{
  "_id": "6a1af78a1d7bb097a09fa673",
  "Package": "sevenbridges",
  "Type": "Package",
  "Title": "Seven Bridges Platform API Client and Common Workflow Language\nTool Builder in R",
  "Version": "1.43.0",
  "Authors@R": "c(\nperson(\"Phil\", \"Webster\", email = \"phil.webster@velsera.com\", role = c(\"aut\", \"cre\")),\nperson(\"Soner\", \"Koc\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-0772-6600\")),\nperson(\"Nan\", \"Xiao\", role = c(\"aut\")),\nperson(\"Tengfei\", \"Yin\", role = c(\"aut\")),\nperson(\"Dusan\", \"Randjelovic\", role = \"ctb\"),\nperson(\"Emile\", \"Young\", role = c(\"ctb\")),\nperson(\"Velsera\", role = c(\"cph\", \"fnd\"))\n)",
  "Maintainer": "Phil Webster <phil.webster@velsera.com>",
  "Description": "R client and utilities for Seven Bridges platform API,\nfrom Cancer Genomics Cloud to other Seven Bridges supported\nplatforms.",
  "License": "Apache License 2.0 | file LICENSE",
  "VignetteBuilder": "knitr",
  "URL": "https://www.sevenbridges.com,\nhttps://sbg.github.io/sevenbridges-r/,\nhttps://github.com/sbg/sevenbridges-r",
  "BugReports": "https://github.com/sbg/sevenbridges-r/issues",
  "biocViews": "Software, DataImport, ThirdPartyClient",
  "NeedsCompilation": "no",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.0",
  "Collate": "sevenbridges-package.R class-all.R api-http.R api-utils.R\napi-misc.R class-filesystem.R class-cwl.R class-auth-utils.R\nclass-auth.R class-item.R class-meta.R class-ratelimit.R\nclass-user.R class-billing.R class-member.R class-project.R\nclass-files.R class-upload.R class-app.R class-tool.R\nclass-flow.R class-task.R class-volume.R class-division.R\nclass-team.R class-teammember.R class-marker.R misc-uploader.R\nmisc-handler.R misc-lift.R zzz.R",
  "Config/pak/sysreqs": "libicu-dev libssl-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:41:48 UTC",
  "RemoteUrl": "https://github.com/bioc/sevenbridges",
  "RemoteRef": "HEAD",
  "RemoteSha": "619d6c744e7d3dc973815a0b4ae97e68c3384df7",
  "Packaged": {
    "Date": "2026-05-30 09:48:01 UTC",
    "User": "root"
  },
  "Author": "Phil Webster [aut, cre],\nSoner Koc [aut] (ORCID: <https://orcid.org/0000-0002-0772-6600>),\nNan Xiao [aut],\nTengfei Yin [aut],\nDusan Randjelovic [ctb],\nEmile Young [ctb],\nVelsera [cph, fnd]",
  "MD5sum": "d6bf2fe580086e18a418ea5adb6f167b",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-30T09:48:01.000Z",
  "_published": "2026-05-30T14:43:22.667Z",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677075164",
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    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "login": "professorp-beep",
    "linkedin": "in/phillipjwebster",
    "description": "",
    "uuid": 83318967
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  "_distro": "noble",
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    },
    {
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      "role": "Depends"
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    {
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      "role": "Depends"
    },
    {
      "package": "httr",
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    {
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      "role": "Imports"
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    {
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    },
    {
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      "role": "Imports"
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    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
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      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
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      "role": "Suggests"
    }
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  "_updates": [
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      "n": 2
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  "_topics": [
    "software",
    "dataimport",
    "thirdpartyclient",
    "api-client",
    "bioconductor",
    "bioinformatics",
    "cloud",
    "common-workflow-language",
    "sevenbridges"
  ],
  "_stars": 37,
  "_contributors": [
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      "uuid": 199363
    },
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    },
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      "count": 1,
      "uuid": 13538375
    }
  ],
  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 446,
    "source": "https://www.bioconductor.org/packages/stats/bioc/sevenbridges"
  },
  "_devurl": "https://github.com/sbg/sevenbridges-r",
  "_pkgdown": "https://sbg.github.io/sevenbridges-r/",
  "_searchresults": 27,
  "_rbuild": "4.6.0",
