Off topic:TopHat aligning with ensembl in Galaxy

Question

[michael.flower.14]

I'm using the Galaxy interface to analyse RNAseq data. I've successfully aligned using the default reference genome, then counted using the gtf file downloaded from UCSC, then done the differential expression analysis with DeSeq2, which gives good results. I wanted to compare against the ensemble reference genome, but am struggling. I downloaded the DNA FASTA from here - http://www.ensembl.org/info/data/ftp/index.html - but can't get TopHat to align with it. Any help would be much appreciated