Installation and User Configuration

The Illumina Preset Protocols (IPP) v2.7 support the integration of Clarity LIMS with established lab protocols.

The integration provides preconfigured workflows that map to lab protocols and steps, and support Illumina library prep kits, reagent kits, assays, and instruments.

This guide provides instructions and describes the components installed in the default configuration of IPP.

Installation Components

IPP Integration v2.7 is distributed as the BaseSpaceLIMS-Illumina-Preset-Protocols RPM package. The RPM package installs the following components:

• The illumina-preset-protocols-installer.sh script for configuration slices.

• Templates for the following uses:

  • Sample sheet generation

  • Sample placement pattern

  • Covid testing setup and reporting

  • Illumina Genomics Architecture (IGA)

• Automation scripts, including scripts to support IGA and Clarity LIMS Product Analytics (CLPA) automation.

• Configuration slices.

• Workflows for applicable instrument integrations.

Sample Sheet Generation Templates

• BCL2FASTQ_Reverse_Complement_Samplesheet.csv

• BCL2FASTQ_Samplesheet.csv

• genomeStudio_Genotyping_SampleSheet_driver_file.csv

• genomeStudio_Methylation_SampleSheet_driver_file.csv

• iSeq_Samplesheet.csv

• iSeqManual_Samplesheet.csv

• miniSeq_Samplesheet.csv

• MiSeqSamplesheetv3.csv

• NextSeq1K2K_Pool1.csv

• NextSeq1K2K_Pool2.csv

• NextSeq1K2K_Pool3.csv

• NovaSeq_BCL2FASTQ_Samplesheet.csv

• NovaSeq_BCL2FASTQ_Samplesheet_v2.csv

• NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv

• NovaSeq_Standard_Bulk_Pool1.csv

• NovaSeq_Standard_Bulk_Pool2.csv

• NovaSeq_Standard_Bulk_Pool3.csv

• NovaSeq_Xp_Bulk_Pool.csv

• NovaSeq_Xp_Bulk_Pool2.csv

• NovaSeq_Xp_Working_Pool.csv

• NovaSeq_Xp_Working_Pool2.csv

• NovaSeqDx_BCL2FASTQ_Samplesheet_v2.csv

• NovaSeqXSeries_Bulk_Pool1.csv

• NovaSeqXSeries_Bulk_Pool2.csv

• NovaSeqXSeries_Dilute_Denature_Calculate_Volumes.csv

Sample Placement Pattern Templates

• Hybrid Pattern_96 well plate_8x1 HD BeadChip.tsv

• Hybrid Pattern_96 well plate_8x1 LCG BeadChip.tsv

• Hybrid Pattern_96 well plate_12x1 HD BeadChip.tsv

• Hybrid Pattern_96 well plate_24x1 HD BeadChip.tsv

• Hybrid Pattern_96 well plate_24x1 HTS BeadChip.tsv

• Hybrid Pattern_96 well plate_24x1 HTS BeadChip Multichannel.tsv

• Hybrid Pattern_96 well plate_24x4 XT BeadChip.tsv

Covid-Related Templates

• 7900sds_container_setup_template.txt

• covid_report_results.csv

Illumina Genomics Architecture (IGA) Templates

• BatchingInputFile_template.csv

• CaptureWashInputFile_template.csv

• ExtractionInputFile_template.csv

• LibInputFile_NFE_template_withoffsets.csv

• LibInputFile_NFPF_template_withoffsets.csv

• LoadToFlowcell_NovaSeqXp_Incomplete_template.csv

• LoadToFlowcell_NovaSeqXp_ManifestForConsolidation_template.csv

• LoadToFlowcell_NovaSeqXp_template.csv

• LoadToLibTubeFile_NovaSeqStd_template.csv

• MakeBPFile_NovaSeq_template.csv

• PlatingInputFile_template.csv

Python Scripts for Automation Support

• autoPlaceCovid7500.py

• clarityapiutil.py

• parseCovidSeqRunReport.py

• verifyBeadChipIDs.py

Python Scripts for IGA Automation Support

• glsapiutil:

  • glsapiutil.py

  • glsapiutil3.py

• hamilton_fast_prep:

