{
  "_id": "6a17e676acfb0bcc41da1508",
  "Package": "AnVILWorkflow",
  "Title": "Run workflows implemented in Terra/AnVIL workspace",
  "Version": "1.13.0",
  "Date": "2023-4-23",
  "Authors@R": "c(person(given = \"Sehyun\",\nfamily = \"Oh\",\nrole = c(\"aut\", \"cre\"),\nemail = \"shbrief@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9490-3061\")),\nperson(\"Marcel\", \"Ramos\", , \"marcel.ramos@sph.cuny.edu\", \"ctb\", c(ORCID = \"0000-0002-3242-0582\")),\nperson(\"Kai\", \"Gravel-Pucillo\", role = \"aut\"))",
  "Description": "The AnVIL is a cloud computing resource developed in part\nby the National Human Genome Research Institute. The main\ncloud-based genomics platform deported by the AnVIL project is\nTerra. The AnVILWorkflow package allows remote access to Terra\nimplemented workflows, enabling end-user to utilize Terra/\nAnVIL provided resources - such as data, workflows, and\nflexible/scalble computing resources - through the conventional\nR functions.",
  "License": "Artistic-2.0",
  "biocViews": "Infrastructure, Software",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/shbrief/AnVILWorkflow",
  "BugReports": "https://github.com/shbrief/AnVILWorkflow/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev libsecret-1-dev libuv1-dev\nlibssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:00:02 UTC",
  "RemoteUrl": "https://github.com/bioc/AnVILWorkflow",
  "RemoteRef": "HEAD",
  "RemoteSha": "1cf359ce862b2cb388881b2222117b72e6acc6c9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 06:32:14 UTC",
    "User": "root"
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  "Author": "Sehyun Oh [aut, cre] (ORCID: <https://orcid.org/0000-0002-9490-3061>),\nMarcel Ramos [ctb] (ORCID: <https://orcid.org/0000-0002-3242-0582>),\nKai Gravel-Pucillo [aut]",
  "Maintainer": "Sehyun Oh <shbrief@gmail.com>",
  "MD5sum": "5ba5341cd0ea8ca83a46bc9b77cd3e7d",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-28T06:32:14.000Z",
  "_published": "2026-05-28T06:53:41.998Z",
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26558665885",
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  "_host": "GitHub-Actions",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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  "_maintainer": {
    "name": "Sehyun Oh",
    "email": "shbrief@gmail.com",
    "login": "shbrief",
    "linkedin": "in/sehyunoh",
    "twitter": "@drsehyun",
    "description": "Molecular Biologist & Bioinformatician",
    "uuid": 15724490,
    "orcid": "0000-0002-9490-3061"
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      "role": "Depends"
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      "role": "Depends"
    },
    {
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    },
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    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "n": 1
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  "_bioc": [
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    "software",
    "anvil",
    "gcp",
    "terra",
    "u24hg010263",
    "workflows"
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  "_stars": 7,
  "_contributors": [
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      "uuid": 15724490
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  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
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    "source": "https://www.bioconductor.org/packages/stats/bioc/AnVILWorkflow"
  },
  "_devurl": "https://github.com/shbrief/anvilworkflow",
  "_searchresults": 3,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/shbrief/anvilworkflow",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "AnVILBrowse",
    "availableAnalysis",
    "cloneWorkspace",
    "currentInput",
    "findInputName",
    "getAllDataTables",
    "getAllWorkflows",
    "getDashboard",
    "getData",
    "getOutput",
    "getWorkflowConfig",
    "getWorkflows",
    "getWorkspaces",
    "monitorWorkflow",
    "runWorkflow",
    "setCloudEnv",
    "stopWorkflow",
    "updateInput"
  ],
  "_help": [
    {
      "page": "dot-getAgeMinMax",
      "title": "Apply to the returned value from '.avSampleData' function",
      "topics": [
        ".getAgeMinMax"
      ]
    },
    {
