For some reason there is still a dependency in biojava-structure-gui to a version of javaws, that is hosted on the biojava specific Maven repo. Let's point it to the system's javaws with
<dependencies>
<dependency>
<groupId>javax.jnlp</groupId>
<artifactId>jnlp-api</artifactId>
<version>7.0</version>
<scope>system</scope>
<systemPath>${java.home}/lib/javaws.jar</systemPath>
</dependency>
</dependencies>
For some reason there is still a dependency in biojava-structure-gui to a version of javaws, that is hosted on the biojava specific Maven repo. Let's point it to the system's javaws with
see also http://stackoverflow.com/questions/4645104/how-to-bundle-jnlp-api-with-maven-project