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.

AuthorNan Xiao [aut, cre], Dusan Randjelovic [aut], Emile Young [ctb], Tengfei Yin [aut], Seven Bridges Genomics [cph]
Date of publicationNone
MaintainerNan Xiao <nan.xiao@sevenbridges.com>
LicenseApache License 2.0 | file LICENSE
Version1.4.9
https://www.sevenbridges.com, https://sbg.github.io/sevenbridges-r/, https://github.com/sbg/sevenbridges-r

View on Bioconductor

Man pages

addIdNum: add '#' prefix to id

api: Core HTTP logic for Seven Bridges API

App-class: Class App

as-methods: Convert a object slots/fields to a list, json, or yaml file

Auth-class: Class Auth

batch: batch function for task batch execution

Binding: Binding

CCBList: characterORCommandLineBindingList Class

cli_list_projects: List projects using Seven Bridges command line uploader

cli_list_tags: List all the tags in project using Seven Bridges command line...

cli_upload: Upload files using Seven Bridges command line uploader

CommandInputParameter-class: CommandInputParameter Class

CommandInputSchema-class: CommandInputSchema Class

CommandLineBinding-class: CommandLineBinding Class

CommandLineTool: CommandLineTool Class

CommandOutputBinding-class: CommandOutputBinding Class

CommandOutputParameter-class: CommandOutputParameter Class

CommandOutputSchema-class: CommandOutputSchema

convert_app: Convert App or a CWL JSON file to Tool or Flow object

CWL: Class CWL

cwl-utils: Get class from CWL JSON file

delete-methods: Delete files

download-methods: Download files

DSCList: DSC list

Enum: Pre-defiend enums

Expression-class: Expression Class

ExpressionTool-class: ExpressionTool Class

File-class: FileList Class

Files-class: Class Files

Flow: Build workflow

Folders-class: Class Folders

FS-class: FS class

get_token: Opens web browser to copy the auth token

get_uploader: Download Seven Bridges command line uploader and extract to a...

Handler-class: Handler instance

input_output_matrix: Get input/output matrix out of JSON CWL file directly

Item-class: Class Item

link: link two nodes to form a new Workflow

link_what: List possible linking methods

Metadata: Meta schema

Parameter: Paramter class (reference class)

Process: Process Class

ProcessRequirement: ProcessRequirement Class

project_details: Returns the details of the project

project_members: Returns a list of all users invited to the project and their...

requirements: Rabix specifc Requirements

response-methods: Get raw response from an Item object

sbg_get_env: Set authentication environment variables for Seven Bridges...

sbg_set_env: Set authentication environment variables for Seven Bridges...

Schema: SchemaList

setListClass: List Class generator.

set_test_env: Set testing env

sevenbridges-package: Seven Bridges Platform API Client and CWL Tool Builder in R

shorthand-cwl: Shorthand functions for cwl packages constructors

status_check: Check request status

tag-methods: Set file tags

TaskHook: set task function hook

test_tool_bunny: Test tools in rabix/bunny

test_tool_cwlrun: Test tools with cwl-runner

test_tool_rabix: Test tools in rabix/rabix-devel (DEPRECATED)

