common-workflow-language/workflow-service

Name: workflow-service

Owner: Common Workflow Language

Description: null

Created: 2015-09-16 05:06:55.0

Updated: 2017-12-13 02:46:33.0

Pushed: 2018-01-03 20:20:00.0

Homepage: null

Size: 47

Language: Python

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README

Workflow as a Service

This provides client and server implementations of the GA4GH Workflow Execution Service API for the Common Workflow Language.

It provides an Arvados backend. It also works with any cwl-runner that supports the CWL standard command line interface: http://www.commonwl.org/v1.0/CommandLineTool.html#Executing_CWL_documents_as_scripts

Installation:

install wes-service

Run a standalone server with default cwl-runner backend:

s-server

Submit a workflow to run:

s-client --host=localhost:8080 myworkflow.cwl myjob.json

List workflows:

s-client --list

Get workflow status:

s-client --get <workflow-id>

Get stderr log from workflow:

s-client --log <workflow-id>

Server Options

Run a standalone server with Arvados backend:

s-server --backend=wes_service.arvados_wes

Use a different executable with cwl_runner backend

s-server --backend=wes_service.cwl_runner --opt runner=cwltoil

Pass parameters to cwl-runner

s-server --backend=wes_service.cwl_runner --opt extra=--workDir=/

Client environment options

Set service endpoint:

port WES_API_HOST=localhost:8080

Set the value to pass in the Authorization header:

port WES_API_AUTH=my_api_token

Set the protocol (one of http, https)

port WES_API_PROTO=http