Installation

Use the prebuilt Jar file

Simply download the latest release of PhenoteFX from the GitHub releases page at https://github.com/monarch-initiative/PhenoteFX/releases.

Note

This is the recommended way of installing for normal users.

Install from Source

You only need to install from source if you want to contribute to the development of PhenoteFX yourself. To use PhenoteFX for annotation, it is recommended to download the prebuilt version.

Prerequisites

For building PhenoteFX, you will need

  1. Java JDK 16 or higher for compiling OntoLib,
  2. Maven for building PhenoteFX, and
  3. Git for getting the sources.

Git Checkout

The following command downloads the sources of PhenoteFX.

# git clone https://github.com/monarch-initiative/PhenoteFX.git
# cd PhenoteFX

Building

You can build PhenoteFX using mvn package.

$ mvn package

You shuld now be able to start the app with the following command.

$ java -jar target/PhenoteFX.jar

Maven Proxy Settings

If you are behind a proxy, you may encounter problems with Maven downloading dependencies. Edit the settings.xml file in your .m2 maven directory to adjust the settings for your proxy server.

<settings>
  <proxies>
   <proxy>
      <active>true</active>
      <protocol>http</protocol>
      <host>proxy.example.com</host>
      <port>8080</port>
      <nonProxyHosts>*.example.com</nonProxyHosts>
    </proxy>
  </proxies>
</settings>
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