semvec/pypi-packages huggingface dataset:
cwl-tes 0.3.0
Common workflow language reference implementation backended     by a GA4GH Task Execution Service
License: Apache 2.0
Requires Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4

[![Build Status](https://travis-ci.org/ohsu-comp-bio/cwl-tes.svg?branch=master)](https://travis-ci.org/ohsu-comp-bio/cwl-tes)
[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

# GA4GH CWL Task Execution

___cwl-tes___ submits your tasks to a TES server. Task submission is parallelized when possible.

[Funnel](https://ohsu-comp-bio.github.io/funnel) is an implementation of the [GA4GH task execution API](https://github.com/ga4gh/task-execution-schemas). It runs your dockerized tasks on slurm, htcondor, google compute engine, aws batch, etc.


## Requirements

* Python 2.7 / 3.5 / 3.6

* [Docker](https://docs.docker.com/)

* [Funnel](https://ohsu-comp-bio.github.io/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](https://virtualenv.pypa.io/en/stable/#) 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](https://github.com/tox-dev/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
```