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 <mnkyboy@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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