Hi guys,

I'm getting this error when running tophat for Illumina:

Error in tophat:

[2013-02-20 16:43:50] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-02-20 16:43:50] Checking for Bowtie
 Bowtie version: 2.0.2.0
[2013-02-20 16:43:50] Checking for Samtools
[2013-02-20 16:43:50] samtools_path: None
[2013-02-20 16:43:50] samtools_path after prog_path:
/usr/local/galaxy/installs/bin/samtools-0.1.18/samtools
Samtools version: 0.1.18.0
[2013-02-20 16:43:50] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files
(/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/BowtieIndex.*.bt2)

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


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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