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?
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
> (b) use the Tophat2 wrapper in conjunction with Bowtie2.
> For (a), you'll want to modify the bowtie_indices.loc; for (b), modify
>> (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: 220.127.116.11
>> [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
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