Prerequisites
- JDK 17
- Tomcat 8 or 9
- Maven 3.8 or later
- git
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}
beROOT
- To deploy to a subdirectory (e.g., https://www.myserver.org/runscanner/), let
${CONTEXT}
be the name of the subdirectory (e.g.,runscanner
)
- To deploy to the root context (e.g., https://www.myrunscanner.org), let
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
- Stop Run Scanner's Tomcat.
- Remove
${CATALINA_HOME}/webapps/${CONTEXT}
directory and${CATALINA_HOME}/webapps/${CONTEXT}.war
file (See note about${CONTEXT}
in Setting Up Run Scanner above). - Copy the
scanner-${VERSION}.war
from the build to${CATALINA_HOME}/webapps/${CONTEXT}.war
. - Start Run Scanner's Tomcat.