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Updated: Nov-04-2024

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 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 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;  LAPACK version 3.10.0
## 
## 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_0.99.7
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3                   bitops_1.0-9               
##   [3] gridExtra_2.3               rlang_1.1.4                
##   [5] magrittr_2.0.3              matrixStats_1.4.1          
##   [7] compiler_4.4.1              RSQLite_2.3.7              
##   [9] systemfonts_1.1.0           vctrs_0.6.5                
##  [11] pkgconfig_2.0.3             crayon_1.5.3               
##  [13] fastmap_1.2.0               dbplyr_2.5.0               
##  [15] XVector_0.46.0              memes_1.14.0               
##  [17] ca_0.71.1                   utf8_1.2.4                 
##  [19] Rsamtools_2.22.0            rmarkdown_2.28             
##  [21] tzdb_0.4.0                  UCSC.utils_1.2.0           
##  [23] ragg_1.3.2                  purrr_1.0.2                
##  [25] bit_4.5.0                   xfun_0.49                  
##  [27] ggseqlogo_0.2               zlibbioc_1.52.0            
##  [29] cachem_1.1.0                GenomeInfoDb_1.42.0        
##  [31] jsonlite_1.8.9              blob_1.2.4                 
##  [33] DelayedArray_0.32.0         BiocParallel_1.40.0        
##  [35] parallel_4.4.1              R6_2.5.1                   
##  [37] bslib_0.8.0                 RColorBrewer_1.1-3         
##  [39] rtracklayer_1.66.0          GenomicRanges_1.58.0       
##  [41] jquerylib_0.1.4             Rcpp_1.0.13-1              
##  [43] assertthat_0.2.1            SummarizedExperiment_1.36.0
##  [45] iterators_1.0.14            knitr_1.48                 
##  [47] readr_2.1.5                 IRanges_2.40.0             
##  [49] Matrix_1.7-0                tidyselect_1.2.1           
##  [51] abind_1.4-8                 yaml_2.3.10                
##  [53] viridis_0.6.5               TSP_1.2-4                  
##  [55] codetools_0.2-20            curl_5.2.3                 
##  [57] lattice_0.22-6              tibble_3.2.1               
##  [59] Biobase_2.66.0              evaluate_1.0.1             
##  [61] desc_1.4.3                  heatmaply_1.5.0            
##  [63] BiocFileCache_2.14.0        universalmotif_1.24.0      
##  [65] Biostrings_2.74.0           pillar_1.9.0               
##  [67] filelock_1.0.3              MatrixGenerics_1.18.0      
##  [69] DT_0.33                     foreach_1.5.2              
##  [71] stats4_4.4.1                plotly_4.10.4              
##  [73] generics_0.1.3              RCurl_1.98-1.16            
##  [75] hms_1.1.3                   S4Vectors_0.44.0           
##  [77] ggplot2_3.5.1               munsell_0.5.1              
##  [79] scales_1.3.0                glue_1.8.0                 
##  [81] lazyeval_0.2.2              tools_4.4.1                
##  [83] dendextend_1.18.1           BiocIO_1.16.0              
##  [85] data.table_1.16.2           BSgenome_1.74.0            
##  [87] webshot_0.5.5               GenomicAlignments_1.42.0   
##  [89] registry_0.5-1              fs_1.6.5                   
##  [91] XML_3.99-0.17               grid_4.4.1                 
##  [93] tidyr_1.3.1                 seriation_1.5.6            
##  [95] colorspace_2.1-1            GenomeInfoDbData_1.2.13    
##  [97] restfulr_0.0.15             cli_3.6.3                  
##  [99] textshaping_0.4.0           fansi_1.0.6                
## [101] S4Arrays_1.6.0              viridisLite_0.4.2          
## [103] dplyr_1.1.4                 gtable_0.3.6               
## [105] sass_0.4.9                  digest_0.6.37              
## [107] BiocGenerics_0.52.0         SparseArray_1.6.0          
## [109] rjson_0.2.23                htmlwidgets_1.6.4          
## [111] memoise_2.0.1               htmltools_0.5.8.1          
## [113] pkgdown_2.1.1               lifecycle_1.0.4            
## [115] httr_1.4.7                  MASS_7.3-61                
## [117] bit64_4.5.2