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.
- Public-facing permalink: http://databio.org/looper
- Documentation: Read the Docs
- Source code: http://github.com/epigen/looper
Looper supports Python 2.7 only and has been tested only in Linux.
pip install https://github.com/epigen/looper/zipball/master
To have the looper executable in your $PATH, add the following line to your .bashrc file:
export PATH=$PATH:~/.local/bin
Looper just requires a yaml format config file passed as an argument, which contains all the settings required. This can, for example, submit each job to SLURM (or SGE, or run them locally).
looper run project_config.yamlLooper can do more than just run your samples through pipelines. Once a pipeline has been run (or is running), you can do some post-processing on the results. These commands help with monitoring running pipelines, summarizing pipeline outputs, etc. This includes looper clean, looper destroy, looper summarize, and more. You can find details about these in the Commands section of the documentation.