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Updated: May-29-2025

Installation

MotifPeeker is now available via ghcr.io as a containerised environment with Rstudio and all necessary dependencies pre-installed.

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/motifpeeker

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/motifpeeker

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://ghcr.io/neurogenomics/motifpeeker

For troubleshooting, see the Singularity documentation.

Usage

Finally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8900/

Session Info

utils::sessionInfo()
## R version 4.5.0 (2025-04-11)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 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-r0.3.26.so;  LAPACK version 3.12.0
## 
## 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: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] MotifPeeker_1.1.1
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3                   bitops_1.0-9               
##   [3] gridExtra_2.3               httr2_1.1.2                
##   [5] rlang_1.1.6                 magrittr_2.0.3             
##   [7] matrixStats_1.5.0           compiler_4.5.0             
##   [9] RSQLite_2.3.11              systemfonts_1.2.3          
##  [11] vctrs_0.6.5                 pkgconfig_2.0.3            
##  [13] crayon_1.5.3                fastmap_1.2.0              
##  [15] dbplyr_2.5.0                XVector_0.49.0             
##  [17] memes_1.17.0                ca_0.71.1                  
##  [19] Rsamtools_2.25.0            rmarkdown_2.29             
##  [21] tzdb_0.5.0                  UCSC.utils_1.5.0           
##  [23] ragg_1.4.0                  purrr_1.0.4                
##  [25] bit_4.6.0                   xfun_0.52                  
##  [27] ggseqlogo_0.2               cachem_1.1.0               
##  [29] GenomeInfoDb_1.45.3         jsonlite_2.0.0             
##  [31] blob_1.2.4                  DelayedArray_0.35.1        
##  [33] BiocParallel_1.43.2         parallel_4.5.0             
##  [35] R6_2.6.1                    bslib_0.9.0                
##  [37] RColorBrewer_1.1-3          rtracklayer_1.69.0         
##  [39] GenomicRanges_1.61.0        jquerylib_0.1.4            
##  [41] Rcpp_1.0.14                 assertthat_0.2.1           
##  [43] SummarizedExperiment_1.39.0 iterators_1.0.14           
##  [45] knitr_1.50                  readr_2.1.5                
##  [47] IRanges_2.43.0              Matrix_1.7-3               
##  [49] tidyselect_1.2.1            abind_1.4-8                
##  [51] yaml_2.3.10                 viridis_0.6.5              
##  [53] TSP_1.2-5                   codetools_0.2-20           
##  [55] curl_6.2.3                  lattice_0.22-7             
##  [57] tibble_3.2.1                Biobase_2.69.0             
##  [59] evaluate_1.0.3              desc_1.4.3                 
##  [61] heatmaply_1.5.0             BiocFileCache_2.99.5       
##  [63] universalmotif_1.27.2       Biostrings_2.77.1          
##  [65] pillar_1.10.2               filelock_1.0.3             
##  [67] MatrixGenerics_1.21.0       DT_0.33                    
##  [69] foreach_1.5.2               stats4_4.5.0               
##  [71] plotly_4.10.4               generics_0.1.4             
##  [73] RCurl_1.98-1.17             S4Vectors_0.47.0           
##  [75] hms_1.1.3                   ggplot2_3.5.2              
##  [77] scales_1.4.0                glue_1.8.0                 
##  [79] lazyeval_0.2.2              tools_4.5.0                
##  [81] dendextend_1.19.0           BiocIO_1.19.0              
##  [83] data.table_1.17.4           BSgenome_1.77.0            
##  [85] webshot_0.5.5               GenomicAlignments_1.45.0   
##  [87] registry_0.5-1              fs_1.6.6                   
##  [89] XML_3.99-0.18               grid_4.5.0                 
##  [91] tidyr_1.3.1                 seriation_1.5.7            
##  [93] restfulr_0.0.15             cli_3.6.5                  
##  [95] rappdirs_0.3.3              textshaping_1.0.1          
##  [97] S4Arrays_1.9.0              viridisLite_0.4.2          
##  [99] dplyr_1.1.4                 gtable_0.3.6               
## [101] sass_0.4.10                 digest_0.6.37              
## [103] BiocGenerics_0.55.0         SparseArray_1.9.0          
## [105] rjson_0.2.23                htmlwidgets_1.6.4          
## [107] farver_2.1.2                memoise_2.0.1              
## [109] htmltools_0.5.8.1           pkgdown_2.1.3              
## [111] lifecycle_1.0.4             httr_1.4.7                 
## [113] MASS_7.3-65                 bit64_4.6.0-1