Tool-class: Class Tool

ToolUI: Create Rabix tool object

upload_complete_all: Reports the complete file upload

upload_complete_part: Reports the completion of the part upload

upload_delete: Abort the upload

upload_info: Returns upload information for the ongoing upload

upload_info_part: Returns AWS S3 signed URL for a part of the file upload

upload_init: Initializes the upload of the specified file

Workflow: Workflow

WorkflowStep: WorkflowStepInputList

Functions

"\%>>\%" Man page
\%>>\% Man page
access_level Man page
addIdNum Man page
add_tag Man page
add_tag,FilesList-method Man page
add_tag,Files-method Man page
age_at_diagnosis Man page
aliquot_id Man page
aliquot_uuid Man page
analysis_uuid Man page
anyReq Man page
AnyRequirement Man page
AnyRequirement-class Man page
api Man page
App Man page
"\%>>\%",App,App-method Man page
"+",App,App-method Man page
\%>>\%,App,App-method Man page
+,App,App-method Man page
App-class Man page
appType Man page
argslist Man page
asJSON Man page
asJSON,ANY-method Man page
asList Man page
asList,ANY-method Man page
asList,CWL-method Man page
asList,DSCList-method Man page
asList,SimpleList-method Man page
asList,SingleEnum-method Man page
asYAML Man page
asYAML,ANY-method Man page
Auth Man page
Auth-class Man page
aws Man page
AWSInstanceTypeRequirement Man page
AWSInstanceTypeRequirement-class Man page
batch Man page
Binding Man page
Binding-class Man page
case_id Man page
case_uuid Man page
CCBList Man page
characterORCommandLineBindingList-class Man page
CLB Man page
cli_list_projects Man page
cli_list_tags Man page
cli_upload Man page
COB Man page
CommandInputParameter Man page
CommandInputParameter-class Man page
CommandInputSchema Man page
CommandInputSchema-class Man page
CommandLineBinding Man page
CommandLineBinding-class Man page
CommandLineTool Man page
CommandLineTool-class Man page
CommandOutputBinding Man page
CommandOutputBinding-class Man page
CommandOutputParameter Man page
CommandOutputParameter-class Man page
CommandOutputSchema Man page
CommandOutputSchema-class Man page
ComplexEnum Man page
ComplexSingleEnum-class Man page
convert_app Man page
cpu Man page
CPURequirement Man page
CPURequirement-class Man page
CreateFileRequirement Man page
CreateFileRequirement-class Man page
CWL Man page
CWL-class Man page
data_format Man page
data_subtype Man page
data_type Man page
DatatypeEnum Man page
DatatypeSingleEnum-class Man page
days_to_death Man page
delete Man page
delete,Files-method Man page
delete,SimpleList-method Man page
delete,Task-method Man page
disease_type Man page
docker Man page
DockerRequirement Man page
DockerRequirement-class Man page
download Man page
download,FilesList-method Man page
download,Files-method Man page
DSCList Man page
DSCList-class Man page
enum Man page
enum-class Man page
EnvironmentDef Man page
EnvironmentDef-class Man page
EnvironmentDefList Man page
EnvironmentDefList-class Man page
EnvVarRequirement Man page
EnvVarRequirement-class Man page
ethnicity Man page
experimental_strategy Man page
Expression Man page
Expression-class Man page
ExpressionEngineRequirement Man page
ExpressionEngineRequirement-class Man page
ExpressionTool Man page
ExpressionTool-class Man page
File Man page
File-class Man page
fileDef Man page
FileDef Man page
FileDef-class Man page
FileDefList Man page
FileDefList-class Man page
file_extension Man page
FileList Man page
FileList-class Man page
Files Man page
Files-class Man page
file_segment_number Man page
FilesList Man page
FilesList-class Man page
Flow Man page
Folders Man page
Folders-class Man page
FS Man page
FS-class Man page
gdc_file_uuid Man page
gender Man page
get_cwl_class Man page
getTaskHook Man page
get_token Man page
get_uploader Man page
Handler Man page
Handler-class Man page
InPar Man page
input Man page
input_matrix Man page
InputParameter Man page
InputParameter-class Man page
InputParameterList Man page
InputParameterList-class Man page
InputSchema Man page
