Hi, Peter.

A couple of things worth checking:

1) Is the file (it's a perl script) executable by the user running the
Galaxy process? Unfortunately the FastQC distro is built in windows
apparently so that script is not executable out of the box - fixing
that may be all you need to do.

2) Does fastqc work correctly when executed by the user running the
Galaxy process - eg is the perl binary path right and executable? It
should open interactively if called directly ?

3) Does it work correctly when executed on all the nodes used to
process Galaxy tasks (eg SGE/PBS etc) ?

If all those 3 are true, it should work.


On Fri, Jul 13, 2012 at 12:05 PM, Peter Schmitt
<peter.r.schm...@dartmouth.edu> wrote:
> I get the following error when attempting to run FastQC from galaxy:
>
> job command line:
> python /opt/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py -i
> /opt/galaxy/galaxy-dist/database/files/000/dataset_75.dat -d
> /opt/galaxy/galaxy-dist/database/job_working_directory/000/114/dataset_128_files
> -o /opt/galaxy/galaxy-dist/database/files/000/dataset_128.dat -n "FastQC" -f
> fastqsanger -j SRS280832_1_FASTQ Groomer on data 14 -e
> /opt/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
> -----------------------------------------------------------------------------
> job stderr:
> Traceback (most recent call last):
>   File "/opt/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 149, in
> <module>
>     assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot
> find executable %s' % opts.executable
> AssertionError: ##rgFastQC.py error - cannot find executable
> /opt/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
>
> The fastqc binary is in galaxy's PATH.  Any help would be appreciated.
>
> --
>
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-- 
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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