Package: AnVIL 1.25.1

Marcel Ramos

AnVIL: Bioconductor on the AnVIL compute environment

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides programatic access to the Dockstore, Leonardo, Rawls, TDR, and Terra RESTful programming interfaces. For platform-specific user-level functionality, see either the AnVILGCP or AnVILAz package.

Authors:Marcel Ramos [aut, cre], Martin Morgan [aut], Kayla Interdonato [aut], Yubo Cheng [aut], Nitesh Turaga [aut], BJ Stubbs [ctb], Vincent Carey [ctb], Sehyun Oh [ctb], Sweta Gopaulakrishnan [ctb], Valerie Obenchain [ctb]

AnVIL_1.25.1.tar.gz
AnVIL_1.25.1.zip(r-4.7)AnVIL_1.25.1.zip(r-4.6)AnVIL_1.25.1.zip(r-4.5)
AnVIL_1.25.1.tgz(r-4.6-any)AnVIL_1.25.1.tgz(r-4.5-any)
AnVIL_1.25.1.tar.gz(r-4.7-any)AnVIL_1.25.1.tar.gz(r-4.6-any)
AnVIL_1.25.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AnVIL/json (API)

# Install 'AnVIL' in R:
install.packages('AnVIL', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/anvil/issues

On BioConductor:AnVIL-1.25.1(bioc 3.24)AnVIL-1.24.0(bioc 3.23)

infrastructureu24hg010263

10.48 score 7 stars 12 packages 306 scripts 2 mentions 23 exports 71 dependencies

Last updated from:92bbfe0fc0. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE184
linux-devel-x86_64OK191
source / vignettesOK190
linux-release-x86_64OK181
macos-release-arm64OK104
macos-oldrel-arm64OK92
windows-develOK94
windows-releaseOK90
windows-oldrelOK90
wasm-releaseOK173

Exports:.Dockstore.gadget_run.Leonardo.Rawls.Service.Terraadd_libpathsanvil_set_auth_jsonavtable_gadgetavworkflow_gadgetavworkspace_gadgetbrowse_workspaceDockstoreempty_objectLeonardooperationsRawlsschemasServiceshowtagsTDRTerra

Dependencies:AnVILBaseaskpassbase64encBiocBaseUtilsbslibcachemclicommonmarkcpp11crosstalkcurldigestdplyrDTevaluatefastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsGCPtoolsgenericsgluehighrhtmltoolshtmlwidgetshttpuvhttrhttr2jquerylibjsonlitekeyringknitrlambda.rlaterlazyevallifecyclemagrittrmemoisemimeminiUIopensslotelpillarpkgconfigpromisespurrrR6rapiclientrappdirsRcpprlangrmarkdownsassshinysourcetoolsstringistringrsystibbletidyrtidyselecttinytexutf8vctrswithrxfunxtableyaml

Introduction to the AnVIL package
Installation | Quick start | Up to speed with AnVIL | Use in the AnVIL cloud | Local use | Graphical interfaces | For end users | Fast binary package installation | Working with Google cloud-based resources | Using gcloud_*() for account management | Using gsutil_*() for file and bucket management | Using av*() to work with AnVIL tables and data | Tables, reference data, and persistent files | Using avtable*() for accessing tables | Using avdata() for accessing Workspace Data | Using avbucket() and workspace files | Using avnotebooks*() for notebook management | Using avworkflows_*() for workflows | Using avworkspace_*() for workspaces | Using drs_*() for resolving DRS (Data Repository Service) URIs | For developers | Set-up | Service APIs | Construction | Invoke endpoints | Process responses | Test endpoints | Service implementations | Extending the Service class to implement your own RESTful interface | Support, bug reports, and source code availability | Appendix | Acknowledgments | Session info
Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2026-05-04
Started: 2020-04-25

Dockstore and Bioconductor for AnVIL
Introduction: Basic concepts of Dockstore and Bioconductor | Working with the Dockstore API in Bioconductor | Appendix | Acknowledgments | Session info
Rendered fromBiocDockstore.Rmdusingknitr::rmarkdown

Last update: 2025-12-09
Started: 2020-04-25

Running an AnVIL workflow within R
Installation | Workflow setup: DESeq2 | Setting up the workspace and choosing a workflow | Retrieving the configuration | Updating workflows | Changing the inputs / outputs | Update configuration locally | Set a workflow configuration for reuse in AnVIL | Running and stopping workflows | Running a workflow | Monitoring workflows | Stopping workflows | Managing workflow output | Workflow files | Workflow information | Session information
Rendered fromRunningWorkflow.Rmdusingknitr::rmarkdown

Last update: 2025-12-09
Started: 2022-01-19

Readme and manuals

Help Manual

Help pageTopics
Functions to implement AnVIL gadget interfaces.gadget_run
Store and retrieve authentication credentials using a secure keyringanvil_set_auth_json
Graphical user interfaces for common AnVIL operationsavtable_gadget avworkflow_gadget avworkspace_gadget browse_workspace
RESTful service constructorService
RESTful services useful for AnVIL developers$,Service-method .DollarNames.Service Dockstore Dockstore-class empty_object Leonardo Leonardo-class operations operations,Dockstore-method operations,Leonardo-method operations,Rawls-method operations,Service-method operations,TDR-method operations,Terra-method Rawls Rawls-class schemas schemas,Rawls-method schemas,Service-method schemas,Terra-method Service-class Services show,Service-method tags TDR TDR-class Terra Terra-class
Utilities for managing library pathsadd_libpaths utilities