89] evaluate_0.21                              
##  [90] lattice_0.21-8                             
##  [91] Biobase_2.61.0                             
##  [92] R.methodsS3_1.8.2                          
##  [93] png_0.1-8                                  
##  [94] Rsamtools_2.17.0                           
##  [95] gargle_1.5.2                               
##  [96] memoise_2.0.1                              
##  [97] bslib_0.5.1                                
##  [98] SparseArray_1.1.11                         
##  [99] xfun_0.40                                  
## [100] fs_1.6.3                                   
## [101] MatrixGenerics_1.13.1                      
## [102] pkgconfig_2.0.3