Added bowtie2 index builder.
Using new conan parameter handling.

Also added stubs for Tophat.
Added some aligners.
Added Trinity and for some existing tools added enums where there were string selection parameters.
Using modified interface for args and processes in Conan.
Finish Aligners
Added Bed tools fasta masker, repeat modeler and updated tophat and repeat masker with more functionality.

Also added ability to chunk read files using the linus "split" command.
Fixed some issues in the repeat tools, and optimized imports.
Added functionality to load and parse repeat masker tbl files.
Finish Release-0.7