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GA4GH Workflow Execution Service reference implementation

Project description

# Workflow as a Service

This provides client and server implementations of the [GA4GH Workflow Execution Service](https://github.com/ga4gh/workflow-execution-schemas) API for the Common Workflow Language.

It provides an (Arvados)[https://github.com/curoverse/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:

` pip install wes-service `

Run a standalone server with default cwl-runner backend:

` $ wes-server `

Submit a workflow to run:

` $ wes-client --host=localhost:8080 myworkflow.cwl myjob.json `

List workflows:

` $ wes-client --list `

Get workflow status:

` $ wes-client --get <workflow-id> `

Get stderr log from workflow:

` $ wes-client --log <workflow-id> `

# Server Options

## Run a standalone server with Arvados backend:

` $ wes-server --backend=wes_service.arvados_wes `

## Use a different executable with cwl_runner backend

` $ wes-server --backend=wes_service.cwl_runner --opt runner=cwltoil `

## Pass parameters to cwl-runner

` $ wes-server --backend=wes_service.cwl_runner --opt extra=--workDir=/ `

# Client environment options

Set service endpoint:

` $ export WES_API_HOST=localhost:8080 `

Set the value to pass in the Authorization header:

` $ export WES_API_AUTH=my_api_token `

Set the protocol (one of http, https)

` $ export WES_API_PROTO=http `

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