Completed functionality

Changed naming:
A0 (a test of a known file) uses B0
A1 (a test of a new GEO file) uses B1
B0 (process single file, fastq to fpkm_tracking) uses D and E
B1 (process single file, sra to fpkm_tracking uses C, D, and E
C (process a single file, sra to fastq) uses sra toolkit
D (process a single file, fastq to bam) uses top hat
E (process a single file, bam to fpkm_tracking) uses samtools and
cufflinks