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?
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