I'm confused.  So I installed tophat-2.0.6.Linux_x86_64 which seems to
contain tophat and tophat2.  Can't galaxy use that tophat?

Am I supposed to also install tophat 1?  Does galaxy somehow failover
to use tophat2 otherwise?  What am I missing?

Thanks,

Greg

On Thu, Dec 13, 2012 at 2:32 PM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
>
> On Dec 13, 2012, at 2:13 PM, greg wrote:
>
>> 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?
>
> You are using Tophat2, not Tophat (note the version at the beginning of the 
> log). You can either
>
> (a) install and use Tophat 1.X
>
> or
>
> (b) use the Tophat2 wrapper in conjunction with Bowtie2.
>
> For (a), you'll want to modify the bowtie_indices.loc; for (b), modify 
> bowtie2_indices.loc
>
> J.
>
>>
>> Thanks,
>>
>> Greg
>>
>> (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: 2.0.2.0
>> [2012-12-13 13:55:01] Checking for Samtools
>>  Samtools version: 0.1.18.0
>> [2012-12-13 13:55:01] Checking for Bowtie index files
>> Error: Could not find Bowtie 2 index files
>> (/tmp/4036894.1.f04.q/tmp4TrEQQ/dataset_75.*.bt2)
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