a pipeline submitting engine

PEP compatible

What is looper?

Looper is a pipeline submitting engine. Looper deploys any command-line pipeline for each sample in a project organized in standard PEP format. You can think of looper as providing a single user interface to running, summarizing, monitoring, and otherwise managing all of your sample-intensive research projects the same way, regardless of data type or pipeline used.

What makes looper better?

Looper's key strength is that it decouples job handling from the pipeline process. In a typical pipeline, job handling (managing how individual jobs are submitted to a cluster) is delicately intertwined with actual pipeline commands (running the actual code for a single compute job). The looper approach is modular, following the the unix principle: looper only manages job submission. This approach leads to several advantages compared with the traditional integrated approach:

  1. running a pipeline on just one or two samples/jobs is simpler, and does not require a full-blown distributed compute environment.
  2. pipelines do not need to independently re-implement job handling code, which is shared.
  3. every project uses a universal structure (expected folders, file names, and sample annotation format), so datasets can more easily move from one pipeline to another.
  4. users must learn only a single interface that works with any of their projects for any pipeline.

Installing

Releases are posted as GitHub releases, or you can install using pip:

pip install --user loopercli

Update with:

pip install --user --upgrade loopercli

If the looper executable in not automatically in your $PATH, add the following line to your .bashrc or .profile:

export PATH=~/.local/bin:$PATH

Quick start

To test looper, follow the Hello Looper example repository to run your first looper project:

# download and unzip the hello_looper repository
wget https://github.com/databio/hello_looper/archive/master.zip
unzip master.zip

# Run looper:
cd hello_looper-master
looper run project/project_config.yaml

Detailed explanation of results is in the Hello world tutorial.