tophat 2.0.6
tophat 2.0.6

- Upgrade to 2.0.6
- Add a patch: intializes variable length arrays to 1 for clang.
- Patch stops a variable length array non-POD element type error.
- Patch reported upstream via email and noted in comments.
- Add an LDFLAG for `-lboost_system-mt` because autoconf doesn't.
- Add a dep on boost because the build requires it and samtools.
- Works with superenv on ML with XCode-4.5.1.

Closes #15716.

Signed-off-by: Adam Vandenberg <34c2b6407fd5a10249a15d699d40f9ed1782e98c@gmail.com>

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