  • 01_A_CFP_Batching_defaultContainerCheck.py

  • 01_CFP_Batching_confirmPlateID.py

  • 01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py

  • 02_ReagentParsing.py

  • 03_checkHamiltonFileNameBarcode.py

  • 04_A_checkIndexPlateBarcodeWithCategory.py

  • 04_B_autoAssignIndexesFromIndexPlanning.py

  • 05_reusedIndexPlateWarning.py

  • countSamples.py

  • countSamplesInPools.py

  • validate_sample_placement.py

• iga_helpers:

  • clarityUIFileHelper.py

  • pop_up_msg.py

  • printCurrentWorkflow.py

• iga_novaseq:

  • 01_NovaSeqStd_confirmPlateIDAndStoreInstrumentID_OptionalFile.py

  • 02_NovaSeqStd_confirmPlateIDAndStoreInstrumentID_OptionalFile_DiluteDenature.py

  • 03_NovaSeqXp_confirmBPPPlateAndStoreInstrumentID.py

  • 03_NovaSeqXp_consolidateBulkPoolFiles.py

  • 04_NovaSeqXp_completeAndConsolidateWPPZipFile.py

  • NovaSeq_automated_warning.py

  • NovaSeq_pooling_warning.py

  • validate_floorcell_container.py

  • validate_flowcell_pools.py

  • validate_multiple_destination_plates.py

• illumina-cobalt-samplesheet-converter:

  • ss_converter:

    • converter.py

    • errors.py

    • v1_builder_plugins.py

    • v1_v2_handler.py

    • v2_converter_plugins.py

• index_correct:

  • apply_correction_factors.py

• make_bpp:

  • apply_multiple_bulk_pools.py

  • calculate_sample_volume.py

• utils:

  • common.py

  • igaapiutil.py

Clarity LIMS Product Analytics Automation Script

• unified-product-analytics-automation.jar

Configuration Slices

The following configuration slices are included in IPP Integration v2.7:

• Illumina_Instruments, including:

  • iScan-v1.0

  • iSeq-100-v1.0

  • Library-Prep-Validation-v2.3

  • miniSeq-v1.0

  • miseq-v3.2

  • NextSeq1k2k-v2.3

  • nextseq550-v1.1

  • novaseq-v3.8

  • novaseqdx-v1.2

  • NovaSeqXSeries-v1.1

• QC_Protocols

  • qc-protocols

• Ampliseq_for_Illumina_Protocols, including:

  • AmpliSeq-Illumina-BRCA-Panel-v1.1

  • AmpliSeq-Illumina-Cancer-HotSpot-Panel-V2-v1.1

  • AmpliSeq-Illumina-Childhood-Cancer-Panel-v1.1

  • AmpliSeq-Illumina-Comprehensive-Cancer-Panel-v1.1

  • AmpliSeq-Illumina-Comprehensive-Panel-v3-v1.1

  • AmpliSeq-Illumina-Custom-DNA-Panel-v1.1

  • AmpliSeq-Illumina-Focus-Panel-v1.1

  • AmpliSeq-Illumina-Immune-Repertoire-Panel-v1.1

  • AmpliSeq-Illumina-Immune-Response-Panel-v1.1

  • AmpliSeq-Illumina-Myeloid-Panel-v1.1

  • AmpliSeq-Illumina-TCR-beta-SR-Panel-v1.1

  • AmpliSeq-Illumina-Transcriptome-Human-Gene-Expression-Panel-v1.1

• Covid, including:

  • CDC-COVID-19-RT-PCR-v1.1

  • Illumina-COVIDSeq-Workflow-v1.5

  • Respiratory-Virus-Panel-v1.0

• DNA_Protocols, including:

  • ILASS-TruSight-Whole-Genome-Assay-v1.2

  • Illumina-DNA-PCR-Free-Library-Prep-Manual-v1.0

  • Illumina-DNA-Prep-M-Tagmentation-v1.0

  • Nextera-Mate-Pair-v1.0

  • Nextera-XT-v2.0

  • TruSeq-DNA-PCR-Free-v2.0

  • TruSeq-Nano-DNA-v1.0

• IGA, including:

  • IGA_Library_Prep_Automated_v2.1

  • IGA_NovaSeq_Sequencing_v2.2

• Infinium_Array, including:

  • Genome-Studio-v1.0

  • ILASS-Infinium-Genotyping-Assay-v1.0

  • Infinium-HD-Methylation-Assay-Manual-v1.2

  • Infinium-HTS-Assay-Manual-v1.2

  • Infinium-LCG-Assay-Manual-v1.2

  • Infinium-XT-Assay-Manual-v1.2

• Methylation_Protocols, including:

