GA4GH CWL Task Execution

cwl-tes submits your tasks to a TES server. Task submission is parallelized when possible.

Funnel is an implementation of the GA4GH task execution API. It runs your dockerized tasks on slurm, htcondor, google compute engine, aws batch, etc.

Requirements

• Python 2.7 / 3.5 / 3.6

• Docker

• Funnel

Quickstart

• Start the task server

funnel server run

• Run your CWL tool/workflow

cwl-tes --tes http://localhost:8000 tests/hashsplitter-workflow.cwl.yml --input tests/resources/test.txt

Install

I strongly recommend using a virtualenv for installation since cwl-tes depends on a specific version of cwltool.

Install from pip:

pip install cwl-tes

Install from source:

python setup.py install

Run the v1.0 conformance tests

To start a funnel server instance automatically and run all of the tests, install tox and run it

$ pip install tox
$ tox

For running only the conformance tests in python 2.7:

$ tox -e py27-unit

In a similar way they can be run on any supported python interpreter.

A more manual approach:

Download the conformance tests:

git submodule update --init --recursive

Start the funnel server.

funnel server --config /path/to/config.yaml

Make sure that TMPDIR is specified in the AllowedDirs of your Local storage configuration.

To run all the tests:

./tests/run_conformance.sh

To run a specifc test:

./tests/run_conformance.sh 10