Installation

Maven Central

Note

This is the recommended way of installing for normal users.

Simply use the following snippet for your pom.xml for using phenol modules in your Maven project.

<dependencies>
  <dependency>
    <groupId>org.monarchinitiative.phenol</groupId>
    <artifactId>phenol-core</artifactId>
    <version>${project.version}</version>
  </dependency>
  <dependency>
    <groupId>org.monarchinitiative.phenol</groupId>
    <artifactId>phenol-io</artifactId>
    <version>${project.version}</version>
  </dependency>
</dependencies>

Install from Source

Note

You only need to install from source if you want to develop Phenol in Java yourself.

Prerequisites

For building Phenol, you will need

• Java JDK 11 (or higher) for compiling phenol,
• Maven 3 for building phenol, and
• Git for getting the sources.

Git Checkout and maven build

The following code snippet downloads the phenol sources and builds them.

git clone https://github.com/monarch-initiative/phenol
cd phenol
mvn package

Maven Proxy Settings

If you are behind a proxy, you will get problems with Maven downloading dependencies. If you run into problems, make sure to also delete ~/.m2/repository. Then, execute the following commands to fill ~/.m2/settings.xml.

.. code-block:: console

$ mkdir -p ~/.m2
$ test -f ~/.m2/settings.xml || cat >~/.m2/settings.xml <<END
<settings>
  <proxies>
   <proxy>
      <active>true</active>
      <protocol>http</protocol>
      <host>proxy.example.com</host>
      <port>8080</port>
      <nonProxyHosts>*.example.com</nonProxyHosts>
    </proxy>
  </proxies>
</settings>
END