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README.md

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Build directly via Maven:

You will need:

Process:

matchbox relies on a modified version of Exomiser (https://github.com/exomiser/Exomiser), its reference data and libraries for the phenotype matching algorithm. Given that these libraries are currently not in a maven repository, we obtain this dependency via first building Exomiser and then followed by matchbox. By building Exomiser first, we put its jars in the local maven repository, where the matchbox build is able to see and use them.

  • Clone the Exomiser package

    • Make sure you have a settings.xml file in your ~/.m2/ directory with the following entry (to activate a local repsitory for Maven to use)

       	<settings>
 		<localRepository>${user.home}/.m3/repository</localRepository>
 	</settings>

    • Clone the repository

      git clone https://github.com/exomiser/Exomiser

    • Build the source files

      clean install package

  • Now download the source code for matchbox and build on your system. It should now see all the Exomiser related dependencies in the local maven repository.

    • Clone the repository

      git clone https://github.com/macarthur-lab/matchbox

    • Update the following lines in the src/main/resources/application.properties appropriately.

      • If you are NOT planning to proxy matchbox behind a HTTPS service, you would have to start server matchbox as HTTPS per MME requirements.

        • Uncomment and populate the server.ssl.* attributes to start matchbox as HTTPS.

      • The "exomiser.data-directory=" field is required by Exomiser for phenotype matching. This reference data can be fetched by,

       	wget https://storage.googleapis.com/seqr-reference-data/1807_phenotype.tar.gz

      Then unzip the file.

      Provide the path of the above untar'ed directory to the "exomiser.data-directory=" and "exomiser.phenotype.data-version" fields

      For example, if your reference data was unzipped into, /dev/apps/ref_data/1807_phenotype

      You would populate the fields as such (note: the "1807_phenotype" in not in the path),

       	exomiser.data-directory=/dev/apps/ref_data
 	exomiser.phenotype.data-version=1807

      Next, populate the MongoDB connection fields as per your MongoDB installation.

    • Now build source files.

      mvn clean install package

    • That should create a directory called "target" with an executable JAR file

    • Start server

      java -jar target/matchbox-<version>.jar

  • NOTE: if you would like to change the default port the server listens on (8080), you can either set/use the environment variable SERVER_PORT or add the argument --server.port after the java -jar incantation. For example

    export SERVER_PORT=9020

    or

    java -jar matchbox-0.1.0.jar --server.port=9020

    It is similarly possible to change any of the variables contained in the application.properties in this manner. The latter is usually a better option as this will be application instance specific rather than as a global system variable.