Updated: Aug-10-2024
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:
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/motifpeekerNOTES
- Make sure to replace
<your_password>above with whatever you want your password to be.
- Change the paths supplied to the
-vflags for your particular use case. - The
-densures 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.
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_0.99.4
##
## loaded via a namespace (and not attached):
## [1] DBI_1.2.3 bitops_1.0-8
## [3] gridExtra_2.3 rlang_1.1.4
## [5] magrittr_2.0.3 matrixStats_1.3.0
## [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_0.45.0 memes_1.13.0
## [17] ca_0.71.1 utf8_1.2.4
## [19] Rsamtools_2.21.0 rmarkdown_2.27
## [21] tzdb_0.4.0 UCSC.utils_1.1.0
## [23] ragg_1.3.2 purrr_1.0.2
## [25] bit_4.0.5 xfun_0.46
## [27] ggseqlogo_0.2 zlibbioc_1.51.1
## [29] cachem_1.1.0 GenomeInfoDb_1.41.1
## [31] jsonlite_1.8.8 blob_1.2.4
## [33] DelayedArray_0.31.11 BiocParallel_1.39.0
## [35] parallel_4.4.1 R6_2.5.1
## [37] bslib_0.8.0 RColorBrewer_1.1-3
## [39] rtracklayer_1.65.0 GenomicRanges_1.57.1
## [41] jquerylib_0.1.4 Rcpp_1.0.13
## [43] assertthat_0.2.1 SummarizedExperiment_1.35.1
## [45] iterators_1.0.14 knitr_1.48
## [47] readr_2.1.5 IRanges_2.39.2
## [49] Matrix_1.7-0 tidyselect_1.2.1
## [51] abind_1.4-5 yaml_2.3.10
## [53] viridis_0.6.5 TSP_1.2-4
## [55] codetools_0.2-20 curl_5.2.1
## [57] lattice_0.22-6 tibble_3.2.1
## [59] Biobase_2.65.0 evaluate_0.24.0
## [61] desc_1.4.3 heatmaply_1.5.0
## [63] BiocFileCache_2.13.0 universalmotif_1.23.0
## [65] Biostrings_2.73.1 pillar_1.9.0
## [67] filelock_1.0.3 MatrixGenerics_1.17.0
## [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_0.43.2
## [77] ggplot2_3.5.1 munsell_0.5.1
## [79] scales_1.3.0 glue_1.7.0
## [81] lazyeval_0.2.2 tools_4.4.1
## [83] dendextend_1.17.1 BiocIO_1.15.0
## [85] data.table_1.15.4 BSgenome_1.73.0
## [87] webshot_0.5.5 GenomicAlignments_1.41.0
## [89] registry_0.5-1 fs_1.6.4
## [91] XML_3.99-0.17 grid_4.4.1
## [93] tidyr_1.3.1 seriation_1.5.5
## [95] colorspace_2.1-1 GenomeInfoDbData_1.2.12
## [97] restfulr_0.0.15 cli_3.6.3
## [99] textshaping_0.4.0 fansi_1.0.6
## [101] S4Arrays_1.5.7 viridisLite_0.4.2
## [103] dplyr_1.1.4 gtable_0.3.5
## [105] sass_0.4.9 digest_0.6.36
## [107] BiocGenerics_0.51.0 SparseArray_1.5.31
## [109] rjson_0.2.21 htmlwidgets_1.6.4
## [111] memoise_2.0.1 htmltools_0.5.8.1
## [113] pkgdown_2.1.0 lifecycle_1.0.4
## [115] httr_1.4.7 MASS_7.3-61
## [117] bit64_4.0.5