Portability fixes for Windows

Hello, on the last few days I worked on the code to change Linux-specific settings (like '/tmp') for others that can work on other OSes (like 'tempfile.gettempdir()'). Windows was unable to pass tests because of that and other issues like executables not found because '.exe' extension was missing, or loggers open filehandles blocking file deletions by rmtree (now they are properly closed just before file deletions). Now all tests pass successfully in Windows and Linux (tested on Windows 8.1 x64 with Python 2.7.8, and Ubuntu 14.04 x64 with Python 2.7.6).

The only test I could not make it work after several experiments and lots of googling was 'test_build_not_writable', since folder permission is changed correctly but it does not transform it into a read-only folder, so added a skip in Windows.

As final note, test_GembaseHMMReport_extract_concurent (test_Report.Test) usually succeeds but sometimes fails (around 2 out of 10 times) producing a "RuntimeError: cannot join current thread". This seems to happen only in Windows but I don't have enough experience with threads to figure out a way to prevent it.

Best regards,

Francisco J. Ossandon