Hi,
I installed bowtie2 and when running tophat I get the following error:

Error in tophat:

[2012-06-19 14:02:39] Beginning TopHat run (v2.0.3)
-----------------------------------------------
[2012-06-19 14:02:39] Checking for Bowtie
		  Bowtie version:	 2.0.0.6
[2012-06-19 14:02:39] Checking for Samtools
		Samtools version:	 0.1.18.0
[2012-06-19 14:02:39] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files (/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2)

I was wondering if I can create the index files using bowtie2 via command line and then change the universe_wsgi.ini to:
# Temporary files are stored in this directory.
new_file_path = database/tmp

and put the index files there. Anyway, why is it not creating the indexes? I created links to all bowtie2 executable files. If I remove bowtie 0.12.8, then I get a error from tophat (bowtie not installed). Is it creating the index with bowtie 0.12.8?
Thank you.

Luciano