  "_assets": [
    "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",
    "extra/sevenbridges.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/sbg/sevenbridges-r",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "%>>%",
    "access_level",
    "add_tag",
    "addIdNum",
    "age_at_diagnosis",
    "aliquot_id",
    "aliquot_uuid",
    "analysis_uuid",
    "anyReq",
    "AnyRequirement",
    "api",
    "App",
    "appType",
    "argslist",
    "asList",
    "Auth",
    "aws",
    "AWSInstanceTypeRequirement",
    "batch",
    "Binding",
    "case_id",
    "case_uuid",
    "CCBList",
    "CLB",
    "cli_list_projects",
    "cli_list_tags",
    "cli_upload",
    "COB",
    "CommandInputParameter",
    "CommandInputSchema",
    "CommandLineBinding",
    "CommandLineTool",
    "CommandOutputBinding",
    "CommandOutputParameter",
    "CommandOutputSchema",
    "ComplexEnum",
    "convert_app",
    "cpu",
    "CPURequirement",
    "CreateFileRequirement",
    "CWL",
    "data_format",
    "data_subtype",
    "data_type",
    "DatatypeEnum",
    "days_to_death",
    "delete",
    "disease_type",
    "docker",
    "DockerRequirement",
    "download",
    "DSCList",
    "enum",
    "EnvironmentDef",
    "EnvironmentDefList",
    "EnvVarRequirement",
    "ethnicity",
    "experimental_strategy",
    "Expression",
    "ExpressionEngineRequirement",
    "ExpressionTool",
    "File",
    "file_extension",
    "file_segment_number",
    "fileDef",
    "FileDef",
    "FileDefList",
    "FileList",
    "Files",
    "FilesList",
    "Flow",
    "FS",
    "gdc_file_uuid",
    "gender",
    "get_cwl_class",
    "get_token",
    "get_uploader",
    "getTaskHook",
    "InPar",
    "input",
    "input_matrix",
    "InputParameter",
    "InputParameterList",
    "InputSchema",
    "investigation",
    "IPList",
    "is_commandlinetool",
    "is_workflow",
    "ItemArray",
    "library_id",
    "link",
    "link_what",
    "mem",
    "MemRequirement",
    "Metadata",
    "misc_get_token",
    "misc_get_uploader",
    "misc_make_metadata",
    "misc_upload_cli",
    "OPList",
    "OutPar",
    "output",
    "output_matrix",
    "OutputParameter",
    "OutputParameterList",
    "OutputSchema",
    "paired_end",
    "Parameter",
    "platform",
    "platform_unit_id",
    "primary_site",
    "PrimitiveEnum",
    "Process",
    "ProcessRequirement",
    "ProcessRequirementList",
    "project_details",
    "project_members",
    "quality_scale",
    "race",
    "reference_genome",
    "requirements",
    "response",
    "response<-",
    "sample_id",
    "sample_type",
    "sample_uuid",
    "sbg_get_env",
    "sbg_set_env",
    "SBGWorkflow",
    "ScatterFeatureRequirement",
    "Schema",
    "SchemaDef",
    "SchemaDefList",
    "SchemaList",
    "set_tag",
    "set_test_env",
    "setTaskHook",
    "SubworkflowFeatureRequirement",
    "test_tool_bunny",
    "test_tool_cwlrun",
    "test_tool_rabix",
    "Tool",
    "upload_complete_all",
    "upload_complete_part",
    "upload_delete",
    "upload_info",
    "upload_info_part",
    "upload_init",
    "vital_status",
    "Workflow",
    "WorkflowOutputParameter",
    "WorkflowOutputParameterList",
    "WorkflowStep",
    "WorkflowStepInput",
    "WorkflowStepInputList",
    "WorkflowStepList",
    "WorkflowStepOutput",
    "WorkflowStepOutputList"
  ],
  "_help": [
    {
      "page": "sevenbridges-package",
      "title": "Seven Bridges Platform API Client and CWL Tool Builder in R",
      "topics": [
        "sevenbridges-package"
      ]
    },
    {
      "page": "addIdNum",
      "title": "add '#' prefix to id",
      "topics": [
        "addIdNum"
      ]
    },
    {
      "page": "api",
      "title": "Core HTTP logic for Seven Bridges API",
      "topics": [
        "api"
      ]
    },
    {
      "page": "App-class",
      "title": "Class App",
      "topics": [
        "App",
        "App-class"
      ]
    },
    {
      "page": "as-methods",
      "title": "Convert a object slots/fields to a list, json, or yaml file",
      "topics": [
        "asList",
        "asList,ANY-method",
        "asList,CWL-method",
        "asList,DSCList-method",
        "asList,SimpleList-method",
        "asList,SingleEnum-method"
      ]
    },
    {
      "page": "Auth-class",
      "title": "Class Auth",
      "topics": [
        "Auth",
        "Auth-class"
      ]
    },
    {
      "page": "batch",
      "title": "batch function for task batch execution",
      "topics": [
        "batch"
      ]
    },
    {
      "page": "Binding",
      "title": "Binding",
      "topics": [
        "Binding",
        "Binding-class"
      ]
    },
    {
      "page": "CCBList",
      "title": "characterORCommandLineBindingList Class",
      "topics": [