      "page": "dot-search_keyword",
      "title": "Search keywords in a given metadata table",
      "topics": [
        ".search_keyword"
      ]
    },
    {
      "page": "dot-tableToString",
      "title": "Summary table into a single string where the column name and the value is separated by 'sep' and columns are separated by 'delim'",
      "topics": [
        ".tableToString"
      ]
    },
    {
      "page": "AnVILBrowse",
      "title": "Search AnVIL workspaces using keywords",
      "topics": [
        "AnVILBrowse"
      ]
    },
    {
      "page": "availableAnalysis",
      "title": "Find the available analysis",
      "topics": [
        "availableAnalysis"
      ]
    },
    {
      "page": "cloneWorkspace",
      "title": "Clone template workspace",
      "topics": [
        "cloneWorkspace"
      ]
    },
    {
      "page": "currentInput",
      "title": "Check the current input arguments",
      "topics": [
        "currentInput"
      ]
    },
    {
      "page": "findInputName",
      "title": "Find the root entity name",
      "topics": [
        "findInputName"
      ]
    },
    {
      "page": "getAllDataTables",
      "title": "Get all the data tables",
      "topics": [
        "getAllDataTables"
      ]
    },
    {
      "page": "getAllWorkflows",
      "title": "Collect workflows from all workspaces a user has access to",
      "topics": [
        "getAllWorkflows"
      ]
    },
    {
      "page": "getAllWorkspaces",
      "title": "Get AnVIL workspaces",
      "topics": [
        "getAllWorkspaces"
      ]
    },
    {
      "page": "getDashboard",
      "title": "Print out Dashboard contents",
      "topics": [
        "getDashboard"
      ]
    },
    {
      "page": "getData",
      "title": "Creates a metadata table of data from all workspaces provided",
      "topics": [
        "getData"
      ]
    },
    {
      "page": "getOutput",
      "title": "Download output files from Terra",
      "topics": [
        "getOutput"
      ]
    },
    {
      "page": "getWorkflowConfig",
      "title": "Check the workflow configuration",
      "topics": [
        "getWorkflowConfig"
      ]
    },
    {
      "page": "getWorkflows",
      "title": "Creates a metadata table of workflows from all workspaces provided",
      "topics": [
        "getWorkflows"
      ]
    },
    {
      "page": "getWorkspaces",
      "title": "Creates a metadata table of all workspaces",
      "topics": [
        "getWorkspaces"
      ]
    },
    {
      "page": "monitorWorkflow",
      "title": "Check the status of submitted jobs",
      "topics": [
        "monitorWorkflow"
      ]
    },
    {
      "page": "runWorkflow",
      "title": "Launch Terra workflow",
      "topics": [
        "runWorkflow"
      ]
    },
    {
      "page": "setCloudEnv",
      "title": "Setup Google Cloud Account and Project",
      "topics": [
        "setCloudEnv"
      ]
    },
    {
      "page": "stopWorkflow",
      "title": "Abort submitted job",
      "topics": [
        "stopWorkflow"
      ]
    },
    {
      "page": "updateInput",
      "title": "Update the input",
      "topics": [
        "updateInput"
      ]
    }
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    "AnVILBase",
    "AnVILGCP",
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      "source": "salmon.Rmd",
      "filename": "salmon.html",
      "title": "AnVILWorkflow: Run batch analysis workflows including non-R tools leveraing Cloud resources",
      "author": "Sehyun Oh",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Citing AnVILWorkflow",
        "Install and load package",
        "Google Cloud SDK",
        "Create Terra account",
        "Major steps",
        "Example in this vignette: bulk RNAseq analysis",
        "Browse AnVIL resources",
        "Setup",
        "Clone workspace",
        "Curated by this package",
        "Any workspace you have access to",
        "Prepare input",
        "Current input",
        "Update input",
        "Run workflow",
        "Monitor progress",
        "Abort submission",
        "Result",
        "Session Info"
      ],
      "created": "2022-10-08 02:12:28",
      "modified": "2026-04-23 17:49:54",
      "commits": 14
    }
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