Pipeline improvements

We have added fixes for issues:

#211 continue processing the next locus if the assembler throws an error

#212 add single ends flag to preprocessor

Alpha 3

Fixes:

• This fixes a race condition while creating the auxiliary database
• A bug in the wrapper code for the Spades assembler

Alpha release for version 2.0

v2.alpha.1

Code reorganization

Trinity 2.2.0

Added newer version of Trinity

Move config.txt path for brew

Config.txt is now located in the main aTRAM dir; functions added to Configuration.pm and configure.pl to deal with this change.

v1.02-brew

Adds a no-interactive option to configure.pl so that brew (and other package managers) can run it without interaction.

v1.01-doi

This is the same code base as v1.01; it is re-released just to trigger a DOI.

Fixes a few file-format errors and path searches.

Fixes Issue #133

Also fixes a bug with DOS paths when looking for the aTRAM/lib path.