PEPPRO is a pipeline designed to process PRO-seq (and GRO-seq) data. For more information see: http://peppro.databio.org/

Install

pip install piper pipestat looper

Note: The pypiper PyPI package is piper (not pypiper, which is an unrelated package).

Testing

Unit tests need no special setup:

pytest tests/test_unit.py -v

Integration tests require bioinformatics tools via bulker. Use the wrapper script:

bash tests/scripts/test-integration.sh

This runs bulker exec databio/peppro:1.1.0 to provide samtools, bowtie2, bedtools, etc. Do NOT run integration tests without bulker — they will fail with missing tools.

Docs

Develop docs with:

mkdocs serve -f mkdocs.yml

Build and deploy with:

mkdocs build -f mkdocs.yml -d $CODEBASE/code.databio.org/peppro

Contributing

Pull requests welcome. Active development should occur in a development or feature branch.

Contributors

• Jason Smith, jasonsmith@virginia.edu
• Michael Guertin, mjg7y@virginia.edu
• Nathan Sheffield, nathan@code.databio.org
• Others... (add your name)