Update maven to create fat jar in the package phase.

[deflaux]

This will create both google-genomics-dataflow-v1beta2-0.11-SNAPSHOT.jar and google-genomics-dataflow-v1beta2-0.11-SNAPSHOT-runnable.jar

This should fix #49 but I need to test a release. Hence sending this pull request to a branch instead of master.

[pgrosu]

Thank you for merging, but I'm not seeing the mvn package in the main Readme.rst webpage for the repository. It still says mvn compile and mvn bundle:bundle.

Also when I run mvn package, the -runnable jar file does not show up under any subdirectory when I perform a find . | grep runnable :( This is the only file that shows up:

$ ls target | grep jar
google-genomics-dataflow-v1beta2-0.11-SNAPSHOT.jar
$
$ find . | grep runnable
$

Also now I seem to get the following error when trying to run it after creating it via mvn package (I removed my project id below):

$ java -cp target/google-genomics-dataflo* com.google.cloud.genomics.dataflow.pipelines.VariantSimilarity  --project=<removed>  --output=test.txt  --secretsFile=client_secrets.json
Exception in thread "main" java.lang.NoClassDefFoundError: com/google/cloud/dataflow/sdk/options/DataflowPipelineOptions
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:760)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:455)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:367)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        at java.lang.Class.getDeclaredMethods0(Native Method)
        at java.lang.Class.privateGetDeclaredMethods(Class.java:2688)
        at java.lang.Class.getMethod0(Class.java:2937)
        at java.lang.Class.getMethod(Class.java:1771)
        at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
        at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
Caused by: java.lang.ClassNotFoundException: com.google.cloud.dataflow.sdk.options.DataflowPipelineOptions
        at java.net.URLClassLoader$1.run(URLClassLoader.java:372)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 18 more
$

~p