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.
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:
Releases are posted as GitHub releases, or you can install using
pip install --user loopercli
pip install --user --upgrade loopercli
looper executable in not automatically in your
$PATH, add the following line to your
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.