Simplified configuration

-Corrected error regarding use of export
-Removed requirement that we maintain multiple copies of B (we always
“run” the sra to count conversion; the configuration file determines
what it actually runs)
-Reformatted 1config (fastq_to_count_by_tophat)
-Includes some scripts that tests the functionality of export
Complete

Code complete and mostly tested
Tests A1 and A3 are currently running (and will probably pass).
Test A4 has not been run.
A5 (the actual analysis) is ready to go.