sevenbridges: Seven Bridges Platform API Client and CWL 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@sbgenomics.com>
LicenseApache License 2.0 | file LICENSE
Version1.4.5
http://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

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

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

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-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/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/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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