Package: sevenbridges 1.37.0

Phil Webster

sevenbridges: Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.

Authors:Phil Webster [aut, cre], Soner Koc [aut], Nan Xiao [aut], Tengfei Yin [aut], Dusan Randjelovic [ctb], Emile Young [ctb], Velsera [cph, fnd]

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sevenbridges.pdf |sevenbridges.html✨
sevenbridges/json (API)
NEWS

# Install 'sevenbridges' in R:
install.packages('sevenbridges', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sbg/sevenbridges-r/issues

On BioConductor:sevenbridges-1.37.0(bioc 3.21)sevenbridges-1.36.0(bioc 3.20)

softwaredataimportthirdpartyclientapi-clientbioconductorbioinformaticscloudcommon-workflow-languagesevenbridges

7.40 score 35 stars 24 scripts 198 downloads 158 exports 24 dependencies

Last updated 23 days agofrom:265369eecd. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:%>>%access_leveladd_tagaddIdNumage_at_diagnosisaliquot_idaliquot_uuidanalysis_uuidanyReqAnyRequirementapiAppappTypeargslistasListAuthawsAWSInstanceTypeRequirementbatchBindingcase_idcase_uuidCCBListCLBcli_list_projectscli_list_tagscli_uploadCOBCommandInputParameterCommandInputSchemaCommandLineBindingCommandLineToolCommandOutputBindingCommandOutputParameterCommandOutputSchemaComplexEnumconvert_appcpuCPURequirementCreateFileRequirementCWLdata_formatdata_subtypedata_typeDatatypeEnumdays_to_deathdeletedisease_typedockerDockerRequirementdownloadDSCListenumEnvironmentDefEnvironmentDefListEnvVarRequirementethnicityexperimental_strategyExpressionExpressionEngineRequirementExpressionToolFilefile_extensionfile_segment_numberfileDefFileDefFileDefListFileListFilesFilesListFlowFSgdc_file_uuidgenderget_cwl_classget_tokenget_uploadergetTaskHookInParinputinput_matrixInputParameterInputParameterListInputSchemainvestigationIPListis_commandlinetoolis_workflowItemArraylibrary_idlinklink_whatmemMemRequirementMetadatamisc_get_tokenmisc_get_uploadermisc_make_metadatamisc_upload_cliOPListOutParoutputoutput_matrixOutputParameterOutputParameterListOutputSchemapaired_endParameterplatformplatform_unit_idprimary_sitePrimitiveEnumProcessProcessRequirementProcessRequirementListproject_detailsproject_membersquality_scaleracereference_genomerequirementsresponseresponse<-sample_idsample_typesample_uuidsbg_get_envsbg_set_envSBGWorkflowScatterFeatureRequirementSchemaSchemaDefSchemaDefListSchemaListset_tagset_test_envsetTaskHookSubworkflowFeatureRequirementtest_tool_bunnytest_tool_cwlruntest_tool_rabixToolupload_complete_allupload_complete_partupload_deleteupload_infoupload_info_partupload_initvital_statusWorkflowWorkflowOutputParameterWorkflowOutputParameterListWorkflowStepWorkflowStepInputWorkflowStepInputListWorkflowStepListWorkflowStepOutputWorkflowStepOutputList

Dependencies:askpassBiocGenericsclicurldata.tabledocoptgluehttrjsonlitelifecyclemagrittrmimeobjectPropertiesobjectSignalsopensslR6rlangS4Vectorsstringistringrsysuuidvctrsyaml

Complete Guide for Seven Bridges API R Client

Rendered fromapi.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-10-15
Started: 2016-03-31

Creating Your Docker Container and Command Line Interface (with docopt)

Rendered fromdocker.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-03-26
Started: 2016-01-22

Describe and Execute CWL Tools/Workflows in R

Rendered fromapps.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-06-03
Started: 2016-01-22

Find Data on CGC via Data Browser and Datasets API

Rendered fromcgc-datasets.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-03-26
Started: 2018-11-15

IDE Container: RStudio Server, Shiny Server, and More

Rendered fromrstudio.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-03-26
Started: 2016-02-09

Master Tutorial: Use R for Cancer Genomics Cloud

Rendered frombioc-workflow.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-03-26
Started: 2016-02-09

