Applying Indexing Patterns to Containers Automatically

The indexing of samples is often performed in patterns, based upon the location of the samples in the container.

This example shows how to automate the default placing of reagents on samples, based on their container position. This greatly reduces the amount of time spent on the Add Labels screen (LIMS v6.x) and also reduces user error.

In this example, reagent labels are assigned to samples in a predetermined pattern as the user enters the Add Reagents screen. This pattern is applied to all containers entering this stage.

Solution

The example AssignIndexPattern.groovy script is configured to run on the Adenylate Ends & Ligate Adapters (TruSeq DNA) 4.0 step.

Parameters

The script accepts the following parameters:

An example command line is shown below:

NOTE: The location of Groovy on your server may be different from the one shown in this example. If this is the case, modify the script accordingly.

Step Configuration

In the Clarity LIMS web interface, for the Adenylate Ends & Ligate Adapters (TruSeq DNA) 4.0 step (in the TruSeq DNA Sample Prep protocol), configure Automation as follows:

Clarity LIMS v6.x

• Trigger Location: Add Labels

• Trigger Style: Automatic upon entry

User Interaction

Assuming the user has added 96 samples and has reached the Adenylate Ends & Ligate Adapters (TruSeq DNA) 4.0 step:

1. The user transfers all 96 samples to a new 96-well plate and proceeds with step.

2. When the user enters the Add Labels screen, the script is initiated. A message box alerts the user that a custom script is in progress.

3. Upon completion, the previously defined success message displays.

About the code

Once the script has processed the input and ensured that all the required information is available, we can start applying the reagents to our samples.

1. To begin, we need to define the reagents and pattern to apply.

   • The storing of reagents can be accomplished by placing the reagents in a Map, comprised of the reagent names indexed by their respective number, i.e. 'AD030' indexed at 30.

   • The pattern can be stored as a List of Lists. This can be arranged as a visual representation of the pattern to be applied.\

Assumptions and Notes

• Your configuration conforms with the script requirements documented in .

• You are running a version of Groovy that is supported by Clarity LIMS, as documented in the Clarity LIMS Technical Requirements.

• The attached Groovy file is placed on the LIMS server, in the following location: /opt/gls/clarity/customextensions

Attachments

Single Indexing ReagentTypes.xml:

AssignIndexPattern.groovy: