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

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

Author
Nan Xiao [aut, cre], Dusan Randjelovic [aut], Emile Young [ctb], Tengfei Yin [aut], Seven Bridges Genomics [cph]
Date of publication
None
Maintainer
Nan Xiao <nan.xiao@sbgenomics.com>
License
Apache License 2.0 | file LICENSE
Version
1.4.4
URLs

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
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
Handler-class
Handler instance
Item-class
Class Item
link
link two nodes to form a new Workflow
link_what
List possible linking methods
Metadata
Meta schema
misc_get_token
Opens web browser to copy the auth token
misc_get_uploader
Download SBG uploader and extract to a specified directory
misc_make_metadata
Specify the parameters of the file metadata and return a...
misc_upload_cli
Upload files using SBG uploader
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
Schema
SchemaList
setListClass
List Class generator.
set_test_env
Set testing env
sevenbridges-package
R Client for Seven Bridges Platform API and CWL Tool Builder...
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

Files in this package

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.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/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/convert_app.Rd
sevenbridges/man/cwl-utils.Rd
sevenbridges/man/delete-methods.Rd
sevenbridges/man/download-methods.Rd
sevenbridges/man/link.Rd
sevenbridges/man/link_what.Rd
sevenbridges/man/misc_get_token.Rd
sevenbridges/man/misc_get_uploader.Rd
sevenbridges/man/misc_make_metadata.Rd
sevenbridges/man/misc_upload_cli.Rd
sevenbridges/man/project_details.Rd
sevenbridges/man/project_members.Rd
sevenbridges/man/requirements.Rd
sevenbridges/man/response-methods.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/rstudio.Rmd