============= CGATReport

CGATReport is a report generator that is implemented as an extension to sphinx_.

Its purpose is to facilitate writing scientific reports interpreting large and changing datasets. It is designed to assist the iterative analysis during the development of a computational scientific pipeline as understanding of the data grows. Once the pipeline settles down, CGATReport permits an easy transition towards the automatic report generation needed when the pipeline is run on new data sets.

CGATReport is easy to use and powerful enough to give all the flexibility needed during the development of computational pipelines and robustness during the production use of a pipeline. It is intended for developers and computational scientists with python_ scripting experience.

CGATReport comes with all the batteries included thanks to python_ and sphinx_, in particular, it

• uses simple markup in the form of restructured text_,
• supports both automated and narrative analysis,
• keeps code, data and text together,
• takes care of indexing and formatting to produce something presentable,
• links with ipython_ notebooks
• produces static html, latex, ps and pdf.

Documentation

Documentation is available here <https://www.cgat.org/downloads/public/CGATReport/documentation>_.

Some quick links are below:

• Contents <https://www.cgat.org/downloads/public/CGATReport/documentation/contents.html>_
• Tutorials <https://www.cgat.org/downloads/public/CGATReport/documentation/Tutorials.html>_
• Reference <https://www.cgat.org/downloads/public/CGATReport/documentation/Reference.html>_

Installation

CGATReport is available on pypi_, to install, type::

pip install CGATReport

CGATReport is under active development, the lastest development snapshot can be found ot github_::

git clone [email protected]:AndreasHeger/CGATReport.git

.. _ipython: http://ipython.org/notebook.html .. _python: http://www.python.org .. _pypi: http://pypi.python.org/pypi/CGATReport .. _github: https://github.com/AndreasHeger/CGATReport .. _restructured text: http://docutils.sourceforge.net/rst.html .. _sphinx: http://sphinx-doc.org/