        "CCBList",
        "characterORCommandLineBindingList-class"
      ]
    },
    {
      "page": "shorthand-cwl",
      "title": "Shorthand functions for cwl packages constructors",
      "topics": [
        "argslist",
        "CLB",
        "COB",
        "InPar",
        "input",
        "IPList",
        "OPList",
        "OutPar",
        "output"
      ]
    },
    {
      "page": "cli_list_projects",
      "title": "List projects using Seven Bridges command line uploader",
      "topics": [
        "cli_list_projects"
      ]
    },
    {
      "page": "cli_list_tags",
      "title": "List all the tags in project using Seven Bridges command line uploader",
      "topics": [
        "cli_list_tags"
      ]
    },
    {
      "page": "cli_upload",
      "title": "Upload files using Seven Bridges command line uploader",
      "topics": [
        "cli_upload",
        "misc_upload_cli"
      ]
    },
    {
      "page": "CommandInputParameter-class",
      "title": "CommandInputParameter Class",
      "topics": [
        "CommandInputParameter",
        "CommandInputParameter-class"
      ]
    },
    {
      "page": "CommandInputSchema-class",
      "title": "CommandInputSchema Class",
      "topics": [
        "CommandInputSchema",
        "CommandInputSchema-class"
      ]
    },
    {
      "page": "CommandLineBinding-class",
      "title": "CommandLineBinding Class",
      "topics": [
        "CommandLineBinding",
        "CommandLineBinding-class"
      ]
    },
    {
      "page": "CommandLineTool",
      "title": "CommandLineTool Class",
      "topics": [
        "CommandLineTool",
        "CommandLineTool-class"
      ]
    },
    {
      "page": "CommandOutputBinding-class",
      "title": "CommandOutputBinding Class",
      "topics": [
        "CommandOutputBinding",
        "CommandOutputBinding-class"
      ]
    },
    {
      "page": "CommandOutputParameter-class",
      "title": "CommandOutputParameter Class",
      "topics": [
        "CommandOutputParameter",
        "CommandOutputParameter-class"
      ]
    },
    {
      "page": "CommandOutputSchema-class",
      "title": "CommandOutputSchema",
      "topics": [
        "CommandOutputSchema",
        "CommandOutputSchema-class"
      ]
    },
    {
      "page": "convert_app",
      "title": "Convert App or a CWL JSON file to Tool or Flow object",
      "topics": [
        "appType",
        "convert_app"
      ]
    },
    {
      "page": "requirements",
      "title": "Rabix specifc Requirements",
      "topics": [
        "anyReq",
        "AnyRequirement",
        "AnyRequirement-class",
        "aws",
        "AWSInstanceTypeRequirement",
        "AWSInstanceTypeRequirement-class",
        "cpu",
        "CPURequirement",
        "CPURequirement-class",
        "docker",
        "fileDef",
        "mem",
        "MemRequirement",
        "MemRequirement-class",
        "requirements"
      ]
    },
    {
      "page": "CWL",
      "title": "Class CWL",
      "topics": [
        "CWL",
        "CWL-class"
      ]
    },
    {
      "page": "delete-methods",
      "title": "Delete files or folders",
      "topics": [
        "delete",
        "delete,Files-method",
        "delete,SimpleList-method",
        "delete,Task-method"
      ]
    },
    {
      "page": "download-methods",
      "title": "Download files",
      "topics": [
        "download",
        "download,Files-method",
        "download,FilesList-method"
      ]
    },
    {
      "page": "DSCList",
      "title": "DSC list",
      "topics": [
        "DSCList",
        "DSCList-class"
      ]
    },
    {
      "page": "Expression-class",
      "title": "Expression Class",
      "topics": [
        "Expression",
        "Expression-class"
      ]
    },
    {
      "page": "ExpressionTool-class",
      "title": "ExpressionTool Class",
      "topics": [
        "ExpressionTool",
        "ExpressionTool-class"
      ]
    },
    {
      "page": "File-class",
      "title": "FileList Class",
      "topics": [
        "File",
        "File-class",
        "FileList",
        "FileList-class"
      ]
    },
    {
      "page": "Files-class",
      "title": "Class Files",
      "topics": [
        "Files",
        "Files-class",
        "FilesList",
        "FilesList-class"
      ]
    },
    {
      "page": "FS-class",
      "title": "FS class",
      "topics": [
        "FS",
        "FS-class"
      ]
    },
    {
      "page": "cwl-utils",
      "title": "Get class from CWL JSON file",
      "topics": [
        "get_cwl_class",
        "is_commandlinetool",
        "is_workflow"
      ]
    },
    {
      "page": "get_token",
      "title": "Opens web browser to copy the auth token",
      "topics": [
