Re: [galaxy-dev] tophat for illumina looking in wrong directory for bowtie2 indexes?

...

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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