  • TruSeq-ChIP-Seq-v1.0

  • TruSeq-Methyl-Capture-EPIC-v2.0

• RNA_Protocols, including:

  • Illumina-Stranded-mRNA-Prep-Ligation-v1.0

  • Illumina-Stranded-Total-RNA-Prep-Ligation-with-Ribo-Zero-Plus-v1.0

  • TruSeq-Small-RNA-v1.0

  • TruSeq-Stranded-mRNA-v2.1

• Targeted_Amplicon_Protocols

  • TruSeq-Custom-Amplicon-v1.0

• Targeted_Enrichment_Protocols, including:

  • Illumina-DNA-Prep-with-Enrichment-S-Tagmentation-v1.1

  • Illumina-RNA-Prep-with-Enrichment-L-Tagmentation-v1.0

  • Nextera-Rapid-Capture-Custom-Enrichment-v2.0

  • TruSeq-DNA-Exome-v2.0

  • TruSeq-RNA-Exome-v1.0

• TruSight_Oncology_Protocols, including:

  • TruSight-Oncology-500-ctDNA-v1.1

  • TruSight-Oncology-500-HT-v1.1

  • TruSight-Oncology-500-v1.1

  • TruSight-Tumor-170-v2.0

Instruments and Workflows

IPP Integration v2.7 contains workflows that are used to integrate the following instruments:

• iScan

• iSeq

• MiSeq

• MiniSeq

• NextSeq 500/550

• NextSeq 1000/2000

• NovaSeq 6000

• NovaSeq 6000Dx

• NovaSeq X Series

The following workflows are included in the integration:

• iScan v1.0

• iSeq 100 v1.0

• Library Prep Validation v2.3.2

• MiniSeq v1.0

• MiSeq Sequencing v3.2

• NextSeq 500/550 Sequencing v1.1

• NovaSeq 6000 v3.8

• NextSeq 1000/2000 Sequencing v2.3

• NovaSeqDx v1.2

• NovaSeq X Series Sequencing v1.1

These workflows require ClarityLIMS-NGS-Package v5.24.0 or later so that the Template File Generator tool can be used.

Protocols and Configuration Slices

IPP Integration v2.7 provides protocols that contain configuration slices. These configuration slices are used to install other workflows and protocols.

QC_Protocols

QC_Protocols configuration component contains the qc-protocols base slice. This configuration does not contain any workflows, but it does provide the following protocols that are used by other workflows:

• DNA Initial QC

• Library Validation QC

• RNA Initial QC

The following table shows the components that are installed with the QC_Protocols configuration.

