Welcome to APE’s documentation!

APE (Automated Pipeline Explorer) is a command line tool and Java 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! 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.

Relevant links

• APE GitHub

• RESTful APE

• Use cases

Web platforms using APE: - Workflomics - APE Web

Contents

Basics

• Introduction to APE
  • About APE
  • Credits
  • License
  • Maven dependencies
  • Contributors
  • References
• Getting Started with APE
  • My first APE run
• Install
  • Requirements
  • Releases
  • Add APE to your project
  • Build APE from source (using Maven)

APE Specifications

• APE Setup
  • Configuration file
  • Domain Model
  • Tool Annotations
  • CWL Annotations
  • Constraints File
• APE as a Java Library
  • Run APE from a Java environment
  • APE API functions
  • APE as a Web plug-in
• APE as a Command Line Tool
  • Run APE from the Command Line

Use cases and Demos

• Overview
• ImageMagick
  • Domain Model
  • Example 1
  • Example 2
• GEO GMT (Generic Mapping Tools)
  • E0 - Initial Workflow
  • E1 - Additional Constraints
  • Domain Model
  • References
• Mass spectronomy-based proteomics
  • No 1

RESTful APE

• Introduction to RESTful APE
  • About RESTful APE
  • License
  • Contributors
• Getting Started with RESTful APE
  • Setting Up Your Environment
  • Making Your First Request
  • Exploring the OpenAPI Documentation
  • Next Steps
• Overview of RESTful APE API
  • Index
  • Data Taxonomy
  • Tools Taxonomy
  • Constraints
  • Run Workflow Synthesis
  • Run Synthesis and Benchmarks
  • Retrieve Workflow Image
  • Retrieve CWL File
  • Retrieve CWL Input File
  • Retrieve Design-Time Benchmarks
  • Retrieve CWL Files as ZIP

APE Web

• Introduction to APE Web
  • About APE Web
  • License
  • Dependencies
  • Contributors
• Setup
  • Requirements
  • Configuration
  • Docker setup
  • Manual setup