GCPtools

GCPtools

GCPtools is a package that provides an interface to Google Cloud Platform (GCP) tools, primarily the gcloud and gsutil utilities. It allows users to interact with GCP services such as Google Cloud Storage (GCS) and Google Compute Engine (GCE) directly from R.

Installation and Load

You can install the latest version of GCPtools from GitHub using the following:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Bioconductor/GCPtools")

After installation, you can load the package using:

library(GCPtools)

gcloud Command Line Utility

Check for gcloud SDK

The gcloud_exists() function is used to check if the gcloud command line utility is available on your system.

gcloud_exists()
#> [1] FALSE

gcloud Help

The package provides a function to display the help for the gcloud command line utility. This can be useful to understand the available commands and options. They can be used in conjunction with gcloud_cmd() to run specific commands.

gcloud_help() |>
    head(10L)

Access Token

The package provides functions to interact with GCP services. For example, you can use gcloud_access_token() to obtain an access token for a specific service. This is currently in use by AnVIL and AnVILGCP R packages.

gcloud_access_token("terra")

Command Execution

You can execute gcloud commands using the gcloud_cmd() function. This function allows you to run any gcloud command directly from R, making it easy to interact with GCP services without leaving the R environment.

gcloud_cmd("version")

List of available functions

The package provides a variety of functions to interact with GCP services.

  • gcloud_exists(): tests whether the gcloud() command can be found.
  • gcloud_account(): report the current gcloud account via ⁠gcloud config get-value account⁠.
  • gcloud_project(): report the current gcloud project via ⁠gcloud config get-value project⁠.
  • gcloud_help(): queries gcloud for help for a command or sub-comand via ⁠gcloud help ....
  • gcloud_cmd(): gcloud command execution via ⁠gcloud .... Use pre-defined functions in preference to this.
  • gcloud_storage(): ⁠gcloud storage⁠ command execution via ⁠gcloud storage ...⁠. Typically used for bucket management commands such as rm and cp.
  • gcloud_storage_buckets(): interface to the ⁠gcloud storage buckets⁠ command. It can create a new bucket via ⁠gcloud storage buckets create ...⁠.

gsutil Command Line Utility

Check for gsutil resources

The gsutil_exists() function checks if a bucket or object exists in Google Cloud Storage (GCS).

gsutil_exists("gs://your-bucket-name")

gsutil Help

The gsutil_help() function displays the help for the gsutil command line utility. This can be useful to understand the available commands and options and how to use them effectively.

gsutil_help()

The package also includes functions to manage Google Cloud Storage buckets and objects, such as gsutil_ls() to list objects in a bucket and gsutil_cp() to copy files to and from GCS.

List of available functions

The package provides a variety of functions to interact with GCS.

  • gsutil_requesterpays(): does the Google bucket require that the requester pay for access?
  • gsutil_requesterpays_flag(): return the -u <gcloud_project> flag if the bucket requires that the requester pay for access.
  • gsutil_exists(): check if the bucket or object exists.
  • gsutil_stat(): print, as a side effect, the status of a bucket, directory, or file.
  • gsutil_rsync(): synchronize a source and a destination.
  • gsutil_cat(): concatenate bucket objects to standard output
  • gsutil_help(): print ‘man’ page for the gsutil command or subcommand.
  • gsutil_pipe(): create a pipe to read from or write to a Google bucket object.

Disclaimer

This package is not an official Google product, nor is it affiliated with or endorsed by Google LLC. It is developed and maintained by the AnVIL team to provide a convenient interface to GCP tools for R users on the AnVIL platform.

Only the above set of gcloud and gsutil commands are supported.

SessionInfo

sessionInfo()
#> R version 4.5.1 (2025-06-13)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.3 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=C              
#>  [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: Etc/UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] GCPtools_1.1.0   BiocStyle_2.37.1
#> 
#> loaded via a namespace (and not attached):
#>  [1] vctrs_0.6.5          httr_1.4.7           cli_3.6.5           
#>  [4] knitr_1.50           rlang_1.1.6          xfun_0.54           
#>  [7] purrr_1.1.0          generics_0.1.4       jsonlite_2.0.0      
#> [10] glue_1.8.0           buildtools_1.0.0     htmltools_0.5.8.1   
#> [13] maketools_1.3.2      BiocBaseUtils_1.11.2 sys_3.4.3           
#> [16] sass_0.4.10          rappdirs_0.3.3       rmarkdown_2.30      
#> [19] tibble_3.3.0         evaluate_1.0.5       jquerylib_0.1.4     
#> [22] fastmap_1.2.0        yaml_2.3.10          lifecycle_1.0.4     
#> [25] httr2_1.2.1          BiocManager_1.30.26  compiler_4.5.1      
#> [28] dplyr_1.1.4          pkgconfig_2.0.3      tidyr_1.3.1         
#> [31] digest_0.6.37        R6_2.6.1             tidyselect_1.2.1    
#> [34] pillar_1.11.1        magrittr_2.0.4       bslib_0.9.0         
#> [37] tools_4.5.1          AnVILBase_1.3.1      cachem_1.1.0