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.goecks@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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