Components Installed with QC_Protocols

Component	Items Installed
Protocols	DNA Initial QC 5.1.2 Library Validation QC 5.1.2 RNA Initial QC 5.1.2
Master Steps	Add Multiple Reagents Adenylate ends & Ligate Adapters (TruSeq DNA) 5.1 Pool Samples Aggregate QC (DNA) 5.1.2 Aggregate QC (Library Validation) 5.1.2 Aggregate QC (RNA) 5.1.2 Bioanalyzer QC (DNA) 5.1.2 Bioanalyzer QC (RNA) 5.1.2 CaliperGX QC 5.1.2 NanoDrop QC (DNA) 5.1.2 NanoDrop QC (RNA) 5.1.2 PicoGreen QC (DNA) 5.1.2 PicoGreen QC (RNA) 5.1.2 Qubit QC (DNA) 5.1.2 Qubit QC (RNA) 5.1.2 Tapestation QC (DNA) 5.1.2 Tapestation QC (RNA) 5.1.2 qPCR QC 5.1.2
Container types	384 well plate 96 well plate BioAnalyzer DNA 1000 Chip BioAnalyzer DNA High Sensitivity Chip BioAnalyzer RNA Nano Chip BioAnalyzer RNA Pico Chip Tube
Label groups/reagent categories	TruSeq Custom Amplicon Adapters (A7-A5) TruSeq DNA LT Adapters (AD series) TruSeq Stranded mRNA LT Adapters (AR series) TruSeq HT Adapters (D7-D5) Nextera Enrichment & Rapid Capture Adapters (N7-E5) Nextera DNA Adapters (N7-N5, S7-S5) NoIndex TruSeq Small RNA Adapters (RPI series)
Reagent kits	TruSeq DNA PCR-Free Kit - Adapter Plate Box TruSeq DNA PCR-Free Kit - Core Reagents Box TruSeq DNA PCR-Free Kit - SP Beads Box
Controls	Endogenous Positive Control Exogenous Positive Control No Amplification Control No Reverse Transcriptase Control No Template Control PhiX v3
Sample custom fields	Application Pooling Progress Reference Genome Sample Buffer Sample Conc. Units Volume (ul) Read Length Sample Type Sequencing Coverage Sequencing Method
Container custom fields	Container Name LIMS ID (Container) Well
Project custom fields	Project Name
Derived sample custom fields	A260/280 ratio Conc. Units Concentration Sample Name Waiting Workflow
Measurement custom fields	28s/18s ratio A260 A260/230 ratio A260/280 ratio BA Sample Name Conc. Units Concentration MW Units Molarity Units Number of Peaks found Number of Regions found Peak 1% Integrated Area Peak 1 Conc. Peak 1 MW Peak 1 Molarity Peak 1 Size - bp Peak 2% Integrated Area Peak 2 Conc. Peak 2 MW Peak 2 Molarity Peak 2 Size - bp Peak 3% Integrated Area Peak 3 Conc. Peak 3 MW Peak 3 Molarity Peak 3 Size - bp Peak 4% Integrated Area Peak 4 Conc. Peak 4 MW Peak 4 Molarity Peak 4 Size - bp Peak 5% Integrated Area Peak 5 Conc. Peak 5 MW Peak 5 Molarity Peak 5 Size - bp RIN RNA Area Region 1% of Total Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2% of Total Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3% of Total Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4% of Total Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5% of Total Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity Sample Comment Size (bp)

AmpliSeq_for_Illumina_Protocols

The following table shows the AmpliSeq_for_Illumina_Protocols configuration slices and the workflows that are installed with IPP Integration v2.7.

AmpliSeq_for_Illumina_Protocols Configuration Slices and Workflows

Configuration Slice	Workflows
AmpliSeq-Illumina-BRCA-Panel-v1.1	Equalizer Workflow AmpliSeq for Illumina BRCA Panel v1.1 Library Prep AmpliSeq for Illumina BRCA Panel v1.1 Standard Workflow AmpliSeq for Illumina BRCA Panel v1.1
AmpliSeq-Illumina-Cancer-HotSpot-Panel-V2-v1.1	Library Prep AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1 Standard Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1
AmpliSeq-Illumina-Childhood-Cancer-Panel-v1.1	DNA Library Prep AmpliSeq for Illumina Childhood Cancer Panel v1.1 Equalizer Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1 RNA Library Prep AmpliSeq for Illumina Childhood Cancer Panel v1.1 Standard Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1
AmpliSeq-Illumina-Comprehensive-Cancer-Panel-v1.1	Equalizer Workflow AmpliSeq for Illumina Comprehensive Cancer Panel v1.1 Library Prep AmpliSeq for Illumina Comprehensive Cancer Panel v1.1 Standard Workflow AmpliSeq for Illumina Comprehensive Cancer Panel v1.1
AmpliSeq-Illumina-Comprehensive-Panel-v3-v1.1	DNA Library Prep AmpliSeq for Illumina Comprehensive Panel v3 v1.1 Equalizer Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1 RNA Library Prep AmpliSeq for Illumina Comprehensive Panel v3 v1.1 Standard Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1
AmpliSeq-Illumina-Custom-DNA-Panel-v1.1	Equalizer Workflow AmpliSeq for Illumina Custom DNA Panel v1.1 Library Prep AmpliSeq for Illumina Custom DNA Panel v1.1 Standard Workflow AmpliSeq for Illumina Custom DNA Panel v1.1
AmpliSeq-Illumina-Focus-Panel-v1.1	DNA Library Prep AmpliSeq for Illumina Focus Panel v1.1 Equalizer AmpliSeq for Illumina Focus Panel v1.1 RNA Library Prep AmpliSeq for Focus Panel v1.1 Standard Workflow AmpliSeq for Illumina Focus Panel v1.1
AmpliSeq-Illumina-Immune-Repertoire-Panel-v1.1	Equalizer AmpliSeq for Illumina Immune Repertoire Panel v1.1 RNA Library Prep AmpliSeq for Illumina Immune Repertoire Panel v1.1 Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.1
AmpliSeq-Illumina-Immune-Response-Panel-v1.1	Equalizer Workflow AmpliSeq for Illumina Immune Response Panel v1.1 RNA Library Prep AmpliSeq for Illumina Immune Response Panel v1.1 Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.1
AmpliSeq-Illumina-Myeloid-Panel-v1.1	DNA Library Prep AmpliSeq for Illumina Myeloid Panel v1.1 Equalizer Workflow AmpliSeq for Illumina Myeloid Panel v1.1 RNA Library Prep AmpliSeq for Illumina Myeloid Panel v1.1 Standard Workflow AmpliSeq for Illumina Myeloid Panel v1.1
AmpliSeq-Illumina-TCR-beta-SR-Panel-v1.1	DNA Library Prep AmpliSeq for Illumina TCR beta-SR Panel v1.1 RNA Library Prep AmpliSeq for Illumina TCR beta-SR Panel v1.1
AmpliSeq-Illumina-Transcriptome-Human-Gene-Expression-Panel-v1.1	Equalizer Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1 RNA Library Prep AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1 Standard Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1

