First Beta Update

Major Changes: CAP3_Pipe, Additional Reporting, and Additional Analysis

Full Changelog:
2015-05-12, V.0.9.1
Added Stat_Analysis Segment
Added Package Segment
Added Test_Pipe Testing Pipeline
Separated Pipes and Segments Into tflow/pipes and tflow/segments, Respectively
Added Unpaired Read Trimming Mode
Added Significantly More Code Commenting to Segments: BUSCO_Analysis, and CEGMA_Analysis
Added Summary Module
Added Warning When User-Supplied Setting is Overridden by Pipe Setting
Fixed Trinity_Pipe Settings that Overrode BUSCO Tissue Type Selection
Added test_TFLOW_setup.sh Convenience Script
Added Significantly More Detail to README.txt
Added CAP3_Pipe Job Templates
Added CAP3 Assembly Pipe: CAP3_Pipe
Minor Bug Fixes