Package: AnVILWorkflow 1.13.0

Sehyun Oh

AnVILWorkflow: Run workflows implemented in Terra/AnVIL workspace

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The main cloud-based genomics platform deported by the AnVIL project is Terra. The AnVILWorkflow package allows remote access to Terra implemented workflows, enabling end-user to utilize Terra/ AnVIL provided resources - such as data, workflows, and flexible/scalble computing resources - through the conventional R functions.

Authors:Sehyun Oh [aut, cre], Marcel Ramos [ctb], Kai Gravel-Pucillo [aut]

AnVILWorkflow_1.13.0.tar.gz
AnVILWorkflow_1.13.0.zip(r-4.7)AnVILWorkflow_1.13.0.zip(r-4.6)AnVILWorkflow_1.13.0.zip(r-4.5)
AnVILWorkflow_1.13.0.tgz(r-4.6-any)AnVILWorkflow_1.13.0.tgz(r-4.5-any)
AnVILWorkflow_1.13.0.tar.gz(r-4.7-any)AnVILWorkflow_1.13.0.tar.gz(r-4.6-any)
AnVILWorkflow_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AnVILWorkflow/json (API)

# Install 'AnVILWorkflow' in R:

install.packages('AnVILWorkflow', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/shbrief/anvilworkflow/issues

On BioConductor:AnVILWorkflow-1.13.0(bioc 3.24)AnVILWorkflow-1.11.0(bioc 3.23)

infrastructure software anvil gcp terra u24hg010263 workflows

5.62 score 7 stars 3 scripts 18 exports 74 dependencies

Last updated from:1cf359ce86. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	174
linux-devel-x86_64	ERROR	211
source / vignettes	OK	212
linux-release-x86_64	ERROR	165
macos-release-arm64	ERROR	99
macos-oldrel-arm64	ERROR	79
windows-devel	ERROR	82
windows-release	ERROR	89
windows-oldrel	ERROR	99
wasm-release	OK	145

Exports:AnVILBrowse availableAnalysis cloneWorkspace currentInput findInputName getAllDataTables getAllWorkflows getDashboard getData getOutput getWorkflowConfig getWorkflows getWorkspaces monitorWorkflow runWorkflow setCloudEnv stopWorkflow updateInput

Dependencies:AnVIL AnVILBase AnVILGCP askpass base64enc BiocBaseUtils bslib cachem cli commonmark cpp11 crosstalk curl digest dplyr DT evaluate fastmap filelock fontawesome formatR fs futile.logger futile.options GCPtools generics glue highr htmltools htmlwidgets httpuv httr httr2 jquerylib jsonlite keyring knitr lambda.r later lazyeval lifecycle magrittr memoise mime miniUI openssl otel pillar pkgconfig plyr promises purrr R6 rapiclient rappdirs Rcpp rlang rmarkdown sass shiny sourcetools stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs withr xfun xtable yaml

AnVILWorkflow: Run batch analysis workflows including non-R tools leveraing Cloud resources

Rendered fromsalmon.Rmdusingknitr::rmarkdown

Last update: 2026-04-23
Started: 2022-10-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Apply to the returned value from '.avSampleData' function	.getAgeMinMax
Search keywords in a given metadata table	.search_keyword
Summary table into a single string where the column name and the value is separated by 'sep' and columns are separated by 'delim'	.tableToString
Search AnVIL workspaces using keywords	AnVILBrowse
Find the available analysis	availableAnalysis
Clone template workspace	cloneWorkspace
Check the current input arguments	currentInput
Find the root entity name	findInputName
Get all the data tables	getAllDataTables
Collect workflows from all workspaces a user has access to	getAllWorkflows
Get AnVIL workspaces	getAllWorkspaces
Print out Dashboard contents	getDashboard
Creates a metadata table of data from all workspaces provided	getData
Download output files from Terra	getOutput
Check the workflow configuration	getWorkflowConfig
Creates a metadata table of workflows from all workspaces provided	getWorkflows
Creates a metadata table of all workspaces	getWorkspaces
Check the status of submitted jobs	monitorWorkflow
Launch Terra workflow	runWorkflow
Setup Google Cloud Account and Project	setCloudEnv
Abort submitted job	stopWorkflow
Update the input	updateInput