Just for fun, I updated galaxy-dist/tool-data/bowtie_indices.loc to be:

mm10    mm10    mm10
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index

And ran it again.

Now it's looking at the correct directory (Bowtie2Index) but still says:

Error: Could not find Bowtie 2 index files
(/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index.*.bt2)

But I do have files there:

>ls -l /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index
total 4904587
-rwxrwxr-x 1 gg scicomp 886713321 May 23  2012 genome.1.bt2
-rwxrwxr-x 1 gg scicomp 661884440 May 23  2012 genome.2.bt2
-rwxrwxr-x 1 gg scicomp      4715 May 23  2012 genome.3.bt2
-rwxrwxr-x 1 gg scicomp 661884433 May 23  2012 genome.4.bt2
lrwxrwxrwx 1 gg scicomp        29 Feb 20 16:19 genome.fa ->
../WholeGenomeFasta/genome.fa
-rwxrwxr-x 1 gg scicomp 886713321 May 23  2012 genome.rev.1.bt2
-rwxrwxr-x 1 gg scicomp 661884440 May 23  2012 genome.rev.2.bt2

Why am I getting that error?

-Greg

On Wed, Feb 20, 2013 at 4:53 PM, greg <margeem...@gmail.com> wrote:
> 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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