pepkit / hello_looper

A Hello World! example repository for looper

Hello World! example for looper

Looper is a pipeline submission engine (see source code and documentation). This repository demonstrates how to install looper and use it to run the included pipeline using PEP project.

This repository contains:

1. A functional, basic example of a looper config file.
2. A pipeline_pipestat directory, specifically for configuring Looper to work with Pipestat
3. An example PEP project (in /project)
4. A looper-compatible pipeline (in /pipeline) that can run on that project.

Documentation for running the above examples can be found here: Looper: Hello World

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❗ This repository is compatible with looper>=v1.5.0. In earlier versions, looper configuration was specified inside the PEP config. The old looper configuration examples can be found under /old_specification.

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Quickstart

1. Install the latest version of looper (requires looper>=1.5.0):

pip install --user --upgrade looper

2. Download and unzip this repository

wget https://github.com/pepkit/hello_looper/archive/master.zip
unzip master.zip

3. Run it:

cd hello_looper

looper run --looper-config .looper.yaml

More information

• Full looper documentation at Read the Docs: http://looper.databio.org
• Detailed description of PEP project format: http://pep.databio.org
• Find fully functional pipelines on the list of looper compatible pipelines.
• More example PEP projects: https://github.com/pepkit/example_peps