        "get_token",
        "misc_get_token"
      ]
    },
    {
      "page": "get_uploader",
      "title": "Download Seven Bridges command line uploader and extract to a specified directory",
      "topics": [
        "get_uploader",
        "misc_get_uploader"
      ]
    },
    {
      "page": "Handler-class",
      "title": "Handler instance",
      "topics": [
        "Handler",
        "Handler-class"
      ]
    },
    {
      "page": "input_output_matrix",
      "title": "Get input/output matrix out of JSON CWL file directly",
      "topics": [
        "input_matrix",
        "output_matrix"
      ]
    },
    {
      "page": "Item-class",
      "title": "Class Item",
      "topics": [
        "Item",
        "Item-class"
      ]
    },
    {
      "page": "link",
      "title": "link two nodes to form a new Workflow",
      "topics": [
        "link",
        "link,App,ToolORWorkflow-method",
        "link,Tool,Tool-method",
        "link,Tool,Workflow-method",
        "link,ToolORWorkflow,App-method",
        "link,Workflow,Tool-method",
        "link,Workflow,Workflow-method"
      ]
    },
    {
      "page": "link_what",
      "title": "List possible linking methods",
      "topics": [
        "link_what",
        "link_what,SBGWorkflow,SBGWorkflow-method",
        "link_what,SBGWorkflow,Tool-method",
        "link_what,Tool,SBGWorkflow-method",
        "link_what,Tool,Tool-method"
      ]
    },
    {
      "page": "Metadata",
      "title": "Meta schema",
      "topics": [
        "access_level",
        "age_at_diagnosis",
        "aliquot_id",
        "aliquot_uuid",
        "analysis_uuid",
        "case_id",
        "case_uuid",
        "data_format",
        "data_subtype",
        "data_type",
        "days_to_death",
        "disease_type",
        "ethnicity",
        "experimental_strategy",
        "file_extension",
        "file_segment_number",
        "gdc_file_uuid",
        "gender",
        "investigation",
        "library_id",
        "Metadata",
        "Metadata-class",
        "misc_make_metadata",
        "paired_end",
        "platform",
        "platform_unit_id",
        "primary_site",
        "quality_scale",
        "race",
        "reference_genome",
        "sample_id",
        "sample_type",
        "sample_uuid",
        "vital_status"
      ]
    },
    {
      "page": "Parameter",
      "title": "Paramter class (reference class)",
      "topics": [
        "InputParameter",
        "InputParameter-class",
        "InputParameterList",
        "InputParameterList-class",
        "OutputParameter",
        "OutputParameter-class",
        "OutputParameterList",
        "OutputParameterList-class",
        "Parameter",
        "Parameter-class"
      ]
    },
    {
      "page": "Enum",
      "title": "Pre-defiend enums",
      "topics": [
        "ComplexEnum",
        "ComplexSingleEnum-class",
        "DatatypeEnum",
        "DatatypeSingleEnum-class",
        "enum",
        "enum-class",
        "ItemArray",
        "ItemArray-class",
        "PrimitiveEnum",
        "PrimitiveSingleEnum-class"
      ]
    },
    {
      "page": "Process",
      "title": "Process Class",
      "topics": [
        "Process",
        "Process-class"
      ]
    },
    {
      "page": "ProcessRequirement",
      "title": "ProcessRequirement Class",
      "topics": [
        "CreateFileRequirement",
        "CreateFileRequirement-class",
        "DockerRequirement",
        "DockerRequirement-class",
        "EnvironmentDef",
        "EnvironmentDef-class",
        "EnvironmentDefList",
        "EnvironmentDefList-class",
        "EnvVarRequirement",
        "EnvVarRequirement-class",
        "ExpressionEngineRequirement",
        "ExpressionEngineRequirement-class",
        "FileDef",
        "FileDef-class",
        "FileDefList",
        "FileDefList-class",
        "ProcessRequirement",
        "ProcessRequirement-class",
        "ProcessRequirementList",
        "ProcessRequirementList-class",
        "ScatterFeatureRequirement",
        "ScatterFeatureRequirement-class",
        "SubworkflowFeatureRequirement",
        "SubworkflowFeatureRequirement-class"
      ]
    },
    {
      "page": "project_details",
      "title": "Returns the details of the project",
      "topics": [
        "project_details"
      ]
    },
    {
      "page": "project_members",
      "title": "Returns a list of all users invited to the project and their privileges",
      "topics": [
        "project_members"
      ]
    },
    {
      "page": "response-methods",
      "title": "Get raw response from an Item object",
      "topics": [
        "response",
        "response,ANY-method",
        "response,Item-method",
        "response,SimpleList-method",
