Metadata-Version: 2.1
Name: cwl-tes
Version: 0.3.0
Summary: Common workflow language reference implementation backended     by a GA4GH Task Execution Service
Home-page: https://github.com/common-workflow-language/cwl-tes
Author: Adam Struck
Author-email: strucka@ohsu.edu
License: Apache 2.0
Description: [![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
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4
Description-Content-Type: text/markdown
Provides-Extra: test
