wes-service

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