Improve custom dependencies handling in travis.

Source the file incase it messes with PATH, etc... and ensure they still have the file.
Improve Travis CI integration.

 - Install samtools - needed for bams. Going with version 0.1.19 - new but not too new.
 - More of a framework for installation of dependencies - provide scripts with some place on the PATH to put things.
 - Prettier reporting of commands being run by planemo at runtime.
 - More output information and repo init time.
Testing bash in debug mode.