        "response<-",
        "response<-,ANY-method",
        "response<-,Item-method",
        "response<-,SimpleList-method"
      ]
    },
    {
      "page": "sbg_get_env",
      "title": "Set authentication environment variables for Seven Bridges API",
      "topics": [
        "sbg_get_env"
      ]
    },
    {
      "page": "sbg_set_env",
      "title": "Set authentication environment variables for Seven Bridges API",
      "topics": [
        "sbg_set_env"
      ]
    },
    {
      "page": "Flow",
      "title": "Build workflow",
      "topics": [
        "\"%>>%\"",
        "\"%>>%\",App,App-method",
        "\"%>>%\",Tool,Tool-method",
        "\"%>>%\",Workflow,App-method",
        "\"%>>%\",Workflow,Tool-method",
        "\"%>>%\",Workflow,Workflow-method",
        "\"+\",App,App-method",
        "\"+\",Tool,Tool-method",
        "\"+\",WorkflowStepList,App-method",
        "\"+\",WorkflowStepList,Tool-method",
        "\"+\",WorkflowStepList,WorkflowStepList-method",
        "%>>%",
        "%>>%,App,App-method",
        "%>>%,Tool,Tool-method",
        "%>>%,Workflow,App-method",
        "%>>%,Workflow,Tool-method",
        "%>>%,Workflow,Workflow-method",
        "+,App,App-method",
        "+,Tool,Tool-method",
        "+,WorkflowStepList,App-method",
        "+,WorkflowStepList,Tool-method",
        "+,WorkflowStepList,WorkflowStepList-method",
        "Flow",
        "SBGWorkflow",
        "SBGWorkflow-class"
      ]
    },
    {
      "page": "Schema",
      "title": "SchemaList",
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        "InputSchema",
        "InputSchema-class",
        "OutputSchema",
        "OutputSchema-class",
        "ScehmaList",
        "Schema",
        "Schema-class",
        "SchemaDef",
        "SchemaDef-class",
        "SchemaDefList",
        "SchemaDefList-class",
        "SchemaList",
        "SchemaList-class"
      ]
    },
    {
      "page": "tag-methods",
      "title": "Set file tags",
      "topics": [
        "add_tag",
        "add_tag,Files-method",
        "add_tag,FilesList-method",
        "set_tag",
        "set_tag,Files-method",
        "set_tag,FilesList-method"
      ]
    },
    {
      "page": "set_test_env",
      "title": "Set testing env",
      "topics": [
        "set_test_env"
      ]
    },
    {
      "page": "setListClass",
      "title": "List Class generator.",
      "topics": [
        "setListClass"
      ]
    },
    {
      "page": "TaskHook",
      "title": "set task function hook",
      "topics": [
        "getTaskHook",
        "setTaskHook"
      ]
    },
    {
      "page": "test_tool_bunny",
      "title": "Test tools in rabix/bunny",
      "topics": [
        "test_tool_bunny"
      ]
    },
    {
      "page": "test_tool_cwlrun",
      "title": "Test tools with cwl-runner",
      "topics": [
        "test_tool_cwlrun"
      ]
    },
    {
      "page": "test_tool_rabix",
      "title": "Test tools in rabix/rabix-devel (DEPRECATED)",
      "topics": [
        "test_tool_rabix"
      ]
    },
    {
      "page": "Tool-class",
      "title": "Class Tool",
      "topics": [
        "Tool",
        "Tool-class"
      ]
    },
    {
      "page": "upload_complete_all",
      "title": "Reports the complete file upload",
      "topics": [
        "upload_complete_all"
      ]
    },
    {
      "page": "upload_complete_part",
      "title": "Reports the completion of the part upload",
      "topics": [
        "upload_complete_part"
      ]
    },
    {
      "page": "upload_delete",
      "title": "Abort the upload",
      "topics": [
        "upload_delete"
      ]
    },
    {
      "page": "upload_info",
      "title": "Returns upload information for the ongoing upload",
      "topics": [
        "upload_info"
      ]
    },
    {
      "page": "upload_info_part",
      "title": "Returns AWS S3 signed URL for a part of the file upload",
      "topics": [
        "upload_info_part"
      ]
    },
    {
      "page": "upload_init",
      "title": "Initializes the upload of the specified file",
      "topics": [
        "upload_init"
      ]
    },
    {
      "page": "Workflow",
      "title": "Workflow",
      "topics": [
        "Workflow",
        "Workflow-class",
        "WorkflowOutputParameter",
        "WorkflowOutputParameter-class",
        "WorkflowOutputParameterList",
        "WorkflowOutputParameterList-class"
      ]
    },
    {
      "page": "WorkflowStep",
      "title": "WorkflowStepInputList",
      "topics": [
        "WorkflowStep",
        "WorkflowStep-class",
        "WorkflowStepInput",
        "WorkflowStepInput-class",
        "WorkflowStepInputList",
        "WorkflowStepInputList-class",
        "WorkflowStepList",
        "WorkflowStepList-class",
