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looper is a command-line job submitting engine. It's the glue that connects your PEP project to command-line pipelines. It can work with any pipeline that takes command-line arguments. It also provides a flexible template system so that it can work with either local compute power or a cluster (using any resource manager, e.g. SLURM, LFS, SGE, etc.). looper makes it easy to run any kind of command-line tool serially across all the samples in your project. looper is not a pipeline workflow engine, which is used to build pipelines; it assumes you already have pipelines built, and it helps you map samples to those pipelines.

We provide a suite of already-built pipelines for ease-of-use, but you can configure it to work with just about anything. You have complete control.

Code and documentation

Quick start

Install with

pip install

Once your PEP project and your pipelines are configured, you run your samples through looper with this command:

looper run project_config.yaml

That command will parse your PEP samples, and build jobs for each one. It’s scalable: by default, it runs your jobs sequentially on the local computer, but with a small configuration change, it will create and submit jobs to any cluster resource manager (like SLURM, SGE, or LFS).

To check on your running jobs, you run:

looper check project_config.yaml

To summarize the statistics of all the pipeline runs, you type:

looper summarize project_config.yaml

Looper pipelines

Here is a list of publicly available looper-compatible pipelines

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