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 <margeemail@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