Peter:

GAlaxy is looking for the FastQC executable at the following location (see last line of error message):


/opt/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc

You wrote that the fastqc binary is somewhere in Galaxy's $PATH, but is it 
really in the above directory?
If not, try moving the fastqc executable there (or create a symlink) and it 
should work.

Best,
Klaus




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Message: 5
Date: Fri, 13 Jul 2012 13:59:03 -0400
From: Ross <ross.laza...@gmail.com>
To: peter.r.schm...@dartmouth.edu
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Configuring FastQC to run
Message-ID:
        <caemhw42rkqja8m6en4rgx32qpttngo1-kxr-69dm0pxzjfa...@mail.gmail.com>
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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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