miso-lims/runscanner

Monitors directories on the file system containing the output from sequencing instruments (e.g. Illumina) and reports their status and metrics

Run Scanner

This is a web service that monitors directories on the file system containing the output from sequencing instruments and serves metadata for runs.

Full instructions for the setup and use of Run Scanner can be found in the Run Scanner User Manual.

Prerequisites

• JDK 17
• Tomcat 8 or 9
• C++ build environment (see runscanner-llumina)
• Maven 3.8 or later
• git

Downloading the latest release

Use the GitHub interface to download the latest release. Extract the .zip or .tar.gz file.

Setting Up Run Scanner

Please refer to Installation & Setup in the Run Scanner User Manual for installation instructions.

Debugging

Retrieving run output

For troublesome runs, you can see the output for a particular run directory using:

java -cp $RUN_SCANNER_HOME/WEB-INF/classes:$RUN_SCANNER_HOME/WEB-INF/lib/'*' ca.on.oicr.gsi.runscanner.scanner.ProcessRun

It will display instructions on how to use it. You will have to set the RUN_SCANNER_HOME to the path containing an unpacked version of the WAR.

List observable runs

To troubleshoot whether a processor can observe a run, you can see a list of all the runs a processor will accept from the filesystem using:

java -cp $RUN_SCANNER_HOME/WEB-INF/classes:$RUN_SCANNER_HOME/WEB-INF/lib/'*' ca.on.oicr.gsi.runscanner.scanner.FindRuns

It will display usage instructions. You will have to set the RUN_SCANNER_HOME to the path containing an unpacked version of the WAR.

Please refer to Troubleshooting in the Run Scanner User Manual for more information.