Additional Configuration Slices

The following table shows additional configuration slices and workflows that are installed with IPP Integration v2.7.

Additional Configuration Slices and Workflows

Configuration Slice	Workflows
Covid	CDC COVID-19 RT PCR v1.1 Qiagen EZ1 Advanced XL CDC COVID-19 RT-PCR v1.1 Qiagen QIAamp DSP Viral RNA Mini Kit CDC COVID-19 RT-PCR v1.1 Roche MagNA Pure 96 CDC COVID-19 RT-PCR v1.1 Roche MagNA Pure Compact CDC COVID-19 RT-PCR v1.1 Roche MagNA Pure LC CDC COVID-19 RT-PCR v1.1 Sort Specimens to Extraction CDC COVID-19 RT-PCR v1.1 bioMerieux EMAG Instrument CDC COVID-19 RT-PCR v1.1 bioMerieux NucliSENS easyMAG Instrument CDC COVID-19 RT-PCR v1.1 Illumina COVIDSeq Workflow v1.5 Respiratory Virus Panel v1.0
DNA_Protocols	ILASS TruSight Whole Genome Assay v1.2 Illumina DNA PCR-Free Library Prep Manual v1.0.2 Illumina DNA Prep (M) Tagmentation v1.0.7 Nextera Mate Pair v1.0.8 Nextera XT DNA v2.0.8 TruSeq DNA PCR-Free v2.0.8 TruSeq Nano DNA v1.0.8
IGA	Illumina Genomics Architecture - Library Prep Automated v2.1 Sample Selection (IGA v2.1) Sample Plating (IGA v2.1) Blood Extraction (IGA v2.1) Saliva Extraction (IGA v2.1) Illumina DNA PCR-Free (IGA v2.1) Illumina DNA with Enrichment (IGA v2.1) Sequencing Platform Selection (IGA v2.1) Illumina Genomics Architecture - NovaSeq Sequencing v2.1 Run Format (IGA v2.1) NovaSeq Standard (IGA v2.1) NovaSeq Xp (IGA v2.1) AUTOMATED - NovaSeq Run (IGA v2.1) ℹ IGA workflows require additional installation steps. For assistance, contact Illumina Technical Support. Note also that Illumina Genomics Architecture - NovaSeq Sequencing v2.1 workflow is not the same workflow as NovaSeq 6000 v3.8.
Infinium_Array	GenomeStudio v1.0 ILASS Infinium Genotyping Assay v1.0 ILASS Infinium Genotyping with PGx v1.0 Infinium HD Methylation Assay Manual v1.2 Infinium HTS Assay Manual v1.2 Infinium LCG Assay Manual v1.2 Infinium XT Assay Manual v1.2
Methylation_Protocols	TruSeq ChIP-Seq v1.0.8 TruSeq Methyl Capture EPIC v2.0.9
RNA_Protocols	Illumina Stranded mRNA Prep Ligation v1.0 Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.0 TruSeq Small RNA v1.0.8 TruSeq Stranded mRNA v2.1.8
Targeted_Amplicon_Protocols	TruSeq Custom Amplicon v1.0.8
Targeted_Enrichment_Protocols	Illumina DNA Prep with Enrichment (S) Tagmentation v1.1 Illumina RNA Prep with Enrichment (L) Tagmentation v1.0 Nextera Rapid Capture Custom Enrichment v2.0.9 TruSeq DNA Exome v2.0.8 TruSeq RNA TruSeq RNA Access v2.0.8 TruSeq RNA Exome v1.0.5
TruSight_Oncology_Protocols	TruSight Oncology 500 ctDNA v1.1 TruSight Oncology 500 HT v1.1 TruSight Oncology 500 v1.1 TruSight Tumor 170 v2.0.8

