migrate to newer and external tool dependencies
code cleanups, remove tempdirs, more PEP8 complient and indentation fixes
remove not needed brackets in if-statements
remove samtools package, it is not needed anymore
remove numpy package, it is not needed anymore
Merge pull request #1 from bgruening/master

Cleanups and migration to newer Tool Shed features, updated by Bjoern Gruening <bjoern.gruening@gmail.com>