Irwin fixes

These fixes are on top of the changes in irwin-binaries.
- Fixed Issue #41. Moved binaries, scripts, and build under tools.
- Added source files for mvicuna.
- Set java tempdir in call to trimmomatic.
- Fixed Issue #38. Stop redistributing maf-convert.py. Instead, during install run 2to3 and edit the result.
- Fixed Issue #37. Download prinseq-lite.pl instead of redistributing it.