Ion Reporter Software Integration Guide

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Torrent Suite Software space on Ion Community

IR Integration TOC

Integration with Ion ReporterSoftware

In your analysis template, you can specify that your Torrent SuiteSoftware results files are automatically transferred to your organization in Ion ReporterSoftware. Your results transfer, including sample definition and workflow launch in Ion Reporter Software, is handled by the IonReporterUploader plugin.

You include the Uploader plugin settings in the run plan that you use for your sequencing run. When yourTorrentSuiteSoftwareanalysis completes, the run planautomaticallylaunches the plugin and beginsyour file transfer. After the transfer, yourIon Reporter Software is automatically launched.

You can run the IonReporterUploader in these three ways to transfer your Ion Reporter Software results files to Ion ReporterSoftware:

• The analysis template wizard In the wizard you use configure your analysis template to use Ion Reporter Software. Then e very Torrent Suite Software analysis that is based on your analysis template automatically transfers results files to your Ion ReporterSoftware organization and defines Ion ReporterSoftware samples from your newly transferred files. You have the option to configure automatic Ion ReporterSoftware launch on the new samples.
  
  
  
  
• On-demand manual plugin launch A o ne-time manual launch from a completed run report (with the Select plugins to run button) transfers your results files and defines samples in Ion Reporter Software . Manual plugin launch does not support automaticIon Reporter Software workflow launch.
  
  
• On-demand one-click transfer to Ion Reporter Software A o ne-time manual launch from a completed run report (with the Upload to IR menu) transfers your results files and defines samples inIon Reporter Software. This transfer does not support automaticIon Reporter Software workflow launch.

Each of these requires that you first configure the IonReporterUploader plugin with your Ion Reporter Software login ID and password.

Integration with Ion Reporter Software

Ion ReporterSoftware uses theTorrent SuiteSoftware output BAM file for analysis. TheIon ReporterSoftware annotation-only workflow also accepts the VCF output file of the Torrent Variant Caller plugin. UsetheIonReporterUploader plugin to transfer these output files toIon ReporterSoftware.

In a run plan template wizard, you can set up theIonReporterUploader plugin to automatically transfer the output files toIon ReporterSoftware, after each completion of yourTorrent SuiteSoftware analyses.

See Integration with Ion ReporterSoftware for an overview of Torrent SuiteSoftware output files and how these files are used with Ion ReporterSoftware.

Configure your IonReporterUploader plugin credentials

A one-time configuration of theUploader plugin is required before its first use. See Configure Your IonReporterUploader Plugin Access Credentials .

Only the user who configures a set of credentials in the IonReporterUploader plugin can upload data to thatIon Reporter Software organization.(This is only important if multiple users on your Torrent Server upload to differentIon Reporter Software organizations, and it ensures data is uploaded to the correct organization.) Multiple Torrent Server users can configure the plugin to upload to the sameIon Reporter Software organization.

When multiple users (with different Torrent SuiteSoftware logins) configure theIonReporterUploader plugin, each user can only see (and use) theIonReporterUploader plugin configuration that they created themselves. Whenmultiple users share one Torrent SuiteSoftware login, those users cansee and use allIonReporterUploader plugin configurations created with thatTorrent SuiteSoftware account.

Add the Ion ReporterSoftwareto a run plan

To set a run plan to automatically transfer files (after the completion of the Torrent SuiteSoftware analysis), y ou define a run plan in the Torrent Browser Plan tab before your sequencing run. Your results files are transferred to Ion Reporter Software and also defined as samples in Ion Reporter Software, and your selection ofIon Reporter Software workflow is automatically launched on your newly-transferred samples.

See Set a Run Plan Template to Transfer to Ion ReporterSoftware .

Manual launch of the Uploader plugin

When you run the Uploader plugin from a completed run report, your results files are transferred to Ion Reporter Software and also defined as samples in Ion Reporter Software. AnIon Reporter Software workflow is not automatically launched.

See Manual Launch of the IonReporterUploader Plugin .

Email notifications

The Uploader plugin sends two email notifications for each plugin run:

• When the plugin begins to transfer your files
• When the upload toIon Reporter Softwareis finished

The notifications are sent to the email address of theIon Reporter Software user whose authentication token was used to configure the plugin.

Prerequisites

• There is a one-time configuration of the plugin in both the Ion Reporter Software UI and the Torrent Browser, before the plugin can be used.
• Because this one-time plugin configuration requires an authentication token from Ion Reporter Software, you (or an administrator) must already have an Ion Reporter Software user account).
• The plugin has these requirements:
  • The plugin only works an completed Torrent Suite Software analyses that have a run plan with the following:
    • IonReporterUploader selected in the run plan wizard Export chevron,
    • The Ion Reporter Software sample name(s), workflow(s), and sample relationships properly defined in the Plan chevron,
    • And, for barcoded runs, the correct barcode kit selected ion the Kits chevron.
  • Manual launches of the plugin (on a completed run report) also depend on the run plan.

Transfer limitations

The following limitations apply to the Uploader plugin:

• The Uploader plugin transfers results files for a completed run plan that executed on the Torrent Server where the plugin is configured. (In addition, each run must have the IonReporterUploader plugin enabled and configured in its run plan.)

• You cannot copy results file from a different Torrent Server and have the plugin transfer those files.
• Only files appearing in the File Links section of a run report are transferred.
• You cannot add supplemental files to the results files of a run, in order to have the plugin transfer those files.

• For barcoded runs:

  • For automatic runs with barcoded data, the Uploader plugin only transfers samples if the barcode kit selection in the run plan wizard is correct. If you correct or add the barcode kit selection on the sequencing instrument, the Uploader plugin still uses the old run plan information and the results file transfer fails.

  • For manual launches of the plugin on barcoded data, the Uploader plugin uses the barcode kit selection that you make on the sequencing instrument.

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