Illumina LIMS Integration

This combination of configuration and python script can be used to set up an integration between BaseSpace Clarity LIMS and Illumina LIMS. There are 2 main parts to this integration:

1. Generating a sample manifest from BaseSpace Clarity LIMS to import the samples into Illumina LIMS.
2. Once the analysis is completed, automatically parsing in the results from Illumina LIMS into BaseSpace Clarity LIMS.

Disclaimer: This application example is provided as is, with the assumption that anyone deploying this to their LIMS server will own the testing and customization of the configuration and scripts provided.

Installation

Using the config-slicer tool, import the configuration file attached (IlluminaLIMSIntegration.xml) as the glsjboss user with the following command:

java -jar /opt/gls/clarity/tools/config-slicer/config-slicer-3.<x>.jar -o import -k IlluminaLIMSIntegration.xml -u <user> -p <password> -a https://<hostname>/api

1. As the glsjboss user on the Basespace Clarity LIMS server, copy the Illumina LIMS manifest template file (IlluminaLIMS_Manifest_Template.csv) attached below to the following folder: /opt/gls/clarity/customextensions/IlluminaLIMS
2. On the Illumina LIMS Windows/Linux workstation create a folder called Clarity_gtc_Parser and do the following :
a. Copy the clarity_gtc_parser_v2.py file into this folder and update the following configuration parameters:

Parameter

Description

USERNAME = <APIUSERNAME>

Clarity user with API access

PASSWORD = <APIPASSWORD>

Password for that user

uri = 'https://<DEMAINNAME>/api/v2/artifacts'

URI to the artifact API endpoint on Clarity

path = '/<PATH>/IlluminaLIMS/gtc_folder_v3/'

Path to gtc files

gtcVersion = 3

gtcfile version

This script supports the current LIMS gtc version (3) and will be compatible with version 5 when available.

b. Download and copy the IlluminaBeadArrayFiles.py to the same folder (also available here). Edit the file with variables: API, gtc file path and username/password for clarity API for the relevant server.
c. Create an empty file called processed_gtc.txt in the gtc files directory.
d. Setup a scheduled task (Windows) or cronjob (Linux) to run this python script every 10 minutes (assuming Python version 2.7.1 is installed and available on the workstation).

Workflow

The configuration attached to this page contains an example protocol with two steps.

Samples have been accessioned into BaseSpace Clarity LIMS with the following sample metadata as Submitted Sample UDFs:

• Is Control
• Institute Sample Label
• Species
• Sex
• Comments
• Volume (ul)
• Conc (ng/ul)
• Extraction Method
• Parent 1
• Parent 2
• Replicate(s)
• WGA Method (if applicable)
• Mass of DNA used in
• WGA
• Tissue Source

This manual step is meant to be merged into the last step of a Sample Prep Protocol. It has the configuration to generate a Derived Sample with the LIMSID in the name so that the name can be unique, and used to match data back using the data parser to the next step.

This requires the user to perform the following steps:

1. Generate the Illumina LIMS Manifest using the button provided called "Generate Illumina LIMS Manifest".
2. Download the manifest and import this to IlluminaLIMS Project Manager under the correct institution.
3. Run the appropriate lab workflow on Illumina LIMS
4. After the Illumina LIMS analysis is complete, allow 10 minutes and come back to Clarity LIMS to find the step in progress. Make sure the following derived sample UDFs are populated:
• Autocall Version
• Call Rate
• Cluster File
• GC 10
• GC 50
• Gender
• Imaging Date
• LogR dev
• Number of Calls
• Number of No Calls
• SNP Manifest
• Sample Plate
• Sample Well
• 50th Percentiles in X:
• 50th Percentiles in Y:
• 5th Percentiles in X:
• 5th Percentiles in Y:
• 95th Percentiles in X:
• 95th Percentiles in Y:
• Number of Calls Number of Intensity Only Calls:
• Number of No Calls

Attachments

clarity_gtc_parser_v2.py.txt

IlluminaBeadArrayFiles.py.txt

IlluminaLIMSIntegration.xml

IlluminaLIMS_Manifest_Template.csv