Installation

Pre-built Binaries

Note

This is the recommended way of installing for normal users.

Pre-built binaries are available from Maven Central. Download jannovar-cli-0.35-SNAPSHOT .jar from here.

Or the jannovar command line tool is available via bioconda. You can install it with the command

$ conda install jannovar-cli

Install from Source

Note

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

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 8 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