# Bioconductor on the AnVIL compute environment

## Documentation for package ‘AnVIL’ version 1.16.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B D E F G I L O P R S T U misc

## -- A --

add_libpaths | Utilities for managing library paths
AnVIL-defunct | Defunct functions in package 'AnVIL'
AnVIL-deprecated | Deprecated AnVIL functionality
as.list.response | Process service responses to tibble and other data structures.
av | TABLE, DATA, files, bucket, runtime, and disk elements
avbucket | TABLE, DATA, files, bucket, runtime, and disk elements
avdata | TABLE, DATA, files, bucket, runtime, and disk elements
avdata_import | TABLE, DATA, files, bucket, runtime, and disk elements
avdisks | TABLE, DATA, files, bucket, runtime, and disk elements
avfiles_backup | TABLE, DATA, files, bucket, runtime, and disk elements
avfiles_ls | TABLE, DATA, files, bucket, runtime, and disk elements
avfiles_restore | TABLE, DATA, files, bucket, runtime, and disk elements
avfiles_rm | TABLE, DATA, files, bucket, runtime, and disk elements
avnotebooks | Notebook management
avnotebooks_delocalize | Notebook management
avnotebooks_localize | Notebook management
avruntime | TABLE, DATA, files, bucket, runtime, and disk elements
avruntimes | TABLE, DATA, files, bucket, runtime, and disk elements
avtable | TABLE, DATA, files, bucket, runtime, and disk elements
avtables | TABLE, DATA, files, bucket, runtime, and disk elements
avtable_delete_values | TABLE, DATA, files, bucket, runtime, and disk elements
avtable_gadget | Graphical user interfaces for common AnVIL operations
avtable_import | TABLE, DATA, files, bucket, runtime, and disk elements
avtable_import_set | TABLE, DATA, files, bucket, runtime, and disk elements
avtable_import_status | TABLE, DATA, files, bucket, runtime, and disk elements
avtable_paged | TABLE, DATA, files, bucket, runtime, and disk elements
avworkflow | Workflow configuration
avworkflows | Workflow submissions and file outputs
avworkflow_configuration | Defunct functions in package 'AnVIL'
avworkflow_configurations | Workflow configuration
avworkflow_configuration_get | Workflow configuration
avworkflow_configuration_inputs | Workflow configuration
avworkflow_configuration_outputs | Workflow configuration
avworkflow_configuration_set | Workflow configuration
avworkflow_configuration_template | Workflow configuration
avworkflow_configuration_update | Workflow configuration
avworkflow_files | Workflow submissions and file outputs
avworkflow_gadget | Graphical user interfaces for common AnVIL operations
avworkflow_import_configuration | Defunct functions in package 'AnVIL'
avworkflow_info | Workflow submissions and file outputs
avworkflow_jobs | Workflow submissions and file outputs
avworkflow_localize | Workflow submissions and file outputs
avworkflow_name | Workflow configuration
avworkflow_namespace | Workflow configuration
avworkflow_run | Workflow submissions and file outputs
avworkflow_stop | Workflow submissions and file outputs
avworkspace | Workspace management
avworkspaces | Workspace management
avworkspace_clone | Workspace management
avworkspace_gadget | Graphical user interfaces for common AnVIL operations
avworkspace_name | Workspace management
avworkspace_namespace | Workspace management

## -- B --

BINARY_BASE_URL | Defunct functions in package 'AnVIL'
browse_workspace | Graphical user interfaces for common AnVIL operations

## -- D --

delocalize | Copy packages, folders, or files to or from google buckets.
Dockstore | RESTful services useful for AnVIL developers
Dockstore-class | RESTful services useful for AnVIL developers
drs_access_url | DRS (Data Repository Service) URL management
drs_cp | DRS (Data Repository Service) URL management
drs_stat | DRS (Data Repository Service) URL management

## -- E --

empty_object | RESTful services useful for AnVIL developers

## -- F --

flatten | Process service responses to tibble and other data structures.
flatten-method | Process service responses to tibble and other data structures.

## -- G --

gcloud | gcloud command line utility interface
gcloud_account | gcloud command line utility interface
gcloud_cmd | gcloud command line utility interface
gcloud_exists | gcloud command line utility interface
gcloud_help | gcloud command line utility interface
gcloud_project | gcloud command line utility interface
gcloud_storage | gcloud command line utility interface
gcloud_storage_buckets | gcloud command line utility interface
Gen3Fence | Defunct functions in package 'AnVIL'
Gen3Indexd | Defunct functions in package 'AnVIL'
Gen3Peregrine | Defunct functions in package 'AnVIL'
Gen3Sheepdog | Defunct functions in package 'AnVIL'
gsutil | gsutil command line utility interface
gsutil_cat | gsutil command line utility interface
gsutil_cp | gsutil command line utility interface
gsutil_exists | gsutil command line utility interface
gsutil_help | gsutil command line utility interface
gsutil_ls | gsutil command line utility interface
gsutil_pipe | gsutil command line utility interface
gsutil_requesterpays | gsutil command line utility interface
gsutil_rm | gsutil command line utility interface
gsutil_rsync | gsutil command line utility interface
gsutil_stat | gsutil command line utility interface

## -- I --

install | Defunct functions in package 'AnVIL'

## -- L --

Leonardo | RESTful services useful for AnVIL developers
Leonardo-class | RESTful services useful for AnVIL developers
localize | Copy packages, folders, or files to or from google buckets.

## -- O --

operations | RESTful services useful for AnVIL developers
operations-method | RESTful services useful for AnVIL developers

## -- P --

print.avworkflow_configuration | Workflow configuration
print.repository_stats | Deprecated AnVIL functionality

## -- R --

Rawls | RESTful services useful for AnVIL developers
Rawls-class | RESTful services useful for AnVIL developers
repositories | Defunct functions in package 'AnVIL'
repository | Defunct functions in package 'AnVIL'
repository_stats | Deprecated AnVIL functionality
Response | Process service responses to tibble and other data structures.

## -- S --

schemas | RESTful services useful for AnVIL developers
schemas-method | RESTful services useful for AnVIL developers
Service | RESTful service constructor
Service-class | RESTful services useful for AnVIL developers
Services | RESTful services useful for AnVIL developers
show-method | RESTful services useful for AnVIL developers
str-method | Process service responses to tibble and other data structures.

## -- T --

tags | RESTful services useful for AnVIL developers
Terra | RESTful services useful for AnVIL developers
Terra-class | RESTful services useful for AnVIL developers

## -- U --

utilities | Utilities for managing library paths

## -- misc --

$-method | RESTful services useful for AnVIL developers
.DollarNames.Service | RESTful services useful for AnVIL developers
.gadget_run | Functions to implement AnVIL gadget interfaces