Installer Parameters and Operations

The IPP Integration v2.5 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

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

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

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 v2.5. 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 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.

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.

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

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 (eg, IPP - LIMS 5 - TruSight_Oncology_Protocols.TruSight-Oncology-500-HT-v1.0).
• Version—The version of the configuration slice that was installed (eg, 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)

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 and omxprops.log files show 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 /opt/gls/clarity/logs/illumina-preset-protocols/<IPP version>/<Time-based Digits>/ directory.

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