InputSchema-class Man page
investigation Man page
IPList Man page
is_commandlinetool Man page
is_workflow Man page
Item Man page
ItemArray Man page
ItemArray-class Man page
Item-class Man page
library_id Man page
link Man page
link,App,ToolORWorkflow-method Man page
link,ToolORWorkflow,App-method Man page
link,Tool,Tool-method Man page
link,Tool,Workflow-method Man page
link_what Man page
link_what,SBGWorkflow,SBGWorkflow-method Man page
link_what,SBGWorkflow,Tool-method Man page
link_what,Tool,SBGWorkflow-method Man page
link_what,Tool,Tool-method Man page
link,Workflow,Tool-method Man page
link,Workflow,Workflow-method Man page
mem Man page
MemRequirement Man page
MemRequirement-class Man page
Metadata Man page
Metadata-class Man page
misc_get_token Man page
misc_get_uploader Man page
misc_make_metadata Man page
misc_upload_cli Man page
OPList Man page
OutPar Man page
output Man page
output_matrix Man page
OutputParameter Man page
OutputParameter-class Man page
OutputParameterList Man page
OutputParameterList-class Man page
OutputSchema Man page
OutputSchema-class Man page
paired_end Man page
Parameter Man page
Parameter-class Man page
platform Man page
platform_unit_id Man page
primary_site Man page
PrimitiveEnum Man page
PrimitiveSingleEnum-class Man page
Process Man page
Process-class Man page
ProcessRequirement Man page
ProcessRequirement-class Man page
ProcessRequirementList Man page
ProcessRequirementList-class Man page
project_details Man page
project_members Man page
quality_scale Man page
race Man page
reference_genome Man page
requirements Man page
response Man page
response<- Man page
response<-,ANY-method Man page
response,ANY-method Man page
response<-,Item-method Man page
response,Item-method Man page
response<-,SimpleList-method Man page
response,SimpleList-method Man page
sample_id Man page
sample_type Man page
sample_uuid Man page
sbg_get_env Man page
sbg_set_env Man page
SBGWorkflow Man page
SBGWorkflow-class Man page
ScatterFeatureRequirement Man page
ScatterFeatureRequirement-class Man page
Schema Man page
Schema-class Man page
SchemaDef Man page
SchemaDef-class Man page
SchemaDefList Man page
SchemaDefList-class Man page
SchemaList Man page
SchemaList-class Man page
setListClass Man page
set_tag Man page
set_tag,FilesList-method Man page
set_tag,Files-method Man page
setTaskHook Man page
set_test_env Man page
sevenbridges-package Man page
status_check Man page
SubworkflowFeatureRequirement Man page
SubworkflowFeatureRequirement-class Man page
test_tool_bunny Man page
test_tool_cwlrun Man page
test_tool_rabix Man page
Tool Man page
Tool-class Man page
"\%>>\%",Tool,Tool-method Man page
"+",Tool,Tool-method Man page
\%>>\%,Tool,Tool-method Man page
+,Tool,Tool-method Man page
ToolUI Man page
upload_complete_all Man page
upload_complete_part Man page
upload_delete Man page
upload_info Man page
upload_info_part Man page
upload_init Man page
vital_status Man page
Workflow Man page
"\%>>\%",Workflow,App-method Man page
\%>>\%,Workflow,App-method Man page
Workflow-class Man page
WorkflowOutputParameter Man page
WorkflowOutputParameter-class Man page
WorkflowOutputParameterList Man page
WorkflowOutputParameterList-class Man page
WorkflowStep Man page
WorkflowStep-class Man page
WorkflowStepInput Man page
WorkflowStepInput-class Man page
WorkflowStepInputList Man page
WorkflowStepInputList-class Man page
WorkflowStepList Man page
"+",WorkflowStepList,App-method Man page
+,WorkflowStepList,App-method Man page
WorkflowStepList-class Man page
"+",WorkflowStepList,Tool-method Man page
+,WorkflowStepList,Tool-method Man page
"+",WorkflowStepList,WorkflowStepList-method Man page
+,WorkflowStepList,WorkflowStepList-method Man page
WorkflowStepOutput Man page
WorkflowStepOutput-class Man page
WorkflowStepOutputList Man page
WorkflowStepOutputList-class Man page
"\%>>\%",Workflow,Tool-method Man page
\%>>\%,Workflow,Tool-method Man page
"\%>>\%",Workflow,Workflow-method Man page
\%>>\%,Workflow,Workflow-method Man page

