README.md

In AnVIL: Bioconductor on the AnVIL compute environment

This archive contains an interface to AnVIL web services. The interface uses Bioconductor/AnVIL_rapiclient (rather than the older CRAN version), and is easily extended. Current implementations are for Leonardo, Terra, and Dockstore; there are Gen3 stubs but these are not complete because I do not know end points.

Install the dependency and this package with

pkgs <- ("Bioconductor/AnVIL_rapiclient", "Bioconductor/AnVIL")
BiocManager::install(pkgs)

The package provides singleton endpoints with tab completion on operations

terra = Terra()
terra$getUserStatus() %>% AnVIL::str()

leonardo = Leonardo()
leonardo
leonardo$listClusters() %>% AnVIL::flatten()
operations(leonardo)
schemas(leonardo)

The return values all require further processing; there are some helper functions str() and flatten(), as well as httr::content().

Some services require client keys, in inst/service/<name>/auth.json.

• For dockstore, visit dockstore.org/accounts and put your token in inst/service/dockstore/auth.json file like

  { "token" : "fff" }

AnVIL documentation built on Nov. 8, 2020, 4:57 p.m.