Skip to main content

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
wes_service-2.9-py2-none-any.whl (28.1 kB) Copy SHA256 hash SHA256 Wheel py2
wes-service-2.9.tar.gz (22.8 kB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page