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.Schmitt@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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