        "WorkflowStepOutput",
        "WorkflowStepOutput-class",
        "WorkflowStepOutputList",
        "WorkflowStepOutputList-class"
      ]
    }
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    "mime",
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    "R6",
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    "S4Vectors",
    "stringi",
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    "yaml"
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      "filename": "api.html",
      "title": "Complete Guide for Seven Bridges API R Client",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "R Client for Seven Bridges API",
        "API General Information",
        "Installation",
        "Quickstart",
        "Create Auth Object",
        "Get User Information",
        "Rate Limit",
        "Show Billing Information",
        "Create Project",
        "Get Details about Existing Project",
        "Copy Public Apps into Your Project",
        "Import CWL App and Run a Task",
        "Execute a New Task",
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        "Get your input files ready",
        "Create a new draft task",
        "Draft a batch task",
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        "Task Monitoring",
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        "Authentication",
        "Direct authentication",
        "Authentication via system environment variables",
        "Authentication via user configuration file",
        "List All API Calls",
        "Offset, Limit, Search, and Advance Access Features",
        "offset and limit",
        "Search by ID",
        "Search by name",
        "Experiment with Advance Access features",
        "Query Parameter 'fields'",
        "Rate Limits",
        "Users",
        "Billing Group and Invoices",
        "For billing",
        "For invoices",
        "Project",
        "List all projects",
        "Partial match project name",
        "Filter by project creation date, modification date, and creator",
        "Create a new project",
        "Create a new project with TCGA controlled data on CGC",
        "Delete a project",
        "Update/edit a project",
        "Project member",
        "List members",
        "Add a member",
        "Update a member",
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        "List all files",
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        "Rule of thumb",
        "Search by name and id",
        "Search by metadata",
        "Search by tags",
        "Search by original task id",
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        "Delete file(s)",
        "Download files",
        "Upload files via API",
        "Upload single file",
        "Upload a folder",
        "Upload a list of files",
        "Upload files via a defined manifest file",
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        "Update a file",
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        "Move files between folders",
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        "Delete a folder",
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        "List all apps",
        "Copy an app",
        "Get an app's CWL description",
        "Add CWL as an app",
        "Describe CWL in R directly",
        "Create test or keep the previous test for Tool",
        "Tasks",
        "List tasks",
        "Create a draft task",
        "Modify a task",
        "Run a task",
        "Abort a running task",
        "Delete a task",
        "Download all files from a completed task",
        "Run tasks in batch mode",
        "Download all files from a batch task",
        "Volumes",
        "Create a volume",
        "List and search all volumes",
        "Get a volume's detail",
        "Delete volume",
        "Import file from volume to project",
        "Export file from project to volume",
        "Public Files and Apps",
        "Public files",
        "Public apps",
        "Actions",
        "Copy files between projects",
        "Send a feedback item",
        "Enterprise",
        "API token for the division context",
        "List all divisions",
        "Get details of a division",
        "Create a team",
        "Get details of a team",
        "Add a team member",
        "List team members",
        "Remove a team member",
        "Rename a team",
        "List your teams in the division",
        "Delete a team",
        "Markers",
        "Create a marker",
        "List markers available on a file",
        "Get details for a marker",
        "Modify a marker",
        "Delete a marker",
        "Get Raw Response from httr",
        "Batch Operation on Project/Files/Tasks",
