Platform API Middle-Layer (PAML)

PAML(Platform API Middle-Layer) is an installable Python package to enable anyone to (easily) write cross-platform launchers. It is used to abstract the specifics of a platform from workflow orchestration. This abstraction of the platform layer enables the orchestration component to be platform independent to support interoperability.

Contents

• Features
• Usage
  • Initial setup
• Versioning
• FAQ
• Contributing

Features

Multiple supported platforms

• Arvados
• SevenBridges
• NGS360 (via the GA4GH WES API)

Usage

Initial setup

1. Create a virtual environment that your launcher will use

   python3 -m venv env
   source env/bin/activate
   

2. Install this package in your virtual environment

   pip install git+https://github.com/NGS360/PAML.git@<tag>#egg=cwl_platform
   

   where <tag> is a release tag such as v0.5.3, listed on the releases page. The v is part of the tag name and is required - @0.5.3 does not resolve to anything.

   Alternatively, if you've cloned this repo and want to install from source,

   pip install .
   

3. Develop Launcher

   Follow ExampleLauncher as an example

Versioning

PAML follows Semantic Versioning. A release is a git tag of the form vMAJOR.MINOR.PATCH, and the package version is derived from that tag, so an installed build always reports where it came from:

import cwl_platform
print(cwl_platform.__version__)

• PATCH (v0.5.1 to v0.5.2) - bug fixes and backwards-compatible changes
• MINOR (v0.5.2 to v0.6.0) - new backwards-compatible functionality
• MAJOR (v0.6.0 to v1.0.0) - breaking changes

The version is below 1.0.0, so the API is not yet stable. SemVer permits a 0.x minor release to break compatibility, so pin an exact tag rather than tracking a branch, and check the CHANGELOG before upgrading.

A few tags predating this convention have only two components (v0.5, for example). They are left as they are, because moving a published tag would break anyone already pinned to it.

See RELEASE_PROCESS.md for how releases are made.

FAQ

This repo hasn't been around long enough to earn a FAQ!

Contributing

Contributions are always welcome!

If you find a bug 🐛, please open a bug report.

If you have an idea for an improvement or new feature 🚀, please open a feature request.

Acknowledgements

• Maggie Chen
• Steve Vasquez-Grinnell