eHive user manual
master

Quickstart

  • Installation and setup
  • Quick start guide
  • Tips (cheat-sheet)

Walkthrough

  • Long Multiplication pipeline 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

  • PipeConfig Files
  • Dataflows
  • Semaphores and other tools to sequence Job execution
  • Accumulators
  • Job parameters
  • Meadows and Resource Classes
  • Standard library of Runnables

Creating runnables

  • Runnables Overview
  • Runnable API
  • IO and Error Handling in Runnables

Advanced usage

  • How to use MPI
  • How to report to Slack
  • Continuously running pipelines
  • Serialising dataflow events with JSON

External plugins

  • Other job schedulers
  • Docker Swarm

Appendix

  • Presentations & Workshop materials
  • Analyses pattern syntax
  • Scripts options quick reference
    • Execution
      • beekeeper
      • init_pipeline
      • seed_pipeline
    • Debugging
      • db_cmd
      • hoover_pipeline
      • runWorker
      • standaloneJob
      • tweak_pipeline
    • Reporting
      • generate_graph
      • generate_timeline
      • load_resource_usage
      • visualize_jobs
  • Schema diagram
  • Table list
  • API Documentation
  • Changelog

Developer documentation

  • eHive development in a nutshell
  • Checklist to release a new eHive version
  • Other repos
  • Build the documentation
eHive user manual
  • Docs »
  • Scripts options quick reference
  • Edit on GitHub

Scripts options quick reference¶

Execution¶

  • beekeeper
  • init_pipeline
  • seed_pipeline

Debugging¶

  • db_cmd
  • hoover_pipeline
  • runWorker
  • standaloneJob
  • tweak_pipeline

Reporting¶

  • generate_graph
  • generate_timeline
  • load_resource_usage
  • visualize_jobs
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© Copyright [2016-2022] EMBL-European Bioinformatics Institute Revision 3a4ed746.

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