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:
[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:
Samtools version:
[2013-02-20 16:43:50] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files

But this is what's in my galaxy-dist/tool-data/bowtie2_indices.loc file:

mm10    mm10    mm10

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?


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