I got this error which executing tophat2 in Galaxy:

Error in tophat:

[2013-02-13 02:02:43] Beginning TopHat run (v2.0.7)
[2013-02-13 02:02:43] Checking for Bowtie
                  Bowtie version:
[2013-02-13 02:02:43] Checking for Samtools
                Samtools version:
[2013-02-13 02:02:43] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files

The tool produced the following additional output:

TopHat v2.0.7
tophat2 -p 4  

I have these files under the Index directory:

genome.1.bt2  genome.2.bt2  genome.3.bt2  genome.4.bt2  genome.fa
genome.rev.1.bt2  genome.rev.2.bt2  tophat_out
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