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:	 2.0.6.0
[2013-02-13 02:02:43] Checking for Samtools
		Samtools version:	 0.1.18.0
[2013-02-13 02:02:43] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files (/data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/.*.bt2)
The tool produced the following additional output:
TopHat v2.0.7
tophat2 -p 4  /data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/ /opt/galaxyprod/galaxy-dist/database/files/000/dataset_197.dat
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

Your path to your indices should like like this:

/data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome

Best,
J.