crisprverse / docker

crisprVerse: ecosystem of R packages for CRISPR gRNA design

• Installation and getting started
• Components
• Reproducibility

Authors: Jean-Philippe Fortin, Luke Hoberecht

Date: July 25, 2022

Installation and getting started

The crisprVerse is a collection of packages for CRISPR guide RNA (gRNA) design that can easily be installed with the crisprVerse package. This provides a convenient way of downloading and installing all crisprVerse packages with a single R command.

The package can be installed from the Bioconductor devel branch using the following commands in an R session:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(version="devel")
BiocManager::install("crisprVerse")

The core crisprVerse includes the packages that are commonly used for gRNA design, and are attached when you attach the crisprVerse package:

library(crisprVerse)

## Warning: multiple methods tables found for 'aperm'

## Warning: replacing previous import 'BiocGenerics::aperm' by
## 'DelayedArray::aperm' when loading 'SummarizedExperiment'

You can check that all crisprVerse packages are up-to-date with crisprVerse_update():

crisprVerse_update()

## The following packages are out of date:
## 
## • crisprDesign (0.99.176 -> 0.99.177)
## • crisprScore  (1.1.15 -> 1.1.16)
## 
## Start a clean R session then run:
## BiocManager::install(c("crisprDesign", "crisprScore"))

The complete documentation for the package can be found here.

Components

The following packages are installed and loaded with the crisprVerse package:

• crisprBase to specify and manipulate CRISPR nucleases.
• crisprBowtie to perform gRNA spacer sequence alignment with Bowtie.
• crisprScore to annotate gRNAs with on-target and off-target scores.
• crisprDesign to design and manipulate gRNAs with GuideSet objects.
• crisprViz to visualize gRNAs.

Reproducibility

sessionInfo()

## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] crisprViz_0.99.22     crisprDesign_0.99.176 crisprScore_1.1.15   
##  [4] crisprScoreData_1.1.3 ExperimentHub_2.5.0   AnnotationHub_3.5.1  
##  [7] BiocFileCache_2.5.0   dbplyr_2.2.1          BiocGenerics_0.43.4  
## [10] crisprBowtie_1.1.1    crisprBase_1.1.8      crisprVerse_0.99.9   
## [13] BiocStyle_2.25.0     
## 
## loaded via a namespace (and not attached):
##   [1] backports_1.4.1               Hmisc_4.7-1                  
##   [3] lazyeval_0.2.2                splines_4.2.1                
##   [5] BiocParallel_1.31.12          GenomeInfoDb_1.33.7          
##   [7] ggplot2_3.3.6                 digest_0.6.29                
##   [9] ensembldb_2.21.4              htmltools_0.5.3              
##  [11] fansi_1.0.3                   checkmate_2.1.0              
##  [13] magrittr_2.0.3                memoise_2.0.1                
##  [15] BSgenome_1.65.2               cluster_2.1.4                
##  [17] tzdb_0.3.0                    Biostrings_2.65.3            
##  [19] readr_2.1.2                   matrixStats_0.62.0           
##  [21] prettyunits_1.1.1             jpeg_0.1-9                   
##  [23] colorspace_2.0-3              blob_1.2.3                   
##  [25] rappdirs_0.3.3                xfun_0.32                    
##  [27] dplyr_1.0.10                  crayon_1.5.1                 
##  [29] RCurl_1.98-1.8                jsonlite_1.8.0               
##  [31] survival_3.4-0                VariantAnnotation_1.43.3     
##  [33] glue_1.6.2                    gtable_0.3.1                 
##  [35] zlibbioc_1.43.0               XVector_0.37.1               
##  [37] DelayedArray_0.23.1           scales_1.2.1                 
##  [39] DBI_1.1.3                     Rcpp_1.0.9                   
##  [41] htmlTable_2.4.1               xtable_1.8-4                 
##  [43] progress_1.2.2                reticulate_1.26              
##  [45] foreign_0.8-82                bit_4.0.4                    
##  [47] Formula_1.2-4                 stats4_4.2.1                 
##  [49] htmlwidgets_1.5.4             httr_1.4.4                   
##  [51] dir.expiry_1.5.1              RColorBrewer_1.1-3           
##  [53] ellipsis_0.3.2                pkgconfig_2.0.3              
##  [55] XML_3.99-0.10                 nnet_7.3-17                  
##  [57] Gviz_1.41.1                   deldir_1.0-6                 
##  [59] utf8_1.2.2                    tidyselect_1.1.2             
##  [61] rlang_1.0.5                   later_1.3.0                  
##  [63] AnnotationDbi_1.59.1          munsell_0.5.0                
##  [65] BiocVersion_3.16.0            tools_4.2.1                  
##  [67] cachem_1.0.6                  cli_3.4.0                    
##  [69] generics_0.1.3                RSQLite_2.2.16               
##  [71] evaluate_0.16                 stringr_1.4.1                
##  [73] fastmap_1.1.0                 yaml_2.3.5                   
##  [75] knitr_1.40                    bit64_4.0.5                  
##  [77] purrr_0.3.4                   randomForest_4.7-1.1         
##  [79] AnnotationFilter_1.21.0       KEGGREST_1.37.3              
##  [81] Rbowtie_1.37.0                mime_0.12                    
##  [83] xml2_1.3.3                    biomaRt_2.53.2               
##  [85] compiler_4.2.1                rstudioapi_0.14              
##  [87] filelock_1.0.2                curl_4.3.2                   
##  [89] png_0.1-7                     interactiveDisplayBase_1.35.0
##  [91] tibble_3.1.8                  stringi_1.7.8                
##  [93] basilisk.utils_1.9.3          GenomicFeatures_1.49.6       
##  [95] lattice_0.20-45               ProtGenerics_1.29.0          
##  [97] Matrix_1.4-1                  vctrs_0.4.1                  
##  [99] pillar_1.8.1                  lifecycle_1.0.1              
## [101] BiocManager_1.30.18           data.table_1.14.2            
## [103] bitops_1.0-7                  httpuv_1.6.5                 
## [105] rtracklayer_1.57.0            GenomicRanges_1.49.1         
## [107] R6_2.5.1                      BiocIO_1.7.1                 
## [109] latticeExtra_0.6-30           promises_1.2.0.1             
## [111] gridExtra_2.3                 IRanges_2.31.2               
## [113] codetools_0.2-18              dichromat_2.0-0.1            
## [115] assertthat_0.2.1              SummarizedExperiment_1.27.2  
## [117] rjson_0.2.21                  GenomicAlignments_1.33.1     
## [119] Rsamtools_2.13.4              S4Vectors_0.35.3             
## [121] GenomeInfoDbData_1.2.8        parallel_4.2.1               
## [123] hms_1.1.2                     rpart_4.1.16                 
## [125] grid_4.2.1                    basilisk_1.9.6               
## [127] rmarkdown_2.16                MatrixGenerics_1.9.1         
## [129] biovizBase_1.45.0             Biobase_2.57.1               
## [131] shiny_1.7.2                   base64enc_0.1-3              
## [133] interp_1.1-3                  restfulr_0.0.15

