• Why isn’t the looper executable in my path?
    By default, Python packages are installed to ~/.local/bin. You can add this location to your path by appending it (export PATH=$PATH:~/.local/bin). See discussion about this issue here: https://github.com/epigen/looper/issues/8
  • How can I run my jobs on a cluster?
    See cluster resource managers.
  • Which configuration file has which settings?
    Here’s a list: config files
  • What’s the difference between looper and pypiper?
    Pypiper and Looper work together as a comprehensive pipeline management system. Pypiper builds individual, single-sample pipelines that can be run one sample at a time. Looper then processes groups of samples, submitting appropriate pipelines to a cluster or server. The two projects are independent and can be used separately, but they are most powerful when combined.
  • Why isn’t looper submitting my pipeline: Not submitting, flag found: ['*_completed.flag']?
    When using looper run, looper first checks the sample output directly for flag files for each sample (which can be _completed.flag, or _running.flag, or _failed.flag). Typically, we don’t want to resubmit a job that’s already running or already finished, so by default, looper will not submit a job when it finds a flag file. This is what the message above is indicating. If you do in fact want to re-rerun a sample (maybe you’ve updated the pipeline, or you want to run restart a failed attempt), you can do so by just passing --ignore-flags to looper at startup. This will skip the flag check for all samples. If you only want to re-run or restart a few samples, it’s best to just delete the flag files for the samples you want to restart.