Readme and manuals

Help Manual

Help pageTopics
Seven Bridges Platform API Client and CWL Tool Builder in Rsevenbridges-package
add '#' prefix to idaddIdNum
Core HTTP logic for Seven Bridges APIapi
Class AppApp App-class
Convert a object slots/fields to a list, json, or yaml fileasList asList,ANY-method asList,CWL-method asList,DSCList-method asList,SimpleList-method asList,SingleEnum-method
Class AuthAuth Auth-class
batch function for task batch executionbatch
BindingBinding Binding-class
characterORCommandLineBindingList ClassCCBList characterORCommandLineBindingList-class
Shorthand functions for cwl packages constructorsargslist CLB COB InPar input IPList OPList OutPar output
List projects using Seven Bridges command line uploadercli_list_projects
List all the tags in project using Seven Bridges command line uploadercli_list_tags
Upload files using Seven Bridges command line uploadercli_upload misc_upload_cli
CommandInputParameter ClassCommandInputParameter CommandInputParameter-class
CommandInputSchema ClassCommandInputSchema CommandInputSchema-class
CommandLineBinding ClassCommandLineBinding CommandLineBinding-class
CommandLineTool ClassCommandLineTool CommandLineTool-class
CommandOutputBinding ClassCommandOutputBinding CommandOutputBinding-class
CommandOutputParameter ClassCommandOutputParameter CommandOutputParameter-class
CommandOutputSchemaCommandOutputSchema CommandOutputSchema-class
Convert App or a CWL JSON file to Tool or Flow objectappType convert_app
Rabix specifc RequirementsanyReq AnyRequirement AnyRequirement-class aws AWSInstanceTypeRequirement AWSInstanceTypeRequirement-class cpu CPURequirement CPURequirement-class docker fileDef mem MemRequirement MemRequirement-class requirements
Class CWLCWL CWL-class
Delete files or foldersdelete delete,Files-method delete,SimpleList-method delete,Task-method
Download filesdownload download,Files-method download,FilesList-method
DSC listDSCList DSCList-class
Expression ClassExpression Expression-class
ExpressionTool ClassExpressionTool ExpressionTool-class
FileList ClassFile File-class FileList FileList-class
Class FilesFiles Files-class FilesList FilesList-class
FS classFS FS-class
Get class from CWL JSON fileget_cwl_class is_commandlinetool is_workflow
Opens web browser to copy the auth tokenget_token misc_get_token
Download Seven Bridges command line uploader and extract to a specified directoryget_uploader misc_get_uploader
Handler instanceHandler Handler-class
Get input/output matrix out of JSON CWL file directlyinput_matrix output_matrix
Class ItemItem Item-class
link two nodes to form a new Workflowlink link,App,ToolORWorkflow-method link,Tool,Tool-method link,Tool,Workflow-method link,ToolORWorkflow,App-method link,Workflow,Tool-method link,Workflow,Workflow-method
List possible linking methodslink_what link_what,SBGWorkflow,SBGWorkflow-method link_what,SBGWorkflow,Tool-method link_what,Tool,SBGWorkflow-method link_what,Tool,Tool-method
Meta schemaaccess_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
Paramter class (reference class)InputParameter InputParameter-class InputParameterList InputParameterList-class OutputParameter OutputParameter-class OutputParameterList OutputParameterList-class Parameter Parameter-class
Pre-defiend enumsComplexEnum ComplexSingleEnum-class DatatypeEnum DatatypeSingleEnum-class enum enum-class ItemArray ItemArray-class PrimitiveEnum PrimitiveSingleEnum-class
Process ClassProcess Process-class
ProcessRequirement ClassCreateFileRequirement 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
Returns the details of the projectproject_details
Returns a list of all users invited to the project and their privilegesproject_members
Get raw response from an Item objectresponse response,ANY-method response,Item-method response,SimpleList-method response<- response<-,ANY-method response<-,Item-method response<-,SimpleList-method
Set authentication environment variables for Seven Bridges APIsbg_get_env
Set authentication environment variables for Seven Bridges APIsbg_set_env
Build workflow"%>>%" "%>>%",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
SchemaListInputSchema InputSchema-class OutputSchema OutputSchema-class ScehmaList Schema Schema-class SchemaDef SchemaDef-class SchemaDefList SchemaDefList-class SchemaList SchemaList-class
Set file tagsadd_tag add_tag,Files-method add_tag,FilesList-method set_tag set_tag,Files-method set_tag,FilesList-method
Set testing envset_test_env
List Class generator.setListClass
set task function hookgetTaskHook setTaskHook
Test tools in rabix/bunnytest_tool_bunny
Test tools with cwl-runnertest_tool_cwlrun
Test tools in rabix/rabix-devel (DEPRECATED)test_tool_rabix
Class ToolTool Tool-class
Reports the complete file uploadupload_complete_all
Reports the completion of the part uploadupload_complete_part
Abort the uploadupload_delete
Returns upload information for the ongoing uploadupload_info
Returns AWS S3 signed URL for a part of the file uploadupload_info_part
Initializes the upload of the specified fileupload_init
WorkflowWorkflow Workflow-class WorkflowOutputParameter WorkflowOutputParameter-class WorkflowOutputParameterList WorkflowOutputParameterList-class
WorkflowStepInputListWorkflowStep WorkflowStep-class WorkflowStepInput WorkflowStepInput-class WorkflowStepInputList WorkflowStepInputList-class WorkflowStepList WorkflowStepList-class WorkflowStepOutput WorkflowStepOutput-class WorkflowStepOutputList WorkflowStepOutputList-class