Package: AnVIL 1.19.3
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 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:
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://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:AnVIL-1.19.0(bioc 3.21)AnVIL-1.18.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 7 days agofrom:08fdcb81df. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 13 2024 |
| R-4.5-win | OK | Nov 13 2024 |
| R-4.5-linux | OK | Nov 13 2024 |
| R-4.4-win | OK | Nov 13 2024 |
| R-4.4-mac | OK | Nov 13 2024 |
| R-4.3-win | OK | Nov 13 2024 |
| R-4.3-mac | OK | Nov 13 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
Rendered fromBiocDockstore.Rmdusingknitr::rmarkdownon Nov 13 2024.Last update: 2024-10-16
Started: 2020-04-25
Introduction to the AnVIL package
Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Nov 13 2024.Last update: 2024-11-12
Started: 2020-04-25
Running an AnVIL workflow within R
Rendered fromRunningWorkflow.Rmdusingknitr::rmarkdownon Nov 13 2024.Last update: 2024-10-22
Started: 2022-01-19
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Functions to implement AnVIL gadget interfaces | .gadget_run |
| TABLE, DATA, files, bucket, runtime, and disk elements | av-defunct avbucket avdata avdata_import avdisks avfiles_backup avfiles_ls avfiles_restore avfiles_rm avruntime avruntimes avtable_import_status avtable_paged |
| DEFUNCT - Workflow configuration | avworkflow 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 outputs | avworkflows avworkflows-defunct avworkflow_files avworkflow_info avworkflow_localize avworkflow_run avworkflow_stop |
| Graphical user interfaces for common AnVIL operations | avtable_gadget avworkflow_gadget avworkspace_gadget browse_workspace |
| DEFUNCT - DRS (Data Repository Service) URL management | drs-defunct drs_access_url drs_cp drs_stat |
| DEFUNCT - gcloud command line utility interface | gcloud gcloud-defunct gcloud_account gcloud_cmd gcloud_exists gcloud_help gcloud_project gcloud_storage gcloud_storage_buckets |
| DEFUNCT - gsutil command line utility interface | gsutil 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 buckets | delocalize localize localize-defunct |
| RESTful service constructor | Service |
| 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 paths | add_libpaths utilities |
