Welcome to APE’s documentation!
===============================

`APE (Automated Pipeline Explorer) <https://github.com/sanctuuary/APE>`_ is a library (available as CLI, Java API and a RESTful API) for the automated exploration of possible computational pipelines (scientific workflows) from large collections of computational tools. It also comes with a RESTful API interface. APE was originally developed at Utrecht University and is now maintained by the Netherlands eScience Center.



.. note:: The APE team can always use your feedback and help to
          improve the tutorials and class references. If
          you don't understand something, or cannot find what you
          are looking for in the docs, help us make the documentation better
          by submitting an issue or pull request on the  `GitHub repository
          <https://github.com/sanctuuary/APE/issues>`_!
          We welcome contributions (bug reports, bug fixes, feature requests, extensions,
          use cases, etc.) to APE. Please get in touch with
          Vedran Kasalica (v.kasalica[at]esciencecenter.nl) if you have any questions regarding
          your contribution. We expect all contributors to follow our
          `Code of Conduct <https://github.com/sanctuuary/APE/blob/master/CODE_OF_CONDUCT.md>`_.

Relevant links
==============

- `APE GitHub <https://github.com/sanctuuary/ape>`_
- `RESTful APE <https://github.com/sanctuuary/restape>`_

- `Use cases <https://github.com/sanctuuary/APE_UseCases>`_

Web platforms using APE:

- `Workflomics <https://github.com/Workflomics/workflomics-frontend>`_

Contents
========

.. example: docs/basics/ape-introduction references to ./docs/basics/ape-introduction.rst

.. toctree::
   :maxdepth: 2
   :caption: Getting Started

   docs/basics/ape-introduction
   docs/basics/gettingstarted

.. toctree::
   :maxdepth: 2
   :caption: Configure APE

   docs/specifications/domain
   docs/specifications/constraints

.. toctree::
   :maxdepth: 2
   :caption: Using APE

   docs/developers/install
   docs/developers/java
   docs/developers/cli
   docs/developers/developers

.. toctree::
   :maxdepth: 2
   :caption: RESTful APE

   docs/restful-ape/introduction
   docs/restful-ape/gettingstarted
   docs/restful-ape/restful-api


.. toctree::
   :maxdepth: 2
   :caption: Use cases and Demos

   docs/demo/demo-overview
   docs/demo/imagemagick/imagemagick
   docs/demo/geo_gmt/geo_gmt
   docs/demo/massspectrometry/massspectrometry

.. toctree::
   :maxdepth: 2
   :caption: APE Web

   docs/ape-web/introduction
   docs/ape-web/setup