Prerequisites

For Illumina support:

  • C++ build environment
  • jsoncpp

Please ensure that your sequencer(s) are supported by Run Scanner. Please refer to Appendix C: Sequencers Supported by Run Scanner for more information.

Downloading the latest release

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

Setting Up Run Scanner

In the following instructions:

  • Let ${CATALINA_HOME} be the directory where Tomcat is installed.
  • Let ${CONTEXT} be the context URL you wish to use for Run Scanner.
    • To deploy to the root context (e.g., https://www.myrunscanner.org), let ${CONTEXT} be ROOT
    • To deploy to a subdirectory (e.g., https://www.myserver.org/runscanner/), let ${CONTEXT} be the name of the subdirectory (e.g., runscanner)

Create a file called ${CONTEXT}.xml in ${CATALINA_HOME}/conf/Catalina/localhost, creating the directory if necessary, and populate it with the following information:

<Context>
   <Parameter name="runscanner.configFile" value="/etc/runscanner.json" override="false"/>
</Context>

/etc/runscanner.json is the default location of the instrument descriptions, however this can be changed if necessary. Create this file, and within, write JSON data describing your instruments. Run Scanner requires one record per instrument, therefore the file will contain a list of instruments:

[
  {
    "path": "/srv/sequencer/hiseq2500_1",
    "platformType": "ILLUMINA",
    "name": "default",
    "timeZone": "America/Toronto",
    "parameters": {}
  },
  {
    "path": "/srv/sequencer/promethion",
    "platformType": "OXFORDNANOPORE",
    "name": "promethion",
    "timeZone": "America/Toronto",
    "parameters": {}
  }
]

The name/platformType combination is used to define how to interpret the sequencer's results. A full list of instrument options can be found in Appendix A: Processor Definitions and a full list of supported sequencers can be found in Appendix C: Sequencers Supported by Run Scanner.

Building Run Scanner

Navigate to $RUNSCANNER_SRC. Build the application using:

mvn clean package

There will be an important build artefact: scanner/target/scanner-$VERSION.war

Enabling Illumina scanning

If you would like to scan for Illumina output, please follow Illumina Setup before deploying.

Deploying

  1. Stop Run Scanner's Tomcat.
  2. Remove ${CATALINA_HOME}/webapps/${CONTEXT} directory and ${CATALINA_HOME}/webapps/${CONTEXT}.war file (See note about ${CONTEXT} in Setting Up Run Scanner above).
  3. Copy the scanner-${VERSION}.war from the build to ${CATALINA_HOME}/webapps/${CONTEXT}.war.
  4. Start Run Scanner's Tomcat.