gxy-wes

A tiny, dependency-light client and command line tool for Galaxy's GA4GH Workflow Execution Service (WES) API. It depends only on requests, so it runs cleanly under uvx and is meant for documentation examples and quick interactive exploration of a Galaxy WES endpoint.

It walks the same flow the Galaxy developer docs describe: discover the service, stage an input dataset, submit a workflow, poll the run, and read outputs and per-task logs.

Scope

This project exists to demonstrate the WES API — it is not meant for production or user-facing applications.

• For user-facing applications, use Planemo.
• For production applications, build on the BioBlend abstractions.

Install

Run it without installing using uv:

$ uvx gxy-wes service-info --galaxy-url http://localhost:8080

Or install it:

$ pip install gxy-wes

Authentication

Every endpoint except service-info needs a Galaxy API key, sent as the x-api-key header. Pass --api-key or set GXY_WES_API_KEY; set the server with --galaxy-url or GXY_WES_URL. Get a key with:

$ curl -s -u you@example.com:password \
    http://localhost:8080/api/authenticate/baseauth

Usage

Each WES endpoint is a subcommand:

$ gxy-wes service-info
$ gxy-wes stage --content $'hello\nworld\n'          # -> {history_id, hda_id}
$ gxy-wes submit --workflow simple.gxwf.yml \
    --params '{"input1": {"src": "hda", "id": "<hda_id>"}}' \
    --engine-parameters '{"history_id": "<history_id>"}'
$ gxy-wes status <run_id>
$ gxy-wes get <run_id>
$ gxy-wes tasks <run_id>
$ gxy-wes task <run_id> 1
$ gxy-wes list
$ gxy-wes cancel <run_id>
$ gxy-wes job-output <job_id> --which stderr

The demo subcommand runs the whole example end to end against a live Galaxy (stage an input, submit the bundled Format2 workflow, poll, print outputs and tasks):

$ export GXY_WES_API_KEY=...
$ uvx gxy-wes demo --galaxy-url http://localhost:8080

As a library

from gxy_wes import WesClient

client = WesClient("http://localhost:8080", api_key="...")
info = client.service_info()
run = client.submit_run(
    workflow_type="gx_workflow_format2",
    workflow_path="simple.gxwf.yml",
    params={"input1": {"src": "hda", "id": hda_id}},
    engine_parameters={"history_id": history_id},
)
status = client.get_run_status(run["run_id"])

Notes

• workflow_type is one of Galaxy's formats: gx_workflow_format2 (Format2 YAML) or gx_workflow_ga (native .ga JSON). It is detected from the workflow content when you pass --workflow.
• WES has no data-staging endpoint; dataset inputs must already exist in Galaxy and are referenced as {"src": "hda", "id": ...}. The stage subcommand uses Galaxy's native API to create those.
• Run success is determined by the WES run state (COMPLETE), not by per-task exit codes — a failed job can be a normal part of a valid workflow.

License

MIT. See LICENSE.