GA4GH Workflow Execution Service reference implementation
Project description
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:
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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