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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