Install and run PEPPRO

We provide several methods to setup PEPPRO. A fundamental challenge of any complex pipeline is that they rely on many independent tools. Installing all of these from scratch can be a chore, although the common use of many of the required bioinformatic tools means they are likely to already be available on an HPC or server. Installation can also be addressed through the use of containers, although that requires setting up and learning to use containers. No single approach appears to resolve all challenges for all users, but we've done our best to provide various ways to ease setup as much as possible.

  1. Run the pipeline using the multi-container environment manager, bulker.
  2. Run the pipeline using a single, monolithic container.
  3. Run the pipeline in a conda environment.
  4. Run the pipeline natively.

Confirm installation

After setting up your environment to run PEPPRO, you can confirm which means of running the pipeline are now executable using the included checkinstall script. This can either be run directly from the peppro/ repository:


or from the web:

curl -sSL | bash