Config Slicer Tool

The Config Slicer tool is used to move small incremental configuration changes, contained in a configuration set, between Clarity LIMS systems. For example, it moves changes between a test system and a production system.

This configuration tool provides granular export/import functionality that allows the management of configurations that support experimental workflows.

Use this tool to back up, copy, deploy, and restore configuration sets. By making small incremental changes, make sure that the modifications made to the production system are minimal.

Review the following key concepts:

• Configuration set—This item may be created by the Illumina Support team or by the customer. It comprises the items (know as entities) that are added to a Clarity LIMS system to allow for customization for a particular scientific experiment or workflow. The Illumina NGS Extensions Package is a good example. See Supported Entities.

• Configuration manifest file—This text file determines the configuration set to be exported from a system. The manifest file does not contain the actual configuration data. It only drives the extraction of configuration from a system.

• Configuration package file—This XML file contains the top-level entities selected by the configuration manifest file, plus any related child entities. For example, for process types, it includes process type UDFs, process templates (protocols), and output UDFs.

Config Slicer tool Export/Import Process Overview

The Config Slicer tool uses an export/import process to transfer configuration sets from a source to a destination server. This process breaks down into the following tasks:

1. On the source Clarity LIMS server, use the Config Slicer tool to create a configuration manifest file.

2. Edit the manifest file so that only the required custom configuration set is preserved.

3. Use the Config Slicer tool to export the edited manifest file to a configuration package file.

4. On the destination Clarity LIMS server, use the Config Slicer tool to import the configuration package file into the system.

A configuration package file can be imported into multiple systems. Use this feature to create and import multiple custom configuration sets, such as the Illumina TruSeq integration. This functionality also provides the Illumina Support team with a scalable way to keep up with constantly changing protocols.

Supported Entities

A configuration set comprises the entities added to a Clarity LIMS system that allow for customization of the system for a particular scientific experiment or workflow. The following entities are currently supported by the Config Slicer tool:

• Sample UDFs and UDTs

• Container UDFs and UDTs

• Project UDFs and UDTs

• Artifact groups (experiments)

• Reagent types

• Control types

• Reagent kits

• Process types (any configured processes – for example, Pool Samples and Add Multiple Reagents)

  • Process UDFs and UDTs

  • Output UDFs

• Process templates - UDFs, UDTs, and parameter strings only (other entities such as instruments and researchers are not supported)

• Protocols

• Workflows

When performing custom manifest generation by workflow, protocol, or process type, the following entities are not exported: Sample, Container, Project UDTs, and UDFs for Project. Account (Lab) and Client (Researcher) UDFs are never exported by config slicer. These are known issues.

Config Slicer does not export/import nonstep automation, nor does it preserve the order of protocols.

Tools and requirements

When working with Config Slicer on the Clarity LIMS application server, there are no additional prerequisites. The latest version of the config-slicer.jar file is installed as part of Clarity LIMS on the Clarity LIMS server. In a default installation, find the file in the following location:

Copy

/opt/gls/clarity/tools/config-slicer 

To work with Config Slicer on a machine other than the Clarity LIMS server, do the following:

1. Make sure that Java is installed.

2. Copy the /opt/gls/clarity/tools/config-slicer directory, and its contents, from the Clarity LIMS server to the machine. The config-slicer directory and the config-slicer package should contain the following:

   • config-slicer-<version>.jar

   • libs subdirectory (which includes all the libraries referenced by config-slicer-<version>.jar, including groovy-all-2.4.8.jar)

   • upgrade-config-slice.jar