Thanks, adding the genome did work!

But I still don't understand why bowtie2 is looking at the
bowtie_indices.loc file instead of the bowtie2_indices.loc file?
Could that be a bug somewhere?

Here's why I think I'm using bowtie 2:

[2013-02-20 16:31:10] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-02-20 16:31:10] Checking for Bowtie
 Bowtie version: 2.0.2.0

-Greg

On Wed, Feb 20, 2013 at 5:44 PM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
> But this is what's in my galaxy-dist/tool-data/bowtie2_indices.loc file:
>
>
> mm10    mm10    mm10
>
> /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index
>
>
> You need:
>
> /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
>
> J.
>
>
>
> Why isn't it looking in that directory for the bowtie2 files?  It's
>
> almost as if it's reading my bowtie_indices.loc file instead?
>
>
> Thanks,
>
>
> Greg
>
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