This is the recommended way of installing for normal users.
Or the jannovar command line tool is available via bioconda. You can install it with the command
$ conda install jannovar-cli
Install from Source¶
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.
For building Jannovar, you will need
In this tutorial, we will download the Jannovar sources and build them in
~ # 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
Then, execute the following commands to fill
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
You can build Jannovar using
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
jannovar # mvn install jannovar # mvn eclipse:eclipse