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• Introduction
• Installing the Analysis Automation Server Plugin
• Running analysis automation
  • Configuring user for running analysis automation service
  • Starting and stopping analysis automation service
  • Monitoring analysis automation service
    • Viewing job status and errors
    • Resetting submission statistics
• Configuring analysis automation
  • Managing automation configurations
    • Adding automation configuration
    • Editing automation configuration
    • Deleting automation configuration
    • Multi-configuration operations
    • Importing and exporting configurations
  • Concept definitions
    • Definition of sample completion
    • Definition of sample grouping
    • Definition of wildcards
    • Definition of placeholders
  • Configuration settings
    • Description
    • Enabled
    • Sequencer type
    • Sequencer folder
    • Workflow matcher
    • Sample completion
    • Sample sheet
    • Sample detection delay
    • Filename pattern
    • Files to ignore
    • Workflow
    • Sample types
    • Output folder
    • Export folder
    • Batch folder
    • Output prefix
    • Execution environment
    • Grid preset
    • File system location
    • Cloud preset
    • S3 bucket
• Troubleshooting
  • Accessing log file
  • Issues
    • Samples produced by sequencer were not submitted for analysis
    • Server cannot check if sequencer is done writing sample file to disk
• System requirements
  • Linux and macOS
    • Support for checking if sequencer is done writing sample file to disk
  • Windows
    • Path length limit

Starting and stopping analysis automation service

Note: Make sure that samples matching the enabled automation configurations are not in the process of being produced when starting the analysis automation service as this could lead to inconsistencies in the selection of sample files submitted for analysis.

The analysis automation service starts a sample submitter for each of the enabled automation configurations. The service can be turned on and off using the ON/OFF switch. The service must be manually started again after each restart of the CLC Genomics Server.

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