Installation

Use Maven Central Binaries

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

  1. Java JDK 8 for compiling phenol,
  2. Maven 3 for building phenol, and
  3. 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.

$ 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