docker's Issues

Container cant anymore be build from Dockerfile

Hi
I realized that the latest container was a bit older and I wanted to try putting the latest version of CrisprVerse in a docker.
Therefore I pulled your Dockerfile.
I realized that there was no version specified for the the CrisprVerse in the instructions and assume that it therefore pulls
the latest version. I am not sure whether it is due to this change in latest version or conda internally, but the build is not anymore successful.
It seems to fail regularly with CrispScore for an issue related with panda.

      File "/home/crisprverse/tmp/pip-install-7BjdyG/pandas/setup.py", line 362, in check_cython_extensions
        """ % src)
    Exception: Cython-generated file 'pandas/index.c' not found.
                    Cython is required to compile pandas from a development branch.
                    Please install Cython or download a release package of pandas.
    
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/crisprverse/usr/local/lib/R/site-library/crisprScore/basilisk/crisprai_basilisk/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/crisprverse/tmp/pip-install-7BjdyG/pandas/setup.py'"'"'; __file__='"'"'/home/crisprverse/tmp/pip-install-7BjdyG/pandas/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /home/crisprverse/tmp/pip-record-PrNX4I/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
Error in setupBasiliskEnv(envpath = file.path(envdir, .getEnvName(current)),  : 
  failed to install additional packages via pip
Calls: <Anonymous> -> setupBasiliskEnv
Execution halted
ERROR: configuration failed for package ‘crisprScore’
* removing ‘/home/crisprverse/usr/local/lib/R/site-library/crisprScore’
* installing *source* package ‘GenomicFeatures’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

I tried to add earlier steps installing cython but it seems that the python environment which is created in the installation process does not pick it up.

Do you have :

• the version for which the previous container build was successful ?
• an idea what changed and how could add/fix the dependencies ?

Thanks for all the work!
Cheers