IPP Integration v2.7 Package Installation

The BaseSpaceLIMS-Ilumina-Preset-Protocols RPM package provides instructions for locating and running the /opt/gls/clarity/config/illumina-preset-protocols-installer.sh bash script that launches the IPP configuration installer.

The RPM package automatically installs template files that are used with Template File Generator (TFG) and Sample Placement Helper. These template files are accessible after the applicable configuration is installed. The files are installed at the following locations:

• /opt/gls/clarity/extensions/conf/driverfiletemplates

• /opt/gls/clarity/extensions/conf/infinium/placementpatterns

• /opt/gls/clarity/extensions/conf/covid

The RPM package automatically installs the CLPA automation that is used for the CLPA integration. This automation is installed at the following location:

/opt/gls/clarity/extensions/unified-product-analytics/automation

If this is a new Clarity LIMS installation, you must install the QC_Protocols before the preconfigured workflows. The base configuration is included in the standard installation process.

After you have selected a workflow, the installer validates the import of that workflow and provides Warning/Error details in STDOUT. This process allows you to proceed with the import or cancel it.

Prerequisites

Before installing the RPM package, make sure that the following software is installed:

• Clarity LIMS v6.2 or later

• NGS-Package v5.24 or later

• SecretUtil v1.2. For more information, refer to Guide to Secret Management in the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

RPM Installation

1. On the server used for the IPP RPM installation, log in as the root user.

2. Use the following yum command to install the RPM:

   The --enablerepo in the command line must be included to enable the repo. The Illumina Support team provides the repo file and the appropriate name to use.

   yum install BaseSpaceLIMS-Illumina-Preset-Protocols --enablerepo=<< repo name info from support >>

3. When prompted to proceed with the RPM package installation, enter y to confirm.

For information on running the installer and supported commands, parameters, and options, refer to Installer Parameters and Operations.

Installer Parameters and Operations

The IPP Integration v2.7 installer uses parameters and operations to assist with the configuration installation.

You must run the installer as the glsjboss user. The following table describes the parameters that are available for use with the installer.

IPP Installer Parameters

Parameter	Description	Example Command
--operation, -o	Specifies the run mode for the installer. Supported modes are as follows: help list install	bash /opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o list
--headless, -h	Run the installer in headless mode. Used for the install operation only.	bash /opt/gls/clarity/config/illumina-preset-protocols-installer.sh --headless -o install QC_Protocols.qc-protocols
--log, -l	Sets the log file name and destination. The default value is ipp-installer.log.	bash /opt/gls/clarity/config/illumina-preset-protocols-installer.sh -l ipp-installer.log

List Operation

Run the installer with the list operation for a list of all configuration installation options in a two-column format. The first column shows the IPP workflow identifier (or Id) that the installer uses when running the install operation. The second column shows the name of the configuration associated with the identifier.

As the glsjboss user, run the following command to view the list of IPP workflows:

/opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o list

Install Operation

Use the install operation to install the configuration slices. Specify both the name of the parent item and the name of the configuration slice, separated by a period, as follows:

/opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install Parent_Item_name.slice_name

For example, to install the qc-protocols slice, run the following command:

/opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install QC_Protocols.qc-protocols

All Operation

The all operation is a special option that is available at the top level and parent item level.

• At the top level, use the operation to install every configuration package from IPP Integration v2.7. To use the all operation at this level, run the following command:

  bash /opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install all

• At the parent item level, use the operation to install the workflows associated with a specific parent item. For example, run the following command to install the workflows associated with the AmpliSeq_for_Illumina_Protocols parent item:

  bash /opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install AmpliSeq_for_Illumina_Protocols.all

There is no all option available for QC_Protocols and Targeted_Amplicon_Protocols as they each contain only one configuration slice. Including all in the install command for these items generates an error.

Headless Mode

Headless mode allows the install operation to complete without prompting for input. Use this mode if you want to automate the installation. When running the installation in headless mode, the process still runs through the validation phase before importing the configuration. However, if a conflict is found, the configuration causing the conflict is skipped automatically.

