Clarity LIMS
Illumina Connected Software
Clarity LIMS v6.3 & Lablink v2.5
Clarity LIMS v6.3 & Lablink v2.5
  • Release Notes Clarity LIMS v6.3
    • Release Notes Clarity LIMS v6.3.1
    • Release Notes Clarity LIMS v6.3.0
  • Technical Overview
    • Technical Requirements
  • Installation
    • Installation Procedure
    • Guide to Secret Management
    • Install/Upgrade Secret Management for Integration Modules
    • Change the Clarity LIMS Hostname
    • Update Server Passwords and Database Connection Details
  • On-Premise Deployments
    • Pre-installation Requirements
      • Install a Purchased SSL/TLS Certificate
      • Configure Your HashiCorp Vault
    • On Premise to On Premise Upgrade Procedures
    • On Premise to On Premise In-place Upgrade Procedures
    • On Premise to Hosted Upgrade Procedures
    • Hosted to On Premise Upgrade Procedures
  • Administration
    • Database Cleanup Procedure
    • Backup and Restore Procedure
    • Receiving and Decrypting Cloud Backup Data
    • LDAP Integration
      • Using the LDAP Checker Tool
    • Illumina Connected Software Platform Integration
    • Clarity LIMS Log Files
    • Customize the Term Used for Projects
    • Enforcing Unique Sample Names Within a Project
    • Container Name Uniqueness
    • Configure Electronic Signatures
    • Creating Enrypted Passwords
    • Config Slicer Tool
      • Managing Configurations with Config Slicer
      • Upgrading a configuration package/manifest file for compatibility with Config Slicer v3.0.x
      • Config Slicer Use Cases
      • Troubleshooting Config Slicer
    • Audit Trail
      • Enabling, Validating and Disabling Audit Trail
    • System Settings
    • Automation Worker Nodes
      • Troubleshooting Automation Worker
  • Clarity LIMS v6.3 Reference Guide
    • Dashboards
      • Overview Dashboard
      • Projects Dashboard
    • Projects and Samples
      • Projects
      • Samples Accessioning
        • Sample List for Batch Import
        • Guidelines and Tips for Batch Sample Import
      • Assign and Process Samples
    • Lab View
      • Requeue and Rework Samples
      • Storing Sample Aliquots for Later Use
      • Modifying Completed Step Details
      • Alert Notifications
    • Configuration
      • Lab Work
        • Steps and Master Steps
          • Step Milestones
          • Derived Sample Naming Convention Tokens
        • Protocols
        • Workflows
      • Consumables
        • Reagents
          • Reagent Kit Lot Manifest for Batch Import
        • Controls
        • Instruments
        • Labels
        • Containers
      • Custom Fields
      • User Management
        • Manage User Access
        • User Roles
        • Configured Role-Based Permissions
        • User and Profile Page
      • Automations
        • Automation Trigger Configuration
        • Copy Custom Fields from Step Input to Output
        • Template Files Associated With Automations
    • Automated Quality Control
      • Configure a QC System
    • Search
      • Basic Search
      • Advanced Search
    • Genealogy View
    • System Performance
      • Queue Performance and Usability
      • Demultiplexing API Endpoint Performance
    • Terms and Definitions
  • LabLink v2.5 Reference Guide
    • Project
      • Email Notifications for Notes
    • Resource Materials & Contact Us
    • Users
    • Configuration
    • Publishing Files and Progress
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  1. Administration
  2. Config Slicer Tool

Config Slicer Use Cases

Create a Configuration Package File for Import to Another System (or for Backup Purposes)

Use a configuration package file to copy a configuration set from one server to another or to back up a particular working configuration at a particular time.

Required steps:

  1. Create a configuration manifest file.

  2. Export to configuration package file.

Import (install) a Configuration Package File on a Production or Test Server

This process involves copying a configuration set from one server to another, by importing a configuration package file.

For example, to move a configuration set to a different environment for testing or troubleshooting purposes, or copy a new configuration set (created and tested on one system) onto another system.

Required steps:

  1. On the source server, create a configuration manifest file, and then export to configuration package file.

  2. On the destination server, import the configuration package file.

Compare Differences between a Working Configuration and a Broken Configuration

There are two approaches:

  • Comparing configuration manifest files provides a way to determine if there are processes or UDFs missing from a system. The information in the manifest files only allows comparing process and UDF names, not the specific way in which a process or UDF is configured.

  • Comparing configuration package files helps check how specific processes are configured. If the systems being compared are meant to be identical, this method is more appropriate to use.

Required steps:

  1. On each system, create a configuration manifest file, or a configuration package file.

  2. Run a diff comparison on the two files.

  3. Edit the broken manifest file, export it, and import the resulting configuration package file into the system to add the missing entities.

There are several tools that available to compare files:

  • Meld (graphical), for Linux, port to MacOS

  • Standard Unix diff (Linux, MacOS) (use -q for a quick check).

  • FileMerge (OSX with XCode installed) - /Developer/Applications/Utilities/FileMerge.app

Merge the Configuration Sets from Multiple Test Systems to a Production System

Combine configuration sets from multiple systems, merge them into a single configuration package file, and then import the file into a new system.

Required steps:

  1. On each source server, create and edit a configuration manifest file.

  2. Merge the entities from all files into a single manifest file.

  3. Export the resulting file to a configuration package file.

  4. On the destination server, import the merged configuration package file.

Back up and Restore a Configuration Set

Copy a configuration set to restore it on another server and use it for testing/troubleshooting purposes.

Required steps:

  1. On the server containing the 'broken' source system, create a full manifest file, containing all of the LIMS system configuration.

  2. Export the manifest to a configuration package file. Save file to media/disk.

  3. On the target server, import the configuration package file created on the source system.

Back up and Upgrade a Configuration Set

To upgrade or add to a configuration set already installed on a server, two configuration package files are needed: one to back up the working configuration set and one containing the new updated configuration that have been created on a test server.

Required steps:

  1. On the server you want to upgrade, create a full manifest file and export this to a configuration package file. Save this file as a backup.

  2. On the test server, create a manifest file and edit it so that it only includes the entities you want to import.

  3. On the server you want to upgrade, import the configuration package file.

Deploy a New Configuration Set from Test to Production Server

You may want to take a configuration that has been created and tested on one system/site (referred to as the source system in the steps below), and deploy it on another system/site (destination system).

Take a configuration that has been created and tested on one system/site (referred to as the source system in the following steps) and deploy it on another system/site (destination system).

As a best practice, make sure that the configuration is backed up by creating a full manifest file and exporting to a configuration package file (see Step 2). The process is also described in Back up and Restore a Configuration Set.

Required steps:

  1. On the source system, create a configuration package file containing the tested configuration to import.

  2. On the destination system, create a full manifest file and export this to a configuration package file. Save this file as a backup.

  3. On the destination system, import the configuration package file that was created in step 1.

PreviousUpgrading a configuration package/manifest file for compatibility with Config Slicer v3.0.xNextTroubleshooting Config Slicer

Last updated 9 months ago

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WinMerge (graphical), for Windows -

http://winmerge.org/