Installation

There are two options of installing Jannovar. The recommended way for most users is to download a prebuilt binary and is well-described in the Quickstart section. This section describes how to build Jannovar from scratch.

Prequisites

For building Jannovar, you will need

1. Java JDK 6 or higher for compiling Jannovar,
2. Maven 3 for building Jannovar, and
3. Git for getting the sources.

Git Checkout

In this tutorial, we will download the Jannovar sources and build them in ~/Development/jannovar.

~ # mkdir -p ~/Development
~ # cd ~/Development
Development # git clone https://github.com/charite/jannovar.git jannovar
Development # cd jannovar

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.

jannovar # mkdir -p ~/.m2
jannovar # 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

Building

You can build Jannovar using mvn package. This will automatically download all dependencies, build Jannovar, and run all tests.

jannovar # mvn package

In case that you have non-compiling test, you can use the -DskipTests=true parameter for skipping them.

jannovar # mvn install -DskipTests=true

Creating Eclipse Projects

Maven can be used to generate Eclipse projects that can be imported by the Eclipse IDE. This can be done calling mvn eclipse:eclipse command after calling mvn install:

jannovar # mvn install
jannovar # mvn eclipse:eclipse