Hi Mathew,
The tool xml has a clunky way of finding the fastqc perl script -
which has to be in the same directory as the jars it requires:
<command interpreter="python">
rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file
-n "$out_prefix" -f $input_file.ext -e
${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc
#if $contaminants.dataset and str($contaminants) > ''
-c "$contaminants"
#end if
</command>
so it's looking for the fastQC install under
[galaxyroot]/tool-data/shared/jars/FastQC
If you want, you could change the -e parameter (in
tools/rgenetics/rgFastQC,xml) to reflect your local installation
choice but it might be easier to symlink the fastQC install directory
to tool_data/shared/jars
I hope this helps...
On Fri, Sep 2, 2011 at 8:57 AM, Matthew J. Thomas
<mnky...@u.washington.edu> wrote:
> 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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--
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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