Looper is a pipeline submission engine that parses sample inputs and submits pipelines for each sample. Looper was conceived to use pypiper pipelines, but does not require this.
You can download the latest version from the releases page.
You can find a list of pre-built pipelines in the hello looper! repository.
- Documentation: Read the Docs
- Source code: http://github.com/epigen/looper
Instructions for installation, usage, tutorials, and advanced options are available in the Read the Docs documentation, and that's the best place to start. To get running quickly, you can install the latest release and put the looper executable in your $PATH:
pip install https://github.com/epigen/looper/zipball/master
export PATH=$PATH:~/.local/bin
Looper supports Python 2.7 only and has been tested only in Linux. To use looper with your project, you must define your project using Looper’s standard project definition format, which is a yaml config file passed as an argument to looper:
looper run project_config.yaml-
After adding tests in
testsfor a new feature or a bug fix, please run the test suite. -
To do so, the only additional dependencies needed beyond those for the package can be installed with:
pip install -r requirements/requirements-dev.txt -
Once those are installed, the tests can be run with
pytest. Alternatively,python setup.py testcan be used.