        "API Cheatsheet"
      ],
      "created": "2016-03-31 19:51:05",
      "modified": "2020-10-15 04:13:42",
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      "source": "docker.Rmd",
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      "engine": "knitr::rmarkdown",
      "headings": [
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        "Existing Docker repos",
        "Rocker Project",
        "Bioconductor Images",
        "Docker Hub",
        "Seven Bridges Docker Registry",
        "Tutorial: Random Number Generator",
        "Using docopt Package",
        "Quick Command Line Interface with commandArgs (Position and Named Args)",
        "Quick Report: Spin and Stich",
        "Executable Report with R Markdown (Advanced)",
        "Setup Docker Hub Automated Build",
        "More Examples"
      ],
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      "modified": "2020-03-26 20:02:17",
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    },
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      "source": "apps.Rmd",
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      "title": "Describe and Execute CWL Tools/Workflows in R",
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        "Apps, Workflows, and Tools",
        "Describe Tools in R",
        "Import from JSON file",
        "Utilitites for Tool object",
        "Create your own tool in R",
        "Introduction",
        "Using existing Docker images and command",
        "Add customized script to existing Docker image",
        "Create formal interface for your command line",
        "Quick command line interface with commandArgs (position and named args)",
        "docopt: a better and formal way to make command line interface",
        "Generate reports",
        "Misc",
        "Describe Wokrflow in R",
        "Import from a JSON file",
        "Utilities for Flow objects",
        "Create your own flow in R",
        "Connect simple linear tools",
        "Connecting tools by input and output id",
        "Connecting tool with workflow by input and output id",
        "Using pipe to construct complicated workflow",
        "Execution",
        "Execute the tool and flow in the cloud",
        "Execute the tool in Rabix -- test locally"
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      "engine": "knitr::rmarkdown",
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        "Graphical Data Browser",
        "Datasets API",
        "Browse TCGA via the Datasets API",
        "Return datasets accessible trough the CGC",
        "Return list of all TCGA entities",
        "Interpreting the list of all entities",
        "Copy files to you project",
        "Post with query",
        "Find samples connected to a case",
        "Find cases with given age at diagnosis",
        "Find cases with a given age at diagnosis and disease",
        "Complex example for filtering TCGA data",
        "Query with multiple filters on a case"
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    },
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      "source": "rstudio.Rmd",
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      "title": "IDE Container: RStudio Server, Shiny Server, and More",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Docker container",
        "Build container locally",
        "Pull from Docker Hub",
        "Launch RStudio Server from Docker container",
        "Launch both RStudio Server and Shiny Server from the same Docker container"
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      "filename": "bioc-workflow.html",
      "title": "Master Tutorial: Use R for Cancer Genomics Cloud",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Prerequisites",
        "Installation",
        "Register on Cancer Genomics Cloud",
        "Authentication",
        "Register on shinyapps.io (Optional)",
        "Report issues",
        "Quickstart",
        "Create a project under your account via API R client",
        "Build a RNA-Seq tool: from bam to report",
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        "Step 2: Create Docker container for your tool",
        "Step 3: Create your command line interface",
        "Step 4: Add default report template to your app",
        "Step 5: Describe your tool in R into CWL",
        "Step 6: Execute your tool with a new task via R API",
        "Build a reporting Tool",
        "What is report tool?",
        "Compose a full workflow",
        "Exercise: bring your own tool",
        "More tutorials"
      ],
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      "modified": "2020-03-26 20:02:17",
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