Torrent Browser Analysis Report Guide

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Torrent Suite Software space on Ion Community

IR Integration TOC

Manual launch of the IonReporterUploader plugin

Unlike a run that is launched through a planned run, a manual launch of the Uploader plugin does not automatically launch the Ion Reporter Software workflow for you. With a manual launch of the Uploader plugin, your Torrent Suite Software results files are transferred to Ion Reporter Software and also defined as samples in Ion Reporter Software.

Display names

The plugin launch uses display names that the Uploader plugin uses to transfer files to the correct version of Ion Reporter Software and to the correct Ion Reporter Software organization. The display names are defined in the admin Plugin tab, in the IonReporterUploader Configure option.

Files transferred

BAM files are the output of the main Torrent Suite Software analysis pipeline. VCF files are the output of the Torrent Variant Caller plugin. The default action is to upload both BAM and VCF files, if available.

A VCF file is only available if the Torrent Variant Caller plugin already completed for this run report.

Information from the run plan

The Uploader's behavior is different if the original Torrent Suite Software analysis was executed because of a run plan than if the analysis did not have a run plan:

• Part of a planned run The Uploader reads the run plan and transfers files based on the run plan.
• Not part of a planned run The Uploader checks for BAM and VCF files and uploads all eligible files.
  
  

Launch

Follow these steps to manually run the Uploader plugin:

1. Go to the Data > Completed Runs & Reports tab, then click the link for your completed analysis run.
   
   
   
   
2. In the run report, scroll down to Plugin Summary tab.
   
   
   
   
3. Click Select plugins to run button, then click IonReporterUploader :
   
   
   
   
   
   
   
   
4. The Select Ion Report Account page opens:
   
   
   
   
   
   
   
   
5. First select the correct Upload Option for this run:
   1. BAM files T he output of the main Torrent Suite Software analysis pipeline.
   2. VCF files The output of the Torrent Variant Caller plugin (if already run and completed for this run report).
      
      
   
   
   
6. When multiple Ion Reporter Software user account are supported, your selection on this page determines which Ion Reporter Software organization receives the transferred files. Click the Launch IRU button for the correct set of credentials and to the correct version of Ion Reporter Software
   
   
   
   
7. If you are sure, click Yes on the confirmation popup.
   
   
   
   
8. Please read the submission notice and do not relaunch the Uploader on this run report without allowing time for this Uploader launch to finish transferring its files. Click OK .
   
   
   
   
9. Click the Refresh Plugin Status button to monitor the Uploader's progress.
   
   The Uploader section is easier to find if you click the Collapse All button.

Monitor the upload progress

Use theplugin's progress table (in Plugin Summary section for IonReporterUploader) to track the progress of the file transfer. While the transfer is in progress, the plugin has the following message.

Click the here link to open the Uploader's progress table in the plugin summary section . The status.html link opens the same progress table, but as the only content in a new browser tab. An example progress table is shown below:

The underlined fields are links to additional information. The progress link is best for seeing how much of the transfer is complete. The log link is the best source for troubleshooting a failure.

• stdout The standard output messages for the plugin run.
• log Plugin log messages, including errors.
• input The input file of plugin parameters and options, in JSON format.
• progress Opens a page of progress bars that track the transfer:

Notes about the Uploader plugin

• Use only IonReporterUploader. Other versions of IonReporterUploader plugins are not compatible with Ion Reporter Software 1.6.x.

• If IonReporterUploader does not appear in the Select Plugin to Run list, it is either not enabled or not configured on your Torrent Server.

• The plugin log file (in the Torrent Browser Plugin Summary area) contains information about the location the data files are transferred to in Ion Reporter Software.

• For Torrent Suite Software analyses that do not have the Ion Reporter Software configured in a run plan (in the IonReporter chevron) , sample names in Ion Reporter Software are created using the Torrent Suite Software analysis name. With barcoded runs, the barcode name is also added to the sample name.

Double submission warning message

This warning is shown when there is the possibility that an upload of the current results is already in progress:

If the Uploader plugin has Error status, you can safely click Yes and retry the upload.

If the Uploader plugin status is Queued or Started, click No . A second submission of the plugin on the same run report causes both submissions to fail.

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