Files

sevenbridges/DESCRIPTION
sevenbridges/LICENSE
sevenbridges/NAMESPACE
sevenbridges/NEWS
sevenbridges/NEWS.md
sevenbridges/R
sevenbridges/R/api-http.R sevenbridges/R/api-misc.R sevenbridges/R/api-utils.R sevenbridges/R/class-all.R sevenbridges/R/class-app.R sevenbridges/R/class-auth-utils.R sevenbridges/R/class-auth.R sevenbridges/R/class-billing.R sevenbridges/R/class-cwl.R sevenbridges/R/class-files.R sevenbridges/R/class-filesystem.R sevenbridges/R/class-flow.R sevenbridges/R/class-folders.R sevenbridges/R/class-item.R sevenbridges/R/class-meta.R sevenbridges/R/class-project.R sevenbridges/R/class-ratelimit.R sevenbridges/R/class-task.R sevenbridges/R/class-tool.R sevenbridges/R/class-upload.R sevenbridges/R/class-user.R sevenbridges/R/class-volume.R sevenbridges/R/misc-addins.R sevenbridges/R/misc-handler.R sevenbridges/R/misc-lift.R sevenbridges/R/misc-uploader.R sevenbridges/R/sevenbridges-package.R sevenbridges/R/zzz.R
sevenbridges/README.md
sevenbridges/build
sevenbridges/build/vignette.rds
sevenbridges/inst
sevenbridges/inst/doc
sevenbridges/inst/doc/api.R
sevenbridges/inst/doc/api.Rmd
sevenbridges/inst/doc/api.html
sevenbridges/inst/doc/apps.R
sevenbridges/inst/doc/apps.Rmd
sevenbridges/inst/doc/apps.html
sevenbridges/inst/doc/bioc-workflow.R
sevenbridges/inst/doc/bioc-workflow.Rmd
sevenbridges/inst/doc/bioc-workflow.html
sevenbridges/inst/doc/cgc-sparql.R
sevenbridges/inst/doc/cgc-sparql.Rmd
sevenbridges/inst/doc/cgc-sparql.html
sevenbridges/inst/doc/docker.R
sevenbridges/inst/doc/docker.Rmd
sevenbridges/inst/doc/docker.html
sevenbridges/inst/doc/rstudio.R
sevenbridges/inst/doc/rstudio.Rmd
sevenbridges/inst/doc/rstudio.html
sevenbridges/inst/docker
sevenbridges/inst/docker/reporttool
sevenbridges/inst/docker/reporttool/Dockerfile
sevenbridges/inst/docker/reporttool/rabix
sevenbridges/inst/docker/reporttool/rabix/generator.R
sevenbridges/inst/docker/reporttool/rabix/reporttool.json
sevenbridges/inst/docker/reporttool/src
sevenbridges/inst/docker/reporttool/src/report.R
sevenbridges/inst/docker/rnaseqGene
sevenbridges/inst/docker/rnaseqGene/Dockerfile
sevenbridges/inst/docker/rnaseqGene/rabix
sevenbridges/inst/docker/rnaseqGene/rabix/generator.R
sevenbridges/inst/docker/rnaseqGene/rabix/rnaseqGene.json
sevenbridges/inst/docker/rnaseqGene/report
sevenbridges/inst/docker/rnaseqGene/report/rnaseqGene.Rmd
sevenbridges/inst/docker/rnaseqGene/src
sevenbridges/inst/docker/rnaseqGene/src/performDE.R
sevenbridges/inst/docker/sevenbridges
sevenbridges/inst/docker/sevenbridges/Dockerfile
sevenbridges/inst/docker/sevenbridges/rabix
sevenbridges/inst/docker/sevenbridges/rabix/generator.R
sevenbridges/inst/docker/sevenbridges/rabix/runif.json
sevenbridges/inst/docker/sevenbridges/rabix/runif2.json
sevenbridges/inst/docker/sevenbridges/report
sevenbridges/inst/docker/sevenbridges/report/report.Rmd
sevenbridges/inst/docker/sevenbridges/src
sevenbridges/inst/docker/sevenbridges/src/runif.R
sevenbridges/inst/docker/sevenbridges/src/runif2spin.R
sevenbridges/inst/docker/sevenbridges/src/runif_args.R
sevenbridges/inst/docker/sevenbridges/src/shiny-server.conf
sevenbridges/inst/docker/sevenbridges/src/shiny-server.sh
sevenbridges/inst/docker/sevenbridges/src/supervisord.conf
sevenbridges/inst/docker/testenv
sevenbridges/inst/docker/testenv/Dockerfile
sevenbridges/inst/extdata
sevenbridges/inst/extdata/app
sevenbridges/inst/extdata/app/dna2protein
sevenbridges/inst/extdata/app/dna2protein/README.md
sevenbridges/inst/extdata/app/dna2protein/data
sevenbridges/inst/extdata/app/dna2protein/data/input.txt
sevenbridges/inst/extdata/app/dna2protein/dna2protein.cwl.json
sevenbridges/inst/extdata/app/dna2protein/inputs.json
