Docker/Singularity Containers

DockerHub

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

Installation

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

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.

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

Usage

Finally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8787/

Session Info

utils::sessionInfo()

## R Under development (unstable) (2022-12-07 r83413)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
## 
## 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: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] MungeSumstats_1.7.10 BiocStyle_2.27.0    
## 
## loaded via a namespace (and not attached):
##   [1] tidyselect_1.2.0            dplyr_1.0.10               
##   [3] blob_1.2.3                  filelock_1.0.2             
##   [5] R.utils_2.12.2              Biostrings_2.67.0          
##   [7] bitops_1.0-7                fastmap_1.1.0              
##   [9] RCurl_1.98-1.9              BiocFileCache_2.7.1        
##  [11] VariantAnnotation_1.45.0    GenomicAlignments_1.35.0   
##  [13] XML_3.99-0.13               digest_0.6.31              
##  [15] lifecycle_1.0.3             ellipsis_0.3.2             
##  [17] KEGGREST_1.39.0             RSQLite_2.2.19             
##  [19] googleAuthR_2.0.0           magrittr_2.0.3             
##  [21] compiler_4.3.0              rlang_1.0.6                
##  [23] sass_0.4.4                  progress_1.2.2             
##  [25] tools_4.3.0                 utf8_1.2.2                 
##  [27] yaml_2.3.6                  data.table_1.14.6          
##  [29] rtracklayer_1.59.0          knitr_1.41                 
##  [31] prettyunits_1.1.1           curl_4.3.3                 
##  [33] bit_4.0.5                   DelayedArray_0.25.0        
##  [35] xml2_1.3.3                  BiocParallel_1.33.6        
##  [37] purrr_0.3.5                 BiocGenerics_0.45.0        
##  [39] desc_1.4.2                  R.oo_1.25.0                
##  [41] grid_4.3.0                  stats4_4.3.0               
##  [43] fansi_1.0.3                 biomaRt_2.55.0             
##  [45] SummarizedExperiment_1.29.1 cli_3.4.1                  
##  [47] rmarkdown_2.18              crayon_1.5.2               
##  [49] generics_0.1.3              ragg_1.2.4                 
##  [51] httr_1.4.4                  rjson_0.2.21               
##  [53] DBI_1.1.3                   cachem_1.0.6               
##  [55] stringr_1.5.0               zlibbioc_1.45.0            
##  [57] assertthat_0.2.1            parallel_4.3.0             
##  [59] AnnotationDbi_1.61.0        BiocManager_1.30.19        
##  [61] XVector_0.39.0              restfulr_0.0.15            
##  [63] matrixStats_0.63.0          vctrs_0.5.1                
##  [65] Matrix_1.5-3                jsonlite_1.8.4             
##  [67] bookdown_0.30               IRanges_2.33.0             
##  [69] hms_1.1.2                   S4Vectors_0.37.3           
##  [71] bit64_4.0.5                 systemfonts_1.0.4          
##  [73] GenomicFeatures_1.51.2      jquerylib_0.1.4            
##  [75] glue_1.6.2                  pkgdown_2.0.6.9000         
##  [77] codetools_0.2-18            stringi_1.7.8              
##  [79] GenomeInfoDb_1.35.5         BiocIO_1.9.1               
##  [81] GenomicRanges_1.51.3        tibble_3.1.8               
##  [83] pillar_1.8.1                rappdirs_0.3.3             
##  [85] htmltools_0.5.4             GenomeInfoDbData_1.2.9     
##  [87] BSgenome_1.67.1             dbplyr_2.2.1               
##  [89] R6_2.5.1                    textshaping_0.3.6          
##  [91] rprojroot_2.0.3             evaluate_0.18              
##  [93] Biobase_2.59.0              lattice_0.20-45            
##  [95] R.methodsS3_1.8.2           png_0.1-8                  
##  [97] Rsamtools_2.15.0            gargle_1.2.1               
##  [99] memoise_2.0.1               bslib_0.4.1                
## [101] Rcpp_1.0.9                  xfun_0.35                  
## [103] fs_1.5.2                    MatrixGenerics_1.11.0      
## [105] pkgconfig_2.0.3

¶ Authors: Alan Murphy, Brian Schilder, Nathan Skene ¶