Added executables that are missing on a native osx install

Was installing ide on new mac book and did see some issues in the unit tests

See merge request !171

Fix for issue #167

See merge request !172

NO more reflective issues, simplify some refs.

Remove reflective calls within GearsTrait.

See merge request !170

Conflicts:
	protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
	public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

Feature gears (metagenomics)

Metagenomics pipeline, start from bam or from FastQ files.

Dependencies:
- Sambamba (v0.5.1+)
- Kraken

See merge request !168

Feature yamsvp

Merging into develop to change the extensions/tools section

keep yamsvp branch for development!

See merge request !122