sevenbridges/inst/extdata/app/dna2protein/transcribe.cwl.json
sevenbridges/inst/extdata/app/dna2protein/translate.cwl.json
sevenbridges/inst/extdata/app/flow_star.json
sevenbridges/inst/extdata/app/tool_star.json
sevenbridges/inst/extdata/app/tool_unpack_fastq.json
sevenbridges/inst/extdata/bam_index.json
sevenbridges/inst/extdata/download.txt
sevenbridges/inst/extdata/runif.json
sevenbridges/inst/extdata/sample1.fastq
sevenbridges/inst/extdata/sample1.fastq.meta
sevenbridges/inst/extdata/test-easy-api.R
sevenbridges/inst/liftr
sevenbridges/inst/liftr/runif.Rmd
sevenbridges/inst/rstudio
sevenbridges/inst/rstudio/addins.dcf
sevenbridges/man
sevenbridges/man/App-class.Rd sevenbridges/man/Auth-class.Rd sevenbridges/man/Binding.Rd sevenbridges/man/CCBList.Rd sevenbridges/man/CWL.Rd sevenbridges/man/CommandInputParameter-class.Rd sevenbridges/man/CommandInputSchema-class.Rd sevenbridges/man/CommandLineBinding-class.Rd sevenbridges/man/CommandLineTool.Rd sevenbridges/man/CommandOutputBinding-class.Rd sevenbridges/man/CommandOutputParameter-class.Rd sevenbridges/man/CommandOutputSchema-class.Rd sevenbridges/man/DSCList.Rd sevenbridges/man/Enum.Rd sevenbridges/man/Expression-class.Rd sevenbridges/man/ExpressionTool-class.Rd sevenbridges/man/FS-class.Rd sevenbridges/man/File-class.Rd sevenbridges/man/Files-class.Rd sevenbridges/man/Flow.Rd sevenbridges/man/Folders-class.Rd sevenbridges/man/Handler-class.Rd sevenbridges/man/Item-class.Rd sevenbridges/man/Metadata.Rd sevenbridges/man/Parameter.Rd sevenbridges/man/Process.Rd sevenbridges/man/ProcessRequirement.Rd sevenbridges/man/Schema.Rd sevenbridges/man/TaskHook.Rd sevenbridges/man/Tool-class.Rd sevenbridges/man/ToolUI.Rd sevenbridges/man/Workflow.Rd sevenbridges/man/WorkflowStep.Rd sevenbridges/man/addIdNum.Rd sevenbridges/man/api.Rd sevenbridges/man/as-methods.Rd sevenbridges/man/batch.Rd sevenbridges/man/cli_list_projects.Rd sevenbridges/man/cli_list_tags.Rd sevenbridges/man/cli_upload.Rd sevenbridges/man/convert_app.Rd sevenbridges/man/cwl-utils.Rd sevenbridges/man/delete-methods.Rd sevenbridges/man/download-methods.Rd sevenbridges/man/get_token.Rd sevenbridges/man/get_uploader.Rd sevenbridges/man/input_output_matrix.Rd sevenbridges/man/link.Rd sevenbridges/man/link_what.Rd sevenbridges/man/project_details.Rd sevenbridges/man/project_members.Rd sevenbridges/man/requirements.Rd sevenbridges/man/response-methods.Rd sevenbridges/man/sbg_get_env.Rd sevenbridges/man/sbg_set_env.Rd sevenbridges/man/setListClass.Rd sevenbridges/man/set_test_env.Rd sevenbridges/man/sevenbridges-package.Rd sevenbridges/man/shorthand-cwl.Rd sevenbridges/man/status_check.Rd sevenbridges/man/tag-methods.Rd sevenbridges/man/test_tool_bunny.Rd sevenbridges/man/test_tool_cwlrun.Rd sevenbridges/man/test_tool_rabix.Rd sevenbridges/man/upload_complete_all.Rd sevenbridges/man/upload_complete_part.Rd sevenbridges/man/upload_delete.Rd sevenbridges/man/upload_info.Rd sevenbridges/man/upload_info_part.Rd sevenbridges/man/upload_init.Rd
sevenbridges/tests
sevenbridges/tests/testthat
sevenbridges/tests/testthat.R
sevenbridges/tests/testthat/test-easy-Auth.R
sevenbridges/tests/testthat/test-test_tools.R
sevenbridges/vignettes
sevenbridges/vignettes/api.Rmd
sevenbridges/vignettes/apps.Rmd
sevenbridges/vignettes/bioc-workflow.Rmd
sevenbridges/vignettes/cgc-sparql.Rmd
sevenbridges/vignettes/docker.Rmd
sevenbridges/vignettes/fig
sevenbridges/vignettes/fig/bwa-mem.png
sevenbridges/vignettes/fig/diagram_rnaseq.png
sevenbridges/vignettes/header.html
sevenbridges/vignettes/rstudio.Rmd
sevenbridges/vignettes/sevenbridges.css

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