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  • Galaxy Error: Could not find Bowtie 2 index files

    Hi Guys

    Im trying to run tophat for illumina in galaxy and I get this error

    Error in tophat:

    [2013-08-04 21:11:20] Beginning TopHat run (v2.0.9)
    -----------------------------------------------
    [2013-08-04 21:11:20] Checking for Bowtie
    Bowtie version: 2.1.0.0
    [2013-08-04 21:11:20] Checking for Samtools
    Samtools version: 0.1.18.0
    [2013-08-04 21:11:20] Checking for Bowtie index files (genome)..
    Error: Could not find Bowtie 2 index files (/db/galaxydb/dm3/bowtie_index/dm3.*.bt2)


    what do i do?

  • #2
    A source download of Galaxy doesn't include many third party dependencies, genomes or indices and requires a fair bit of additional installation and tweaking to get everything working - eg see http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

    Without knowing a lot more, it looks like you need to download and index the dm3 genome with bowtie2-build as described on the Galaxy wiki, in the directory where bowtie is looking for it as indicated in your error message:

    Error: Could not find Bowtie 2 index files (/db/galaxydb/dm3/bowtie_index/dm3.*.bt2)

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