Installation Validation

The IPP installer validates the configuration import. If conflicts are found during the validation, a warning message displays. This message provides the following options:

• f/Import anyway

• s/Skip this workflow

• a/Abort

The f/Import anyway option runs the import command of the config slicer tool. It also allows the tool to handle conflicts. This option does not run the config slicer tool in importAndOverwrite mode.

The s/Skip this workflow option does not import workflows where conflicts were found, but continues to import the other selected slices.

The a/Abort option aborts all import operations. The conflicts found are captured in the log files and can be reviewed.

Track and Log the Installation

The IPP installer tracks the installation process in the installhistory table and generates log files that can be reviewed after the installation is complete.

Viewing the installhistory Table

After installation is complete, a record is stored in the installhistory table in the database.

To view the installation record, use the following command:

java -jar /opt/gls/clarity/tools/propertytool/omxprops-ConfigTool.jar getInstallHistory

If a configuration slice is installed multiple times, there are multiple entries in the record. This scenario can happen during an upgrade or if there are attempts to resolve conflicts during installation. The log shows the following information for each slice:

• Product — The name of the slice (e.g., IPP - LIMS 5 - TruSight_Oncology_Protocols.TruSight-Oncology-500-HT-v1.0).

• Version — The version of the configuration slice that was installed (e.g., 2.0.0.25).

• InstallDate — The time stamp for when the slice was installed. The date displays first (in YYYY-MM-DD format), followed by the time (in HH:MM:SS format)

Viewing the Log Files

After the configuration package is installed, the following log files are available:

• ipp-installer.log

• configslicer.log

• omxprops.log

The ipp-installer.log file captures the output of the IPP installer tool. The name and location of this file can be changed with the command line options described previously. The default location is as follows:

/opt/gls/clarity/logs/illumina-preset-protocols/{IPP version}/{Time-based Digits}/

The configslicer.log and omxprops.log files are raw outputs from their respective tools. These files contain more detail than the ipp-installer.log file. For example, if a conflict is identified in the ipp-installer.log file, the configslicer.log file shows the specific entry causing the conflict. Some workflow selections, such as the MiSeq and NextSeq integration workflows, import database properties in addition to a configuration slice.

By default, only the ipp-installer.log file is generated in the following directory:

/opt/gls/clarity/logs/illumina-preset-protocols/{IPP version}/{Time-based Digits}/

When the -l operation is specified during installation, all three log files are available in the current working directory.

IPP Integration v2.7 Workflow Upgrades

There are some expected conflicts when upgrading from IPP Integration v2.6.

In IPP v2.7, new flow cell types are supported that cause a conflict with the NovaSeq X Flowcell Type derived sample custom field. The following workflows can be affected and lead to conflicts when upgrading from IPP v2.6 to v2.7:

• Illumina DNA Prep (M) Tagmentation v1.0.6

• Nextera Mate Pair v1.0.7

• Nextera XT DNA v2.0.7

• TruSeq DNA PCR-Free v2.0.7

• TruSeq Nano DNA v1.0.7

• Library Prep Validation v2.3.1

• TruSeq ChIP-Seq v1.0.7

• TruSeq Methyl Capture EPIC v2.0.8

• TruSeq Small RNA v1.0.7

• TruSeq Stranded mRNA v2.1.7

• TruSeq Custom Amplicon v1.0.7

• Nextera Rapid Capture Custom Enrichment v2.0.8

• TruSeq DNA Exome v2.0.7

• TruSeq RNA Exome v1.0.5

• TruSeq RNA Access v2.0.7

• TruSight Tumor 170 v2.0.7

To resolve these conflicts, perform the following actions:

1. When the expected conflicts are encountered during the IPP workflow installation, enter f to import the workflow when prompted. An example of the prompt is as follows.

   Conflicts were detected between this slice and the existing configuration in the LIMS!
   What would you like to do with this slice? [(f|Import anyway)|(s|Skip this workflow)|(a|Abort)]:

2. After the workflow is installed, resolve the conflicts as follows.

   1. From Configuration, select the Custom Fields tab.

   2. From the Custom Fields tab, select the Global Fields tab.

   3. Search for NovaSeq X Flowcell Type.

   4. For Additional Options, update the Dropdown Items with the following options:

      • 1.5B

      • 10B

      • 25B