Matthew J. Thomas <mnkyboy <at> u.washington.edu> writes:

> 
> 
> 
> Hello,
>  
> I am working on a local install of Galaxy and when running a test data set I 
get this error when invoking the Fastqc commans:
>  
> /home/mnkyboy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 20
> class FastQC():
> ^
> SyntaxError: invalid syntax
>  
> This is Illumina data from a single tile of qseq.txt data  converted to 
FASTQ and run through the FASTQ groomer.  Fastqc is working properly outside 
of Galaxy so any advice would be appreciated.
>  
> Thanks,
> Matt T.
>  
>  
> 
> 
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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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