Package: AnVIL 1.19.3

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 end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.

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_1.19.3.tar.gz
AnVIL_1.19.3.zip(r-4.5)AnVIL_1.19.3.zip(r-4.4)AnVIL_1.19.3.zip(r-4.3)
AnVIL_1.19.3.tgz(r-4.4-any)AnVIL_1.19.3.tgz(r-4.3-any)
AnVIL_1.19.3.tar.gz(r-4.5-noble)AnVIL_1.19.3.tar.gz(r-4.4-noble)
AnVIL_1.19.3.tgz(r-4.4-emscripten)AnVIL_1.19.3.tgz(r-4.3-emscripten)
AnVIL.pdf |AnVIL.html✨
AnVIL/json (API)
NEWS

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

Peer review:

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

On BioConductor:AnVIL-1.19.0(bioc 3.21)AnVIL-1.18.0(bioc 3.20)

infrastructure

10.31 score 8 stars 10 packages 226 scripts 71 exports 69 dependencies

Last updated 12 days agofrom:08fdcb81df. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

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

Dependencies:AnVILBaseaskpassbase64encBiocBaseUtilsbslibcachemclicommonmarkcpp11crayoncrosstalkcurldigestdplyrDTevaluatefansifastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsgluehighrhtmltoolshtmlwidgetshttpuvhttrhttr2jquerylibjsonliteknitrlambda.rlaterlazyevallifecyclemagrittrmemoisemimeminiUIopensslpillarpkgconfigpromisespurrrR6rapiclientrappdirsRcpprlangrmarkdownsassshinysourcetoolsstringistringrsystibbletidyrtidyselecttinytexutf8vctrswithrxfunxtableyaml

Dockstore and Bioconductor for AnVIL

BJ Stubbs, S Gopaulakrishnan, Nitesh Truaga, Martin Morgan, Vincent Carey

Rendered fromBiocDockstore.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-10-16
Started: 2020-04-25

Introduction to the AnVIL package

Nitesh Turaga, Vincent Carey, BJ Stubbs, Marcel Ramos, Martin Morgan

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-11-12
Started: 2020-04-25

Running an AnVIL workflow within R

Kayla Interdonato, Yubo Cheng, Martin Morgan

Rendered fromRunningWorkflow.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-10-22
Started: 2022-01-19

Readme and manuals

Help Manual

Help pageTopics
Functions to implement AnVIL gadget interfaces.gadget_run
TABLE, DATA, files, bucket, runtime, and disk elementsav-defunct avbucket avdata avdata_import avdisks avfiles_backup avfiles_ls avfiles_restore avfiles_rm avruntime avruntimes avtable_import_status avtable_paged
DEFUNCT - Workflow configurationavworkflow avworkflow_config-defunct avworkflow_configurations avworkflow_configuration_get avworkflow_configuration_inputs avworkflow_configuration_outputs avworkflow_configuration_set avworkflow_configuration_template avworkflow_configuration_update avworkflow_name avworkflow_namespace print.avworkflow_configuration
DEFUNCT - Workflow submissions and file outputsavworkflows avworkflows-defunct avworkflow_files avworkflow_info avworkflow_localize avworkflow_run avworkflow_stop
Graphical user interfaces for common AnVIL operationsavtable_gadget avworkflow_gadget avworkspace_gadget browse_workspace
DEFUNCT - DRS (Data Repository Service) URL managementdrs-defunct drs_access_url drs_cp drs_stat
DEFUNCT - gcloud command line utility interfacegcloud gcloud-defunct gcloud_account gcloud_cmd gcloud_exists gcloud_help gcloud_project gcloud_storage gcloud_storage_buckets
DEFUNCT - gsutil command line utility interfacegsutil gsutil-defunct gsutil_cat gsutil_cp gsutil_exists gsutil_help gsutil_ls gsutil_pipe gsutil_requesterpays gsutil_rm gsutil_rsync gsutil_stat
DEFUNCT - Copy packages, folders, or files to or from google bucketsdelocalize localize localize-defunct
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