tophat 2.0.10
tophat 2.0.10

 * patches from 2.0.9 are still necessary and still apply
 * added test step based on example at http://tophat.cbcb.umd.edu/tutorial.shtml#ref
 * added recommended dependency to bowtie2 as it is required to execute tophat

Closes #496

pditommaso/homebrew-science,kozo2/homebrew-science,philippbayer/homebrew-science,goxberry/homebrew-science,aeantipov/homebrew-science,parcollet/homebrew-science,maplesond/homebrew-science,joshbode/homebrew-science,DabeDotCom/homebrew-science,dpo/homebrew-science,quantumsteve/homebrew-science,heuermh/homebrew-science,ge11232002/homebrew-science,pmelsted/homebrew-science,andrewjpage/homebrew-science,ahundt/homebrew-science