switched back to bowtie2
add bowtie2 back to deps
removing reorder option from bowtie2
Merge branch 'bowtie' of github.com:cboursnell/transrate into cboursnell-bowtie

Conflicts:
	deps/deps.yaml
	lib/transrate/read_metrics.rb
fix tests
Merge branch 'cboursnell-bowtie' into bowtie