I've recently set up a local instance of galaxy in our office. I've downloaded the data mangers for Bowtie and Bowtie 2 and have been able to use these to index the reference genomes for both these tools.

However our tophat for illumina and tophat 2 installations do not show any reference genomes. I was under the impression that these tools used the same genomes as Bowtie and Bowtie 2 respectively and thought that the data managers would also index the genomes for these tools.

Is this correct or will I need to set the indexes up manually using the .loc files?