Hi, Antonio - yes, that's right - FastQC is not 'bundled' and has to
be obtained from the tool authors - we just provide a wrapper to make
it work inside Galaxy.

The Galaxy distribution includes code for some of the inbuilt tools
like the fastq groomer, but most of the distribution tool wrappers
rely on popular third party packages such as cufflinks, bwa, FastQC,
R/BioC packages and so on. There's a list of third party dependencies
at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies - they
have to be available on the computational nodes for Galaxy jobs
requiring them to run.

On Sun, Sep 25, 2011 at 9:33 PM, Antonio Ribeiro <acbello...@gmail.com> wrote:


> Hi Ross and Matthew,
> I'm a newbie to Galaxy and got the same error while trying to process some
> Illumina data... Thanks for your posting and tips!
>
> So, just to confirm the understanding: when installing a local instance of
> Galaxy you'd still need to install the FASTQC package independently and,
> subsequently, provide the "linkage" of GALAXY and FASTQC by, for instance,
> using the symlink approach suggested by Ross, right? This means that FASTQC is
> not "bundled" in the Galaxy local instance package, right?
>
> Thanks again for your attention and regards,
> Antonio
>
> ***************************************************************
>
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-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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