I'm seeing the error below when I try to run Tophat for Illumina.

Has anyone seen this before?  Could I have installed bowtie
incorrectly or am I simply running with the wrong data/parameters?



(I'm also really confused why the error is mentioned /tmp/* paths.  I
never assigned anything to /tmp in the universe_wsgi.ini.  Where is it
getting that from?)

Error in tophat:

[2012-12-13 13:55:01] Beginning TopHat run (v2.0.6)
[2012-12-13 13:55:01] Checking for Bowtie
 Bowtie version:
[2012-12-13 13:55:01] Checking for Samtools
  Samtools version:
[2012-12-13 13:55:01] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files
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