Welcome to the eHive user manual
This manual describes how to run, develop, and troubleshoot eHive pipelines. It describes eHive’s “swarm of autonomous agents” paradigm, shows how different components work together, and provides code examples. There are also links to API documentation for eHive classes.
The code is open source, and available on GitHub.
The main documentation for eHive is organized into a couple sections:
User documentation
Quickstart
- Installation and setup
- Quick start guide
- Tips (cheat-sheet)
- Quick “Rules” for writing hive pipelines
- Debugging
- Running a pipeline
- Writing a RunnableDB
- Writing a Runnable
- Creating your own input ids
- Dataflow betweeen analyses
- Using semaphore (funnels)
- Creating a pipeline configuration
- Creating a configuration file
- Parameters and command line
- Deleting databases you create in your pipeline
- Naming your databases
- Getting blast parameters
- Generating the pipeline diagram
- Worker lifespan
- input id template
- Pipeline wide parameters
- Input ids
- SystemCmd
- Substitution
- Crazy substitution with #expr()expr#
- Using customised tables
- Required parameters
- Checking the parameter is defined
- GuiHive
Walkthrough
Running pipelines
- Initialising pipelines
- Running a pipeline and running Jobs
- Tools for monitoring your pipeline
- Tools and techniques for managing running pipelines
- Changing and viewing pipeline configuration
- Error Recovery
- Troubleshooting
Creating pipelines
Creating runnables
Advanced usage
External plugins
Developer documentation
Developer documentation